## Installation
+
+```bash
+pip install datajoint
```
-pip3 install datajoint
-```
-If you already have an older version of DataJoint installed using `pip`, upgrade with
+or with Conda:
+
```bash
-pip3 install --upgrade datajoint
+conda install -c conda-forge datajoint
```
-## Documentation and Tutorials
-A number of labs are currently adopting DataJoint and we are quickly getting the documentation in shape in February 2017.
+## Example Pipeline
+
+
+
+**Cite DataJoint:** [Yatsenko et al., 2026](https://arxiv.org/abs/2602.16585) — RRID: [SCR_014543](https://scicrunch.org/resolver/SCR_014543)
+
+## Resources
+
+- **[Documentation](https://docs.datajoint.com)** — Complete guides and reference
+ - [Tutorials](https://docs.datajoint.com/tutorials/) — Learn by example
+ - [How-To Guides](https://docs.datajoint.com/how-to/) — Task-oriented guides
+ - [API Reference](https://docs.datajoint.com/api/) — Complete API documentation
+ - [Migration Guide](https://docs.datajoint.com/how-to/migrate-to-v20/) — Upgrade from legacy versions
+- **[DataJoint Elements](https://docs.datajoint.com/elements/)** — Example pipelines for neuroscience
+- **[GitHub Discussions](https://github.com/datajoint/datajoint-python/discussions)** — Community support
+
+## Contributing
-* https://datajoint.github.com -- start page
-* https://docs.datajoint.io -- up-to-date documentation
-* https://tutorials.datajoint.io -- step by step tutorials
+See [CONTRIBUTING.md](https://github.com/datajoint/datajoint-python/blob/master/CONTRIBUTING.md) for development setup and guidelines.
diff --git a/RELEASE_MEMO.md b/RELEASE_MEMO.md
new file mode 100644
index 000000000..73700b602
--- /dev/null
+++ b/RELEASE_MEMO.md
@@ -0,0 +1,227 @@
+# DataJoint Release Memo
+
+## Branch Structure
+
+| Branch | Purpose | Version |
+|--------|---------|---------|
+| `master` | Main development | 2.1.x |
+| `maint/2.0` | Maintenance releases | 2.0.x |
+
+For 2.0.x bugfixes:
+1. Commit to `maint/2.0`
+2. Tag and release as v2.0.x
+3. Cherry-pick to master if applicable
+
+---
+
+## Writing Release Notes
+
+Good release notes help users understand what changed and whether they need to take action.
+
+### Categories
+
+Organize changes into these categories (in order):
+
+| Category | When to Use | Example |
+|----------|-------------|---------|
+| **BREAKING** | Changes that require user action | API changes, removed features |
+| **Added** | New features | New methods, new options |
+| **Changed** | Behavior changes (non-breaking) | Performance improvements, defaults |
+| **Deprecated** | Features marked for removal | Old syntax warnings |
+| **Fixed** | Bug fixes | Error corrections |
+| **Security** | Security patches | Vulnerability fixes |
+
+### Format
+
+```markdown
+## What's Changed
+
+### BREAKING CHANGES
+- **`fetch()` removed** — Use `to_dicts()`, `to_pandas()`, or `to_arrays()` instead (#123)
+
+### Added
+- New `to_polars()` method for Polars DataFrame output (#456)
+- Support for custom codecs via `@codec` decorator (#789)
+
+### Changed
+- Improved query performance for complex joins (2-3x faster)
+- Default connection timeout increased to 30s
+
+### Fixed
+- Fixed incorrect NULL handling in aggregations (#234)
+
+### Full Changelog
+https://github.com/datajoint/datajoint-python/compare/v2.0.0...v2.1.0
+```
+
+### Guidelines
+
+1. **Lead with breaking changes** — Users need to see these first
+2. **Explain the "why"** — Not just what changed, but why it matters
+3. **Link to PRs/issues** — For users who want details
+4. **Use imperative mood** — "Add feature" not "Added feature"
+5. **Be concise** — One line per change, details in PR
+
+### PR Labels
+
+The release drafter uses PR labels to categorize changes:
+
+| Label | Category |
+|-------|----------|
+| `breaking` | BREAKING CHANGES |
+| `enhancement` | Added |
+| `bug` | Fixed |
+| `documentation` | (usually excluded) |
+
+Ensure PRs have appropriate labels before merging.
+
+---
+
+## PyPI Release Process
+
+### Steps
+
+1. **Add labels to merged PRs** for release-drafter categorization
+2. **Run "Manual Draft Release" workflow** on GitHub Actions
+3. **Edit the draft release**:
+ - Set release name to `Release X.Y.Z`
+ - Set tag to `vX.Y.Z`
+ - Review and edit release notes
+4. **Publish the release**
+5. Automation will:
+ - Update `version.py` to `X.Y.Z`
+ - Build and publish to PyPI
+ - Create PR to merge version update back to master
+
+### Version Note
+
+The release drafter computes version from the previous tag. You may need to **manually edit** the release name for major version changes.
+
+The regex in `post_draft_release_published.yaml` extracts version from the release name:
+```bash
+VERSION=$(echo "${{ github.event.release.name }}" | grep -oP '\d+\.\d+\.\d+')
+```
+
+---
+
+## Conda-Forge Release Process
+
+DataJoint has a [conda-forge feedstock](https://github.com/conda-forge/datajoint-feedstock).
+
+### How Conda-Forge Updates Work
+
+Conda-forge has **automated bots** that detect new PyPI releases and create PRs automatically:
+
+1. **You publish to PyPI** (via the GitHub release workflow)
+2. **regro-cf-autotick-bot** detects the new version within ~24 hours
+3. **Bot creates a PR** to the feedstock with updated version and hash
+4. **Maintainers review and merge**
+5. **Package builds automatically** for all platforms
+
+### Manual Update (if bot doesn't trigger)
+
+If the bot doesn't create a PR, manually update the feedstock:
+
+1. **Fork** [conda-forge/datajoint-feedstock](https://github.com/conda-forge/datajoint-feedstock)
+
+2. **Edit `recipe/meta.yaml`**:
+ ```yaml
+ {% set version = "2.1.0" %}
+
+ package:
+ name: datajoint
+ version: {{ version }}
+
+ source:
+ url: https://pypi.io/packages/source/d/datajoint/datajoint-{{ version }}.tar.gz
+ sha256:
+
+ build:
+ number: 0 # Reset to 0 for new version
+ ```
+
+3. **Get the SHA256 hash**:
+ ```bash
+ curl -sL https://pypi.org/pypi/datajoint/2.1.0/json | jq -r '.urls[] | select(.packagetype=="sdist") | .digests.sha256'
+ ```
+
+4. **Check dependencies** match `pyproject.toml`:
+ ```yaml
+ requirements:
+ host:
+ - python {{ python_min }}
+ - pip
+ - setuptools >=62.0
+ run:
+ - python >={{ python_min }}
+ - numpy
+ - pandas
+ - pymysql >=1.0
+ - minio
+ - packaging
+ # ... etc
+ ```
+
+5. **Submit PR** to the feedstock
+
+### Verification
+
+After release:
+```bash
+conda search datajoint -c conda-forge
+```
+
+---
+
+## Documentation Release Process
+
+Documentation is hosted at [docs.datajoint.com](https://docs.datajoint.com) and built from [datajoint-docs](https://github.com/datajoint/datajoint-docs).
+
+### How Documentation Builds Work
+
+The documentation build:
+1. Checks out `datajoint-python` from the `master` branch
+2. Uses mkdocstrings to generate API docs from source docstrings
+3. Builds static site with MkDocs
+4. Deploys to `gh-pages` branch
+
+### Triggering a Documentation Build
+
+Documentation rebuilds automatically when:
+- Changes are pushed to `datajoint-docs` main branch
+
+To manually trigger a rebuild (e.g., after updating docstrings in datajoint-python):
+```bash
+gh workflow run development.yml --repo datajoint/datajoint-docs
+```
+
+Or use the "Run workflow" button in GitHub Actions.
+
+### Updating Documentation
+
+1. **For docstring changes**: Update docstrings in `datajoint-python`, then trigger a docs rebuild
+2. **For content changes**: Edit files in `datajoint-docs/src/`, push to main
+3. **Docstring style**: Use NumPy-style docstrings (see CONTRIBUTING.md)
+
+### Verification
+
+After build completes:
+- Check [docs.datajoint.com](https://docs.datajoint.com)
+- Verify API reference pages show updated content
+
+---
+
+## Maintainers
+
+- @datajointbot
+- @dimitri-yatsenko
+- @ttngu207
+
+## Links
+
+- [datajoint-python on GitHub](https://github.com/datajoint/datajoint-python)
+- [datajoint-docs on GitHub](https://github.com/datajoint/datajoint-docs)
+- [datajoint-feedstock on GitHub](https://github.com/conda-forge/datajoint-feedstock)
+- [datajoint on Anaconda.org](https://anaconda.org/conda-forge/datajoint)
+- [datajoint on PyPI](https://pypi.org/project/datajoint/)
+- [docs.datajoint.com](https://docs.datajoint.com)
diff --git a/activate.sh b/activate.sh
new file mode 100644
index 000000000..1632accc8
--- /dev/null
+++ b/activate.sh
@@ -0,0 +1,4 @@
+#! /usr/bin/bash
+# This script registers dot plugins so that we can use graphviz
+# to write png images
+dot -c
\ No newline at end of file
diff --git a/datajoint/__init__.py b/datajoint/__init__.py
deleted file mode 100644
index 0f5276205..000000000
--- a/datajoint/__init__.py
+++ /dev/null
@@ -1,89 +0,0 @@
-"""
-DataJoint for Python is a high-level programming interface for MySQL databases
-to support data processing chains in science labs. DataJoint is built on the
-foundation of the relational data model and prescribes a consistent method for
-organizing, populating, and querying data.
-
-DataJoint is free software under the LGPL License. In addition, we request
-that any use of DataJoint leading to a publication be acknowledged in the publication.
-
-Please cite:
- http://biorxiv.org/content/early/2015/11/14/031658
- http://dx.doi.org/10.1101/031658
-"""
-
-import logging
-import os
-from types import ModuleType
-from .version import __version__
-
-__author__ = "Dimitri Yatsenko, Edgar Y. Walker, and Fabian Sinz at Baylor College of Medicine"
-__date__ = "July 26, 2017"
-__all__ = ['__author__', '__version__',
- 'config', 'conn', 'kill', 'BaseRelation',
- 'Connection', 'Heading', 'FreeRelation', 'Not', 'schema',
- 'Manual', 'Lookup', 'Imported', 'Computed', 'Part',
- 'AndList', 'OrList', 'ERD', 'U',
- 'set_password']
-
-
-class key:
- """
- object that allows requesting the primary key in Fetch.__getitem__
- """
- pass
-
-
-class DataJointError(Exception):
- """
- Base class for errors specific to DataJoint internal operation.
- """
- pass
-
-# ----------- loads local configuration from file ----------------
-from .settings import Config, LOCALCONFIG, GLOBALCONFIG, logger, log_levels
-config = Config()
-config_files = (os.path.expanduser(n) for n in (LOCALCONFIG, os.path.join('~', GLOBALCONFIG)))
-try:
- config_file = next(n for n in config_files if os.path.exists(n))
-except StopIteration:
- config.add_history('No config file found, using default settings.')
-else:
- config.load(config_file)
-
-# override login credentials with environment variables
-mapping = {k: v for k, v in zip(
- ('database.host', 'database.user', 'database.password'),
- map(os.getenv, ('DJ_HOST', 'DJ_USER', 'DJ_PASS')))
- if v is not None}
-for k in mapping:
- config.add_history('Updated login credentials from %s' % k)
-config.update(mapping)
-
-logger.setLevel(log_levels[config['loglevel']])
-
-# ------------- flatten import hierarchy -------------------------
-from .connection import conn, Connection
-from .base_relation import FreeRelation, BaseRelation
-from .user_relations import Manual, Lookup, Imported, Computed, Part
-from .relational_operand import Not, AndList, OrList, U
-from .heading import Heading
-from .schema import Schema as schema
-from .erd import ERD
-from .admin import set_password, kill
-
-
-def create_virtual_module(modulename, dbname):
- """
- Creates a python module with the given name from a database name in mysql with datajoint tables.
- Automatically creates the classes of the appropriate tier in the module.
-
- :param modulename: desired name of the module
- :param dbname: name of the database in mysql
- :return: the python module
- """
- mod = ModuleType(modulename)
- s = schema(dbname, mod.__dict__)
- s.spawn_missing_classes()
- mod.__dict__['schema'] = s
- return mod
diff --git a/datajoint/admin.py b/datajoint/admin.py
deleted file mode 100644
index 172f89237..000000000
--- a/datajoint/admin.py
+++ /dev/null
@@ -1,58 +0,0 @@
-import pymysql
-from . import conn
-from getpass import getpass
-
-
-def set_password(new_password=None, connection=None): # pragma: no cover
- connection = conn() if connection is None else connection
- if new_password is None:
- new_password = getpass('New password: ')
- confirm_password = getpass('Confirm password: ')
- if new_password != confirm_password:
- print('Failed to confirm the password! Aborting password change.')
- return
- connection.query("SET PASSWORD = PASSWORD('%s')" % new_password)
- print('Password updated.')
-
-
-def kill(restriction=None, connection=None): # pragma: no cover
- """
- view and kill database connections.
- :param restriction: restriction to be applied to processlist
- :param connection: a datajoint.Connection object. Default calls datajoint.conn()
-
- Restrictions are specified as strings and can involve any of the attributes of
- information_schema.processlist: ID, USER, HOST, DB, COMMAND, TIME, STATE, INFO.
-
- Examples:
- dj.kill('HOST LIKE "%compute%"') lists only connections from hosts containing "compute".
- dj.kill('TIME > 600') lists only connections older than 10 minutes.
- """
-
- if connection is None:
- connection = conn()
-
- query = 'SELECT * FROM information_schema.processlist WHERE id <> CONNECTION_ID()' + (
- "" if restriction is None else ' AND (%s)' % restriction)
-
- while True:
- print(' ID USER STATE TIME INFO')
- print('+--+ +----------+ +-----------+ +--+')
- for process in connection.query(query, as_dict=True).fetchall():
- try:
- print('{ID:>4d} {USER:<12s} {STATE:<12s} {TIME:>5d} {INFO}'.format(**process))
- except TypeError:
- print(process)
- response = input('process to kill or "q" to quit > ')
- if response == 'q':
- break
- if response:
- try:
- pid = int(response)
- except ValueError:
- pass # ignore non-numeric input
- else:
- try:
- connection.query('kill %d' % pid)
- except pymysql.err.InternalError:
- print('Process not found')
diff --git a/datajoint/autopopulate.py b/datajoint/autopopulate.py
deleted file mode 100644
index 9e3a7a824..000000000
--- a/datajoint/autopopulate.py
+++ /dev/null
@@ -1,158 +0,0 @@
-"""autopopulate containing the dj.AutoPopulate class. See `dj.AutoPopulate` for more info."""
-import logging
-import datetime
-import random
-from pymysql import OperationalError
-from .relational_operand import RelationalOperand, AndList
-from . import DataJointError
-from . import key as KEY
-from .base_relation import FreeRelation
-import signal
-
-# noinspection PyExceptionInherit,PyCallingNonCallable
-
-logger = logging.getLogger(__name__)
-
-
-class AutoPopulate:
- """
- AutoPopulate is a mixin class that adds the method populate() to a Relation class.
- Auto-populated relations must inherit from both Relation and AutoPopulate,
- must define the property `key_source`, and must define the callback method _make_tuples.
- """
- _key_source = None
-
- @property
- def key_source(self):
- """
- :return: the relation whose primary key values are passed, sequentially, to the
- `_make_tuples` method when populate() is called.The default value is the
- join of the parent relations. Users may override to change the granularity
- or the scope of populate() calls.
- """
- if self._key_source is None:
- self.connection.dependencies.load(self.full_table_name)
- parents = list(self.target.parents(primary=True))
- if not parents:
- raise DataJointError('A relation must have parent relations to be able to be populated')
- self._key_source = FreeRelation(self.connection, parents.pop(0)).proj()
- while parents:
- self._key_source *= FreeRelation(self.connection, parents.pop(0)).proj()
- return self._key_source
-
- def _make_tuples(self, key):
- """
- Derived classes must implement method _make_tuples that fetches data from tables that are
- above them in the dependency hierarchy, restricting by the given key, computes dependent
- attributes, and inserts the new tuples into self.
- """
- raise NotImplementedError('Subclasses of AutoPopulate must implement the method "_make_tuples"')
-
- @property
- def target(self):
- """
- relation to be populated.
- Typically, AutoPopulate are mixed into a Relation object and the target is self.
- """
- return self
-
- def _job_key(self, key):
- """
- :param key: they key returned for the job from the key source
- :return: the dict to use to generate the job reservation hash
- """
- return key
-
- def populate(self, *restrictions, suppress_errors=False, reserve_jobs=False, order="original", limit=None):
- """
- rel.populate() calls rel._make_tuples(key) for every primary key in self.key_source
- for which there is not already a tuple in rel.
-
- :param restrictions: a list of restrictions each restrict (rel.key_source - target.proj())
- :param suppress_errors: suppresses error if true
- :param reserve_jobs: if true, reserves job to populate in asynchronous fashion
- :param order: "original"|"reverse"|"random" - the order of execution
- :param limit: if not None, populates at max that many keys
- """
- if self.connection.in_transaction:
- raise DataJointError('Populate cannot be called during a transaction.')
-
- valid_order = ['original', 'reverse', 'random']
- if order not in valid_order:
- raise DataJointError('The order argument must be one of %s' % str(valid_order))
-
- todo = self.key_source
- if not isinstance(todo, RelationalOperand):
- raise DataJointError('Invalid key_source value')
- todo = todo.proj() & AndList(restrictions)
-
- error_list = [] if suppress_errors else None
-
- jobs = self.connection.jobs[self.target.database] if reserve_jobs else None
-
- # define and setup signal handler for SIGTERM
- if reserve_jobs:
- def handler(signum, frame):
- logger.info('Populate terminated by SIGTERM')
- raise SystemExit('SIGTERM received')
- old_handler = signal.signal(signal.SIGTERM, handler)
-
- todo -= self.target
- keys = todo.fetch(KEY, limit=limit)
- if order == "reverse":
- keys.reverse()
- elif order == "random":
- random.shuffle(keys)
-
- logger.info('Found %d keys to populate' % len(keys))
- for key in keys:
- if not reserve_jobs or jobs.reserve(self.target.table_name, self._job_key(key)):
- self.connection.start_transaction()
- if key in self.target: # already populated
- self.connection.cancel_transaction()
- if reserve_jobs:
- jobs.complete(self.target.table_name, self._job_key(key))
- else:
- logger.info('Populating: ' + str(key))
- try:
- self._make_tuples(dict(key))
- except (KeyboardInterrupt, SystemExit, Exception) as error:
- try:
- self.connection.cancel_transaction()
- except OperationalError:
- pass
- if reserve_jobs:
- # show error name and error message (if any)
- error_message = ': '.join([error.__class__.__name__, str(error)]).strip(': ')
- jobs.error(self.target.table_name, self._job_key(key), error_message=error_message)
-
- if not suppress_errors or isinstance(error, SystemExit):
- raise
- else:
- logger.error(error)
- error_list.append((key, error))
- else:
- self.connection.commit_transaction()
- if reserve_jobs:
- jobs.complete(self.target.table_name, self._job_key(key))
-
- # place back the original signal handler
- if reserve_jobs:
- signal.signal(signal.SIGTERM, old_handler)
-
- return error_list
-
- def progress(self, *restrictions, display=True):
- """
- report progress of populating this table
- :return: remaining, total -- tuples to be populated
- """
- todo = self.key_source & AndList(restrictions)
- total = len(todo)
- remaining = len(todo.proj() - self.target)
- if display:
- print('%-20s' % self.__class__.__name__,
- 'Completed %d of %d (%2.1f%%) %s' % (
- total - remaining, total, 100 - 100 * remaining / (total+1e-12),
- datetime.datetime.strftime(datetime.datetime.now(), '%Y-%m-%d %H:%M:%S')), flush=True)
- return remaining, total
diff --git a/datajoint/base_relation.py b/datajoint/base_relation.py
deleted file mode 100644
index c033d0f88..000000000
--- a/datajoint/base_relation.py
+++ /dev/null
@@ -1,579 +0,0 @@
-import collections
-import itertools
-import inspect
-import platform
-import numpy as np
-import pymysql
-import logging
-from . import config, DataJointError
-from .declare import declare
-from .relational_operand import RelationalOperand
-from .blob import pack
-from .utils import user_choice
-from .heading import Heading
-from .settings import server_error_codes
-from . import __version__ as version
-
-logger = logging.getLogger(__name__)
-
-
-class BaseRelation(RelationalOperand):
- """
- BaseRelation is an abstract class that represents a base relation, i.e. a table in the database.
- To make it a concrete class, override the abstract properties specifying the connection,
- table name, database, context, and definition.
- A Relation implements insert and delete methods in addition to inherited relational operators.
- """
- _heading = None
- _context = None
- database = None
- _log_ = None
-
- # -------------- required by RelationalOperand ----------------- #
- @property
- def heading(self):
- """
- Returns the table heading. If the table is not declared, attempts to declare it and return heading.
- :return: table heading
- """
- if self._heading is None:
- self._heading = Heading() # instance-level heading
- if not self._heading: # lazy loading of heading
- self._heading.init_from_database(self.connection, self.database, self.table_name)
- return self._heading
-
- @property
- def context(self):
- return self._context
-
- def declare(self):
- """
- Loads the table heading. If the table is not declared, use self.definition to declare
- """
- try:
- self.connection.query(
- declare(self.full_table_name, self.definition, self._context))
- except pymysql.OperationalError as error:
- if error.args[0] == server_error_codes['command denied']:
- logger.warning(error.args[1])
- else:
- self._log('Declared ' + self.full_table_name)
-
- @property
- def from_clause(self):
- """
- :return: the FROM clause of SQL SELECT statements.
- """
- return self.full_table_name
-
- def get_select_fields(self, select_fields=None):
- """
- :return: the selected attributes from the SQL SELECT statement.
- """
- return '*' if select_fields is None else self.heading.project(select_fields).as_sql
-
- def parents(self, primary=None):
- """
- :param primary: if None, then all parents are returned. If True, then only foreign keys composed of
- primary key attributes are considered. If False, the only foreign keys including at least one non-primary
- attribute are considered.
-
- :return: dict of tables referenced with self's foreign keys
- """
- return dict(p[::2] for p in self.connection.dependencies.in_edges(self.full_table_name, data=True)
- if primary is None or p[2]['primary'] == primary)
-
- def children(self, primary=None):
- """
- :param primary: if None, then all parents are returned. If True, then only foreign keys composed of
- primary key attributes are considered. If False, the only foreign keys including at least one non-primary
- attribute are considered.
-
- :return: dict of tables with foreign keys referencing self
- """
- return dict(p[1:3] for p in self.connection.dependencies.out_edges(self.full_table_name, data=True)
- if primary is None or p[2]['primary'] == primary)
-
- @property
- def is_declared(self):
- """
- :return: True is the table is declared in the database
- """
- return self.connection.query(
- 'SHOW TABLES in `{database}` LIKE "{table_name}"'.format(
- database=self.database, table_name=self.table_name)).rowcount > 0
-
- @property
- def full_table_name(self):
- """
- :return: full table name in the database
- """
- return r"`{0:s}`.`{1:s}`".format(self.database, self.table_name)
-
- @property
- def _log(self):
- if self._log_ is None:
- self._log_ = Log(self.connection, database=self.database)
- return self._log_
-
- def insert1(self, row, **kwargs):
- """
- Insert one data record or one Mapping (like a dict).
- :param row: a numpy record, a dict-like object, or an ordered sequence to be inserted as one row.
- For kwargs, see insert()
- """
- self.insert((row,), **kwargs)
-
- def insert(self, rows, replace=False, ignore_errors=False, skip_duplicates=False, ignore_extra_fields=False):
- """
- Insert a collection of rows.
-
- :param rows: An iterable where an element is a numpy record, a dict-like object, or an ordered sequence.
- rows may also be another relation with the same heading.
- :param replace: If True, replaces the existing tuple.
- :param ignore_errors: If True, ignore errors: e.g. constraint violations.
- :param skip_duplicates: If True, silently skip duplicate inserts.
- :param ignore_extra_fields: If False, fields that are not in the heading raise error.
-
- Example::
- >>> relation.insert([
- >>> dict(subject_id=7, species="mouse", date_of_birth="2014-09-01"),
- >>> dict(subject_id=8, species="mouse", date_of_birth="2014-09-02")])
- """
-
- if isinstance(rows, RelationalOperand):
- # INSERT FROM SELECT
- query = 'INSERT{ignore} INTO {table} ({fields}) {select}'.format(
- ignore=" IGNORE" if ignore_errors or skip_duplicates else "",
- table=self.full_table_name,
- fields='`'+'`,`'.join(rows.heading.names)+'`',
- select=rows.make_sql())
- self.connection.query(query)
- return
-
- heading = self.heading
- if heading.attributes is None:
- logger.warning('Could not access table {table}'.format(table=self.full_table_name))
- return
-
- field_list = None # ensures that all rows have the same attributes in the same order as the first row.
-
- def make_row_to_insert(row):
- """
- :param row: A tuple to insert
- :return: a dict with fields 'names', 'placeholders', 'values'
- """
-
- def make_placeholder(name, value):
- """
- For a given attribute `name` with `value`, return its processed value or value placeholder
- as a string to be included in the query and the value, if any, to be submitted for
- processing by mysql API.
- :param name:
- :param value:
- """
- if ignore_extra_fields and name not in heading:
- return None
- if heading[name].is_blob:
- value = pack(value)
- placeholder = '%s'
- elif heading[name].numeric:
- if value is None or value == '' or np.isnan(np.float(value)): # nans are turned into NULLs
- placeholder = 'NULL'
- value = None
- else:
- placeholder = '%s'
- value = str(int(value) if isinstance(value, bool) else value)
- else:
- placeholder = '%s'
- return name, placeholder, value
-
- def check_fields(fields):
- """
- Validates that all items in `fields` are valid attributes in the heading
- :param fields: field names of a tuple
- """
- if field_list is None:
- if not ignore_extra_fields:
- for field in fields:
- if field not in heading:
- raise KeyError(u'`{0:s}` is not in the table heading'.format(field))
- elif set(field_list) != set(fields).intersection(heading.names):
- raise DataJointError('Attempt to insert rows with different fields')
-
- if isinstance(row, np.void): # np.array
- check_fields(row.dtype.fields)
- attributes = [make_placeholder(name, row[name])
- for name in heading if name in row.dtype.fields]
- elif isinstance(row, collections.abc.Mapping): # dict-based
- check_fields(row.keys())
- attributes = [make_placeholder(name, row[name]) for name in heading if name in row]
- else: # positional
- try:
- if len(row) != len(heading):
- raise DataJointError(
- 'Invalid insert argument. Incorrect number of attributes: '
- '{given} given; {expected} expected'.format(
- given=len(row), expected=len(heading)))
- except TypeError:
- raise DataJointError('Datatype %s cannot be inserted' % type(row))
- else:
- attributes = [make_placeholder(name, value) for name, value in zip(heading, row)]
- if ignore_extra_fields:
- attributes = [a for a in attributes if a is not None]
-
- assert len(attributes), 'Empty tuple'
- row_to_insert = dict(zip(('names', 'placeholders', 'values'), zip(*attributes)))
- nonlocal field_list
- if field_list is None:
- # first row sets the composition of the field list
- field_list = row_to_insert['names']
- else:
- # reorder attributes in row_to_insert to match field_list
- order = list(row_to_insert['names'].index(field) for field in field_list)
- row_to_insert['names'] = list(row_to_insert['names'][i] for i in order)
- row_to_insert['placeholders'] = list(row_to_insert['placeholders'][i] for i in order)
- row_to_insert['values'] = list(row_to_insert['values'][i] for i in order)
-
- return row_to_insert
-
- rows = list(make_row_to_insert(row) for row in rows)
- if rows:
- try:
- self.connection.query(
- "{command} INTO {destination}(`{fields}`) VALUES {placeholders}".format(
- command='REPLACE' if replace else 'INSERT IGNORE' if ignore_errors or skip_duplicates else 'INSERT',
- destination=self.from_clause,
- fields='`,`'.join(field_list),
- placeholders=','.join('(' + ','.join(row['placeholders']) + ')' for row in rows)),
- args=list(itertools.chain.from_iterable((v for v in r['values'] if v is not None) for r in rows)))
- except pymysql.err.OperationalError as err:
- if err.args[0] == server_error_codes['command denied']:
- raise DataJointError('Command denied: %s' % err.args[1])
- else:
- raise
-
- def delete_quick(self):
- """
- Deletes the table without cascading and without user prompt. If this table has any dependent
- table(s), this will fail.
- """
- query = 'DELETE FROM ' + self.full_table_name + self.where_clause
- self.connection.query(query)
- self._log(query[0:255])
-
- def delete(self):
- """
- Deletes the contents of the table and its dependent tables, recursively.
- User is prompted for confirmation if config['safemode'] is set to True.
- """
- self.connection.dependencies.load()
-
- relations_to_delete = collections.OrderedDict(
- (r, FreeRelation(self.connection, r))
- for r in self.connection.dependencies.descendants(self.full_table_name))
-
- # construct restrictions for each relation
- restrict_by_me = set()
- restrictions = collections.defaultdict(list)
- if self.restrictions:
- restrict_by_me.add(self.full_table_name)
- restrictions[self.full_table_name].append(self.restrictions) # copy own restrictions
- for r in relations_to_delete.values():
- restrict_by_me.update(r.children(primary=False))
- for name, r in relations_to_delete.items():
- for dep in r.children():
- if name in restrict_by_me:
- restrictions[dep].append(r)
- else:
- restrictions[dep].extend(restrictions[name])
-
- # apply restrictions
- for name, r in relations_to_delete.items():
- if restrictions[name]: # do not restrict by an empty list
- r.restrict([r.proj() if isinstance(r, RelationalOperand) else r
- for r in restrictions[name]]) # project
- # execute
- do_delete = False # indicate if there is anything to delete
- if config['safemode']: # pragma: no cover
- print('The contents of the following tables are about to be deleted:')
- for relation in list(relations_to_delete.values()):
- count = len(relation)
- if count:
- do_delete = True
- if config['safemode']:
- print(relation.full_table_name, '(%d tuples)' % count)
- else:
- relations_to_delete.pop(relation.full_table_name)
- if not do_delete:
- if config['safemode']:
- print('Nothing to delete')
- else:
- if not config['safemode'] or user_choice("Proceed?", default='no') == 'yes':
- already_in_transaction = self.connection._in_transaction
- if not already_in_transaction:
- self.connection.start_transaction()
- for r in reversed(list(relations_to_delete.values())):
- r.delete_quick()
- if not already_in_transaction:
- self.connection.commit_transaction()
- print('Done')
-
- def drop_quick(self):
- """
- Drops the table associated with this relation without cascading and without user prompt.
- If the table has any dependent table(s), this call will fail with an error.
- """
- if self.is_declared:
- query = 'DROP TABLE %s' % self.full_table_name
- self.connection.query(query)
- logger.info("Dropped table %s" % self.full_table_name)
- self._log(query[0:255])
- else:
- logger.info("Nothing to drop: table %s is not declared" % self.full_table_name)
-
- def drop(self):
- """
- Drop the table and all tables that reference it, recursively.
- User is prompted for confirmation if config['safemode'] is set to True.
- """
- self.connection.dependencies.load()
- do_drop = True
- tables = self.connection.dependencies.descendants(self.full_table_name)
- if config['safemode']:
- for table in tables:
- print(table, '(%d tuples)' % len(FreeRelation(self.connection, table)))
- do_drop = user_choice("Proceed?", default='no') == 'yes'
- if do_drop:
- for table in reversed(tables):
- FreeRelation(self.connection, table).drop_quick()
- print('Tables dropped. Restart kernel.')
-
- @property
- def size_on_disk(self):
- """
- :return: size of data and indices in bytes on the storage device
- """
- ret = self.connection.query(
- 'SHOW TABLE STATUS FROM `{database}` WHERE NAME="{table}"'.format(
- database=self.database, table=self.table_name), as_dict=True).fetchone()
- return ret['Data_length'] + ret['Index_length']
-
- def show_definition(self):
- logger.warn('show_definition is deprecated. Use describe instead.')
- return self.describe()
-
- def describe(self):
- """
- :return: the definition string for the relation using DataJoint DDL.
- This does not yet work for aliased foreign keys.
- """
- self.connection.dependencies.load()
- parents = self.parents()
- in_key = True
- definition = '# ' + self.heading.table_info['comment'] + '\n'
- attributes_thus_far = set()
- attributes_declared = set()
- for attr in self.heading.attributes.values():
- if in_key and not attr.in_key:
- definition += '---\n'
- in_key = False
- attributes_thus_far.add(attr.name)
- do_include = True
- for parent_name, fk_props in list(parents.items()): # need list() to force a copy
- if attr.name in fk_props['referencing_attributes']:
- do_include = False
- if attributes_thus_far.issuperset(fk_props['referencing_attributes']):
- # simple foreign keys
- parents.pop(parent_name)
- if not parent_name.isdigit():
- definition += '-> {class_name}\n'.format(
- class_name=lookup_class_name(parent_name, self.context) or parent_name)
- else:
- # aliased foreign key
- parent_name = self.connection.dependencies.in_edges(parent_name)[0][0]
- lst = [(attr, ref) for attr, ref in zip(
- fk_props['referencing_attributes'], fk_props['referenced_attributes'])
- if ref != attr]
- definition += '({attr_list}) -> {class_name}{ref_list}\n'.format(
- attr_list=','.join(r[0] for r in lst),
- class_name=lookup_class_name(parent_name, self.context) or parent_name,
- ref_list=('' if len(attributes_thus_far) - len(attributes_declared) == 1
- else '(%s)' % ','.join(r[1] for r in lst)))
- attributes_declared.update(fk_props['referencing_attributes'])
- if do_include:
- attributes_declared.add(attr.name)
- definition += '%-20s : %-28s # %s\n' % (
- attr.name if attr.default is None else '%s=%s' % (attr.name, attr.default),
- '%s%s' % (attr.type, 'auto_increment' if attr.autoincrement else ''), attr.comment)
- print(definition)
- return definition
-
- def _update(self, attrname, value=None):
- """
- Updates a field in an existing tuple. This is not a datajoyous operation and should not be used
- routinely. Relational database maintain referential integrity on the level of a tuple. Therefore,
- the UPDATE operator can violate referential integrity. The datajoyous way to update information is
- to delete the entire tuple and insert the entire update tuple.
-
- Safety constraints:
- 1. self must be restricted to exactly one tuple
- 2. the update attribute must not be in primary key
-
- Example
-
- >>> (v2p.Mice() & key).update('mouse_dob', '2011-01-01')
- >>> (v2p.Mice() & key).update( 'lens') # set the value to NULL
-
- """
- if len(self) != 1:
- raise DataJointError('Update is only allowed on one tuple at a time')
- if attrname not in self.heading:
- raise DataJointError('Invalid attribute name')
- if attrname in self.heading.primary_key:
- raise DataJointError('Cannot update a key value.')
-
- attr = self.heading[attrname]
-
- if attr.is_blob:
- value = pack(value)
- placeholder = '%s'
- elif attr.numeric:
- if value is None or np.isnan(np.float(value)): # nans are turned into NULLs
- placeholder = 'NULL'
- value = None
- else:
- placeholder = '%s'
- value = str(int(value) if isinstance(value, bool) else value)
- else:
- placeholder = '%s'
- command = "UPDATE {full_table_name} SET `{attrname}`={placeholder} {where_clause}".format(
- full_table_name=self.from_clause,
- attrname=attrname,
- placeholder=placeholder,
- where_clause=self.where_clause
- )
- self.connection.query(command, args=(value, ) if value is not None else ())
-
-
-def lookup_class_name(name, context, depth=3):
- """
- given a table name in the form `database`.`table_name`, find its class in the context.
- :param name: `database`.`table_name`
- :param context: dictionary representing the namespace
- :param depth: search depth into imported modules, helps avoid infinite recursion.
- :return: class name found in the context or None if not found
- """
- # breadth-first search
- nodes = [dict(context=context, context_name='', depth=depth)]
- while nodes:
- node = nodes.pop(0)
- for member_name, member in node['context'].items():
- if inspect.isclass(member) and issubclass(member, BaseRelation):
- if member.full_table_name == name: # found it!
- return '.'.join([node['context_name'], member_name]).lstrip('.')
- try: # look for part tables
- parts = member._ordered_class_members
- except AttributeError:
- pass # not a UserRelation -- cannot have part tables.
- else:
- for part in (getattr(member, p) for p in parts):
- if inspect.isclass(part) and issubclass(part, BaseRelation) and part.full_table_name == name:
- return '.'.join([node['context_name'], member_name, part.__name__]).lstrip('.')
- elif node['depth'] > 0 and inspect.ismodule(member) and member.__name__ != 'datajoint':
- try:
- nodes.append(
- dict(context=dict(inspect.getmembers(member)),
- context_name=node['context_name'] + '.' + member_name,
- depth=node['depth']-1))
- except ImportError:
- pass # could not import, so do not attempt
- return None
-
-
-class FreeRelation(BaseRelation):
- """
- A base relation without a dedicated class. Each instance is associated with a table
- specified by full_table_name.
- :param arg: a dj.Connection or a dj.FreeRelation
- """
-
- def __init__(self, arg, full_table_name=None):
- super().__init__()
- if isinstance(arg, FreeRelation):
- # copy constructor
- self.database = arg.database
- self._table_name = arg._table_name
- self._connection = arg._connection
- else:
- self.database, self._table_name = (s.strip('`') for s in full_table_name.split('.'))
- self._connection = arg
-
- def __repr__(self):
- return "FreeRelation(`%s`.`%s`)" % (self.database, self._table_name)
-
- @property
- def table_name(self):
- """
- :return: the table name in the database
- """
- return self._table_name
-
-
-class Log(BaseRelation):
- """
- The log table for each database.
- Instances are callable. Calls log the time and identifying information along with the event.
- """
-
- def __init__(self, arg, database=None):
- super().__init__()
-
- if isinstance(arg, Log):
- # copy constructor
- self.database = arg.database
- self._connection = arg._connection
- self._definition = arg._definition
- self._user = arg._user
- return
-
- self.database = database
- self._connection = arg
- self._definition = """ # event logging table for `{database}`
- timestamp = CURRENT_TIMESTAMP : timestamp
- ---
- version :varchar(12) # datajoint version
- user :varchar(255) # user@host
- host="" :varchar(255) # system hostname
- event="" :varchar(255) # custom message
- """.format(database=database)
-
- if not self.is_declared:
- self.declare()
- self._user = self.connection.get_user()
-
- @property
- def definition(self):
- return self._definition
-
- @property
- def table_name(self):
- return '~log'
-
- def __call__(self, event):
- try:
- self.insert1(dict(
- user=self._user,
- version=version + 'py',
- host=platform.uname().node,
- event=event), ignore_errors=True, ignore_extra_fields=True)
- except pymysql.err.OperationalError:
- logger.info('could not log event in table ~log')
-
- def delete(self):
- """bypass interactive prompts and cascading dependencies"""
- self.delete_quick()
-
- def drop(self):
- """bypass interactive prompts and cascading dependencies"""
- self.drop_quick()
diff --git a/datajoint/blob.py b/datajoint/blob.py
deleted file mode 100644
index 139a6ca30..000000000
--- a/datajoint/blob.py
+++ /dev/null
@@ -1,301 +0,0 @@
-"""
-Provides serialization methods for numpy.ndarrays that ensure compatibility with Matlab.
-"""
-
-import zlib
-from collections import OrderedDict, Mapping, Iterable
-import numpy as np
-from . import DataJointError
-
-mxClassID = OrderedDict((
- # see http://www.mathworks.com/help/techdoc/apiref/mxclassid.html
- ('mxUNKNOWN_CLASS', None),
- ('mxCELL_CLASS', None),
- ('mxSTRUCT_CLASS', None),
- ('mxLOGICAL_CLASS', np.dtype('bool')),
- ('mxCHAR_CLASS', np.dtype('c')),
- ('mxVOID_CLASS', None),
- ('mxDOUBLE_CLASS', np.dtype('float64')),
- ('mxSINGLE_CLASS', np.dtype('float32')),
- ('mxINT8_CLASS', np.dtype('int8')),
- ('mxUINT8_CLASS', np.dtype('uint8')),
- ('mxINT16_CLASS', np.dtype('int16')),
- ('mxUINT16_CLASS', np.dtype('uint16')),
- ('mxINT32_CLASS', np.dtype('int32')),
- ('mxUINT32_CLASS', np.dtype('uint32')),
- ('mxINT64_CLASS', np.dtype('int64')),
- ('mxUINT64_CLASS', np.dtype('uint64')),
- ('mxFUNCTION_CLASS', None)))
-
-rev_class_id = {dtype: i for i, dtype in enumerate(mxClassID.values())}
-dtype_list = list(mxClassID.values())
-
-decode_lookup = {
- b'ZL123\0': zlib.decompress
-}
-
-
-class BlobReader:
- def __init__(self, blob, squeeze=False, as_dict=False):
- self._squeeze = squeeze
- self._blob = blob
- self._pos = 0
- self._as_dict = as_dict
-
- @property
- def pos(self):
- return self._pos
-
- @pos.setter
- def pos(self, val):
- self._pos = val
-
- def reset(self):
- self.pos = 0
-
- def decompress(self):
- for pattern, decoder in decode_lookup.items():
- if self._blob[self.pos:].startswith(pattern):
- self.pos += len(pattern)
- blob_size = self.read_value('uint64')
- blob = decoder(self._blob[self.pos:])
- assert len(blob) == blob_size
- self._blob = blob
- self._pos = 0
- break
-
- def unpack(self):
- self.decompress()
- blob_format = self.read_string()
- if blob_format == 'mYm':
- return self.read_mym_data(n_bytes=-1)
-
- def read_mym_data(self, n_bytes=None):
- if n_bytes is not None:
- if n_bytes == -1:
- n_bytes = len(self._blob) - self.pos
- n_bytes -= 1
-
- type_id = self.read_value('c')
- if type_id == b'A':
- return self.read_array(n_bytes=n_bytes)
- elif type_id == b'S':
- return self.read_structure(n_bytes=n_bytes)
- elif type_id == b'C':
- return self.read_cell_array(n_bytes=n_bytes)
-
- def read_array(self, advance=True, n_bytes=None):
- start = self.pos
- n_dims = int(self.read_value('uint64'))
- shape = self.read_value('uint64', count=n_dims)
- n_elem = int(np.prod(shape))
- dtype_id = self.read_value('uint32')
- dtype = dtype_list[dtype_id]
- is_complex = self.read_value('uint32')
-
- if dtype_id == 4: # if dealing with character array
- data = self.read_value(dtype, count=2 * n_elem)
- data = data[::2].astype('U1')
- if n_dims == 2 and shape[0] == 1 or n_dims == 1:
- compact = data.squeeze()
- data = compact if compact.shape == () else np.array(''.join(data.squeeze()))
- shape = (1,)
- else:
- if is_complex:
- n_elem *= 2 # read real and imaginary parts
- data = self.read_value(dtype, count=n_elem)
- if is_complex:
- data = data[:n_elem//2] + 1j * data[n_elem//2:]
-
- if n_bytes is not None:
- assert self.pos - start == n_bytes
-
- if not advance:
- self.pos = start
-
- return self.squeeze(data.reshape(shape, order='F'))
-
- def read_structure(self, advance=True, n_bytes=None):
- start = self.pos
- n_dims = self.read_value('uint64').item()
- shape = self.read_value('uint64', count=n_dims)
- n_elem = int(np.prod(shape))
- n_field = int(self.read_value('uint32'))
- field_names = []
- for i in range(n_field):
- field_names.append(self.read_string())
- if not field_names:
- # return an empty array
- return np.array(None)
- dt = [(f, np.object) for f in field_names]
- raw_data = []
- for k in range(n_elem):
- values = []
- for i in range(n_field):
- nb = int(self.read_value('uint64')) # dealing with a weird bug of numpy
- values.append(self.read_mym_data(n_bytes=nb))
- raw_data.append(tuple(values))
- if n_bytes is not None:
- assert self.pos - start == n_bytes
- if not advance:
- self.pos = start
-
- if self._as_dict and n_elem == 1:
- data = dict(zip(field_names, values))
- return data
- else:
- data = np.rec.array(raw_data, dtype=dt)
- return self.squeeze(data.reshape(shape, order='F'))
-
- def squeeze(self, array):
- """
- Simplify the given array as much as possible - squeeze out all singleton
- dimensions and also convert a zero dimensional array into array scalar
- """
- if not self._squeeze:
- return array
- array = array.copy()
- array = array.squeeze()
- if array.ndim == 0:
- array = array[()]
- return array
-
- def read_cell_array(self, advance=True, n_bytes=None):
- start = self.pos
- n_dims = self.read_value('uint64').item()
- shape = self.read_value('uint64', count=n_dims)
- n_elem = int(np.prod(shape))
- data = np.empty(n_elem, dtype=np.object)
- for i in range(n_elem):
- nb = self.read_value('uint64').item()
- data[i] = self.read_mym_data(n_bytes=nb)
- if n_bytes is not None:
- assert self.pos - start == n_bytes
- if not advance:
- self.pos = start
- return data
-
- def read_string(self, advance=True):
- """
- Read a string terminated by null byte '\0'. The returned string
- object is ASCII decoded, and will not include the terminating null byte.
- """
- target = self._blob.find(b'\0', self.pos)
- assert target >= self._pos
- data = self._blob[self._pos:target]
- if advance:
- self._pos = target + 1
- return data.decode('ascii')
-
- def read_value(self, dtype='uint64', count=1, advance=True):
- """
- Read one or more scalars of the indicated dtype. Count specifies the number of
- scalars to be read in.
- """
- data = np.frombuffer(self._blob, dtype=dtype, count=count, offset=self.pos)
- if advance:
- # probably the same thing as data.nbytes * 8
- self._pos += data.dtype.itemsize * data.size
- if count == 1:
- data = data[0]
- return data
-
- def __repr__(self):
- return repr(self._blob[self.pos:])
-
- def __str__(self):
- return str(self._blob[self.pos:])
-
-
-def pack(obj, compress=True):
- blob = b"mYm\0"
- blob += pack_obj(obj)
-
- if compress:
- compressed = b'ZL123\0' + np.uint64(len(blob)).tostring() + zlib.compress(blob)
- if len(compressed) < len(blob):
- blob = compressed
-
- return blob
-
-
-def pack_obj(obj):
- blob = b''
- if isinstance(obj, np.ndarray):
- blob += pack_array(obj)
- elif isinstance(obj, Mapping): # TODO: check if this is a good inheritance check for dict etc.
- blob += pack_dict(obj)
- elif isinstance(obj, str):
- blob += pack_array(np.array(obj, dtype=np.dtype('c')))
- elif isinstance(obj, Iterable):
- blob += pack_array(np.array(list(obj)))
- elif isinstance(obj, int) or isinstance(obj, float):
- blob += pack_array(np.array(obj))
- else:
- raise DataJointError("Packing object of type %s currently not supported!" % type(obj))
-
- return blob
-
-
-def pack_array(array):
- if not isinstance(array, np.ndarray):
- raise ValueError("argument must be a numpy array!")
-
- blob = b"A"
- blob += np.array((len(array.shape), ) + array.shape, dtype=np.uint64).tostring()
-
- is_complex = np.iscomplexobj(array)
- if is_complex:
- array, imaginary = np.real(array), np.imag(array)
-
- type_number = rev_class_id[array.dtype]
-
- if dtype_list[type_number] is None:
- raise DataJointError("Type %s is ambiguous or unknown" % array.dtype)
-
- blob += np.array(type_number, dtype=np.uint32).tostring()
-
- blob += np.int32(is_complex).tostring()
- if type_number == 4: # if dealing with character array
- blob += ('\x00'.join(array.tostring(order='F').decode()) + '\x00').encode()
- else:
- blob += array.tostring(order='F')
-
- if is_complex:
- blob += imaginary.tostring(order='F')
-
- return blob
-
-
-def pack_string(value):
- return value.encode('ascii') + b'\0'
-
-
-def pack_dict(obj):
- """
- Write dictionary object as a singular structure array
- :param obj: dictionary object to serialize. The fields must be simple scalar or an array.
- """
- obj = OrderedDict(obj)
- blob = b'S'
- blob += np.array((1, 1), dtype=np.uint64).tostring()
- blob += np.array(len(obj), dtype=np.uint32).tostring()
-
- # write out field names
- for k in obj:
- blob += pack_string(k)
-
- for k, v in obj.items():
- blob_part = pack_obj(v)
- blob += np.array(len(blob_part), dtype=np.uint64).tostring()
- blob += blob_part
-
- return blob
-
-
-def unpack(blob, **kwargs):
- if blob is None:
- return None
-
- return BlobReader(blob, **kwargs).unpack()
-
diff --git a/datajoint/connection.py b/datajoint/connection.py
deleted file mode 100644
index c5ac20ecd..000000000
--- a/datajoint/connection.py
+++ /dev/null
@@ -1,211 +0,0 @@
-"""
-This module hosts the Connection class that manages the connection to the mysql database,
- and the `conn` function that provides access to a persistent connection in datajoint.
-"""
-import warnings
-from contextlib import contextmanager
-import pymysql as client
-import logging
-from getpass import getpass
-
-from . import config
-from . import DataJointError
-from .dependencies import Dependencies
-from .jobs import JobManager
-from pymysql import err
-
-logger = logging.getLogger(__name__)
-
-
-def conn(host=None, user=None, password=None, init_fun=None, reset=False):
- """
- Returns a persistent connection object to be shared by multiple modules.
- If the connection is not yet established or reset=True, a new connection is set up.
- If connection information is not provided, it is taken from config which takes the
- information from dj_local_conf.json. If the password is not specified in that file
- datajoint prompts for the password.
-
- :param host: hostname
- :param user: mysql user
- :param password: mysql password
- :param init_fun: initialization function
- :param reset: whether the connection should be reset or not
- """
- if not hasattr(conn, 'connection') or reset:
- host = host if host is not None else config['database.host']
- user = user if user is not None else config['database.user']
- password = password if password is not None else config['database.password']
- if user is None: # pragma: no cover
- user = input("Please enter DataJoint username: ")
- if password is None: # pragma: no cover
- password = getpass(prompt="Please enter DataJoint password: ")
- init_fun = init_fun if init_fun is not None else config['connection.init_function']
- conn.connection = Connection(host, user, password, init_fun)
- return conn.connection
-
-
-class Connection:
- """
- A dj.Connection object manages a connection to a database server.
- It also catalogues modules, schemas, tables, and their dependencies (foreign keys).
-
- Most of the parameters below should be set in the local configuration file.
-
- :param host: host name
- :param user: user name
- :param password: password
- :param init_fun: connection initialization function (SQL)
- """
-
- def __init__(self, host, user, password, init_fun=None):
- if ':' in host:
- host, port = host.split(':')
- port = int(port)
- else:
- port = config['database.port']
- self.conn_info = dict(host=host, port=port, user=user, passwd=password)
- self.init_fun = init_fun
- print("Connecting {user}@{host}:{port}".format(**self.conn_info))
- self._conn = None
- self.connect()
- if self.is_connected:
- logger.info("Connected {user}@{host}:{port}".format(**self.conn_info))
- self.connection_id = self.query('SELECT connection_id()').fetchone()[0]
- else:
- raise DataJointError('Connection failed.')
- self._conn.autocommit(True)
- self._in_transaction = False
- self.jobs = JobManager(self)
- self.schemas = dict()
- self.dependencies = Dependencies(self)
-
- def __eq__(self, other):
- return self.conn_info == other.conn_info
-
- def __repr__(self):
- connected = "connected" if self.is_connected else "disconnected"
- return "DataJoint connection ({connected}) {user}@{host}:{port}".format(
- connected=connected, **self.conn_info)
-
- def connect(self):
- """
- Connects to the database server.
- """
- self._conn = client.connect(init_command=self.init_fun, **self.conn_info)
-
- def register(self, schema):
- self.schemas[schema.database] = schema
-
- @property
- def is_connected(self):
- """
- Returns true if the object is connected to the database server.
- """
- return self._conn.ping()
-
- def query(self, query, args=(), as_dict=False):
- """
- Execute the specified query and return the tuple generator (cursor).
-
- :param query: mysql query
- :param args: additional arguments for the client.cursor
- :param as_dict: If as_dict is set to True, the returned cursor objects returns
- query results as dictionary.
- """
-
- cursor = client.cursors.DictCursor if as_dict else client.cursors.Cursor
- cur = self._conn.cursor(cursor=cursor)
-
- try:
- # Log the query
- logger.debug("Executing SQL:" + query[0:300])
- # suppress all warnings arising from underlying SQL library
- with warnings.catch_warnings():
- warnings.simplefilter("ignore")
- cur.execute(query, args)
- except err.OperationalError as e:
- if 'MySQL server has gone away' in str(e) and config['database.reconnect']:
- warnings.warn('''Mysql server has gone away.
- Reconnected to the server. Data from transactions might be lost and referential constraints may
- be violated. You can switch off this behavior by setting the 'database.reconnect' to False.
- ''')
- self.connect()
- logger.debug("Re-executing SQL: " + query[0:300])
- cur.execute(query, args)
- else:
- raise
- except err.ProgrammingError as e:
- print('Error in query:')
- print(query)
- raise
- return cur
-
- def get_user(self):
- """
- :return: the user name and host name provided by the client to the server.
- """
- return self.query('SELECT user()').fetchone()[0]
-
- # ---------- transaction processing
- @property
- def in_transaction(self):
- """
- :return: True if there is an open transaction.
- """
- self._in_transaction = self._in_transaction and self.is_connected
- return self._in_transaction
-
- def start_transaction(self):
- """
- Starts a transaction error.
-
- :raise DataJointError: if there is an ongoing transaction.
- """
- if self.in_transaction:
- raise DataJointError("Nested connections are not supported.")
- self.query('START TRANSACTION WITH CONSISTENT SNAPSHOT')
- self._in_transaction = True
- logger.info("Transaction started")
-
- def cancel_transaction(self):
- """
- Cancels the current transaction and rolls back all changes made during the transaction.
-
- """
- self.query('ROLLBACK')
- self._in_transaction = False
- logger.info("Transaction cancelled. Rolling back ...")
-
- def commit_transaction(self):
- """
- Commit all changes made during the transaction and close it.
-
- """
- self.query('COMMIT')
- self._in_transaction = False
- logger.info("Transaction committed and closed.")
-
- # -------- context manager for transactions
- @property
- @contextmanager
- def transaction(self):
- """
- Context manager for transactions. Opens an transaction and closes it after the with statement.
- If an error is caught during the transaction, the commits are automatically rolled back.
- All errors are raised again.
-
- Example:
-
- >>> import datajoint as dj
- >>> with dj.conn().transaction as conn:
- >>> # transaction is open here
-
- """
- try:
- self.start_transaction()
- yield self
- except:
- self.cancel_transaction()
- raise
- else:
- self.commit_transaction()
diff --git a/datajoint/declare.py b/datajoint/declare.py
deleted file mode 100644
index 5c7a10ab5..000000000
--- a/datajoint/declare.py
+++ /dev/null
@@ -1,181 +0,0 @@
-"""
-This module hosts functions to convert DataJoint table definitions into mysql table definitions, and to
-declare the corresponding mysql tables.
-"""
-import re
-import pyparsing as pp
-import logging
-
-from . import DataJointError
-
-logger = logging.getLogger(__name__)
-
-
-def build_foreign_key_parser():
- left = pp.Literal('(').suppress()
- right = pp.Literal(')').suppress()
- attribute_name = pp.Word(pp.srange('[a-z]'), pp.srange('[a-z0-9_]'))
- new_attrs = pp.Optional(left + pp.delimitedList(attribute_name) + right).setResultsName('new_attrs')
- arrow = pp.Literal('->').suppress()
- lbracket = pp.Literal('[').suppress()
- rbracket = pp.Literal(']').suppress()
- option = pp.Word(pp.srange('[a-zA-Z]'))
- options = pp.Optional(lbracket + pp.delimitedList(option) + rbracket)
- ref_table = pp.Word(pp.alphas, pp.alphanums + '._').setResultsName('ref_table')
- ref_attrs = pp.Optional(left + pp.delimitedList(attribute_name) + right).setResultsName('ref_attrs')
- return new_attrs + arrow + options + ref_table + ref_attrs
-
-
-def build_attribute_parser():
- quoted = pp.Or(pp.QuotedString('"'), pp.QuotedString("'"))
- colon = pp.Literal(':').suppress()
- attribute_name = pp.Word(pp.srange('[a-z]'), pp.srange('[a-z0-9_]')).setResultsName('name')
- data_type = pp.Combine(pp.Word(pp.alphas) + pp.SkipTo("#", ignore=quoted)).setResultsName('type')
- default = pp.Literal('=').suppress() + pp.SkipTo(colon, ignore=quoted).setResultsName('default')
- comment = pp.Literal('#').suppress() + pp.restOfLine.setResultsName('comment')
- return attribute_name + pp.Optional(default) + colon + data_type + comment
-
-
-foreign_key_parser = build_foreign_key_parser()
-attribute_parser = build_attribute_parser()
-
-
-def is_foreign_key(line):
- """
- :param line: a line from the table definition
- :return: true if the line appears to be a foreign key definition
- """
- arrow_position = line.find('->')
- return arrow_position >= 0 and not any(c in line[0:arrow_position] for c in '"#\'')
-
-
-def compile_foreign_key(line, context, attributes, primary_key, attr_sql, foreign_key_sql):
- """
- :param line: a line from a table definition
- :param context: namespace containing referenced objects
- :param attributes: list of attribute names already in the declaration -- to be updated by this function
- :param primary_key: None if the current foreign key is made from the dependent section. Otherwise it is the list
- of primary key attributes thus far -- to be updated by the function
- :param attr_sql: a list of sql statements defining attributes -- to be updated by this function.
- :param foreign_key_sql: a list of sql statements specifying foreign key constraints -- to be updated by this function.
- """
- from .base_relation import BaseRelation
- try:
- result = foreign_key_parser.parseString(line)
- except pp.ParseException as err:
- raise DataJointError('Parsing error in line "%s". %s.' % line, err)
- try:
- referenced_class = eval(result.ref_table, context)
- except NameError:
- raise DataJointError('Foreign key reference %s could not be resolved' % result.ref_table)
- if not issubclass(referenced_class, BaseRelation):
- raise DataJointError('Foreign key reference %s must be a subclass of UserRelation' % result.ref_table)
- ref = referenced_class()
- if not all(r in ref.primary_key for r in result.ref_attrs):
- raise DataJointError('Invalid foreign key attributes in "%s"' % line)
-
- # match new attributes and referenced attributes and create foreign keys
- missing_attrs = [attr for attr in ref.primary_key if attr not in attributes] or (
- len(result.new_attrs) == len(ref.primary_key) == 1 and ref.primary_key)
- new_attrs = result.new_attrs or missing_attrs
- ref_attrs = result.ref_attrs or missing_attrs
- if len(new_attrs) != len(ref_attrs):
- raise DataJointError('Mismatched attributes in foreign key "%s"' % line)
-
- # declare foreign key attributes and foreign keys
- lookup = dict(zip(ref_attrs, new_attrs))
- for attr in missing_attrs:
- new_attr = lookup.get(attr, attr)
- attributes.append(new_attr)
- if primary_key is not None:
- primary_key.append(new_attr)
- attr_sql.append(ref.heading[attr].sql.replace(attr, new_attr, 1))
- fk = [lookup.get(attr, attr) for attr in ref.primary_key]
- foreign_key_sql.append(
- 'FOREIGN KEY (`{fk}`) REFERENCES {ref} (`{pk}`) ON UPDATE CASCADE ON DELETE RESTRICT'.format(
- fk='`,`'.join(fk), pk='`,`'.join(ref.primary_key), ref=ref.full_table_name))
-
-
-def declare(full_table_name, definition, context):
- """
- Parse declaration and create new SQL table accordingly.
-
- :param full_table_name: full name of the table
- :param definition: DataJoint table definition
- :param context: dictionary of objects that might be referred to in the table. Usually this will be locals()
- """
- # split definition into lines
- definition = re.split(r'\s*\n\s*', definition.strip())
- # check for optional table comment
- table_comment = definition.pop(0)[1:].strip() if definition[0].startswith('#') else ''
- in_key = True # parse primary keys
- primary_key = []
- attributes = []
- attribute_sql = []
- foreign_key_sql = []
- index_sql = []
-
- for line in definition:
- if line.startswith('#'): # additional comments are ignored
- pass
- elif line.startswith('---') or line.startswith('___'):
- in_key = False # start parsing dependent attributes
- elif is_foreign_key(line):
- compile_foreign_key(line, context, attributes,
- primary_key if in_key else None,
- attribute_sql, foreign_key_sql)
- elif re.match(r'^(unique\s+)?index[^:]*$', line, re.I): # index
- index_sql.append(line) # the SQL syntax is identical to DataJoint's
- else:
- name, sql = compile_attribute(line, in_key)
- if in_key and name not in primary_key:
- primary_key.append(name)
- if name not in attributes:
- attributes.append(name)
- attribute_sql.append(sql)
- # compile SQL
- if not primary_key:
- raise DataJointError('Table must have a primary key')
- return ('CREATE TABLE IF NOT EXISTS %s (\n' % full_table_name +
- ',\n'.join(attribute_sql +
- ['PRIMARY KEY (`' + '`,`'.join(primary_key) + '`)'] +
- foreign_key_sql +
- index_sql) +
- '\n) ENGINE=InnoDB, COMMENT "%s"' % table_comment)
-
-
-def compile_attribute(line, in_key=False):
- """
- Convert attribute definition from DataJoint format to SQL
-
- :param line: attribution line
- :param in_key: set to True if attribute is in primary key set
- :returns: (name, sql) -- attribute name and sql code for its declaration
- """
-
- try:
- match = attribute_parser.parseString(line+'#', parseAll=True)
- except pp.ParseException as err:
- raise DataJointError('Declaration error in position {pos} in line:\n {line}\n{msg}'.format(
- line=err.args[0], pos=err.args[1], msg=err.args[2]))
- match['comment'] = match['comment'].rstrip('#')
- if 'default' not in match:
- match['default'] = ''
- match = {k: v.strip() for k, v in match.items()}
- match['nullable'] = match['default'].lower() == 'null'
-
- literals = ['CURRENT_TIMESTAMP'] # not to be enclosed in quotes
- if match['nullable']:
- if in_key:
- raise DataJointError('Primary key attributes cannot be nullable in line %s' % line)
- match['default'] = 'DEFAULT NULL' # nullable attributes default to null
- else:
- if match['default']:
- quote = match['default'].upper() not in literals and match['default'][0] not in '"\''
- match['default'] = ('NOT NULL DEFAULT ' +
- ('"%s"' if quote else "%s") % match['default'])
- else:
- match['default'] = 'NOT NULL'
- match['comment'] = match['comment'].replace('"', '\\"') # escape double quotes in comment
- sql = ('`{name}` {type} {default}' + (' COMMENT "{comment}"' if match['comment'] else '')).format(**match)
- return match['name'], sql
diff --git a/datajoint/dependencies.py b/datajoint/dependencies.py
deleted file mode 100644
index 172c058a5..000000000
--- a/datajoint/dependencies.py
+++ /dev/null
@@ -1,101 +0,0 @@
-import pyparsing as pp
-import networkx as nx
-import itertools
-from . import DataJointError
-
-
-class Dependencies(nx.DiGraph):
- """
- The graph of dependencies (foreign keys) between loaded tables.
- """
- __primary_key_parser = (pp.CaselessLiteral('PRIMARY KEY') +
- pp.QuotedString('(', endQuoteChar=')').setResultsName('primary_key'))
-
- def __init__(self, connection):
- self._conn = connection
- self.loaded_tables = set()
- self._node_alias_count = itertools.count()
- super().__init__(self)
-
- @staticmethod
- def __foreign_key_parser(database):
- def paste_database(unused1, unused2, toc):
- return ['`{database}`.`{table}`'.format(database=database, table=toc[0])]
-
- return (pp.CaselessLiteral('CONSTRAINT').suppress() +
- pp.QuotedString('`').suppress() +
- pp.CaselessLiteral('FOREIGN KEY').suppress() +
- pp.QuotedString('(', endQuoteChar=')').setResultsName('attributes') +
- pp.CaselessLiteral('REFERENCES') +
- pp.Or([
- pp.QuotedString('`').setParseAction(paste_database),
- pp.Combine(pp.QuotedString('`', unquoteResults=False) + '.' +
- pp.QuotedString('`', unquoteResults=False))]).setResultsName('referenced_table') +
- pp.QuotedString('(', endQuoteChar=')').setResultsName('referenced_attributes'))
-
- def add_table(self, table_name):
- """
- Adds table to the dependency graph
- :param table_name: in format `schema`.`table`
- """
- if table_name in self.loaded_tables:
- return
- fk_parser = self.__foreign_key_parser(table_name.split('.')[0].strip('`'))
- self.loaded_tables.add(table_name)
- self.add_node(table_name)
- create_statement = self._conn.query('SHOW CREATE TABLE %s' % table_name).fetchone()[1].split('\n')
- primary_key = None
- for line in create_statement:
- if primary_key is None:
- try:
- result = self.__primary_key_parser.parseString(line)
- except pp.ParseException:
- pass
- else:
- primary_key = [s.strip(' `') for s in result.primary_key.split(',')]
- try:
- result = fk_parser.parseString(line)
- except pp.ParseException:
- pass
- else:
- referencing_attributes = [r.strip('` ') for r in result.attributes.split(',')]
- referenced_attributes = [r.strip('` ') for r in result.referenced_attributes.split(',')]
- props = dict(
- primary=all(a in primary_key for a in referencing_attributes),
- referencing_attributes=referencing_attributes,
- referenced_attributes=referenced_attributes,
- aliased=not all(a == b for a, b in zip(referencing_attributes, referenced_attributes)),
- multi=not all(a in referencing_attributes for a in primary_key))
- if not props['aliased']:
- self.add_edge(result.referenced_table, table_name, **props)
- else:
- # for aliased dependencies, add an extra node in the format '1', '2', etc
- alias_node = '%d' % next(self._node_alias_count)
- self.add_node(alias_node)
- self.add_edge(result.referenced_table, alias_node, **props)
- self.add_edge(alias_node, table_name, **props)
-
- def load(self, target=None):
- """
- Load dependencies for all loaded schemas.
- This method gets called before any operation that requires dependencies: delete, drop, populate, progress.
- """
- if target is not None and '.' in target: # `database`.`table`
- self.add_table(target)
- else:
- databases = self._conn.schemas if target is None else [target]
- for database in databases:
- for row in self._conn.query('SHOW TABLES FROM `{database}`'.format(database=database)):
- table = row[0]
- if not table.startswith('~'): # exclude service tables
- self.add_table('`{db}`.`{tab}`'.format(db=database, tab=table))
- if not nx.is_directed_acyclic_graph(self): # pragma: no cover
- raise DataJointError('DataJoint can only work with acyclic dependencies')
-
- def descendants(self, full_table_name):
- """
- :param full_table_name: In form `schema`.`table_name`
- :return: all dependent tables sorted in topological order. Self is included.
- """
- nodes = nx.algorithms.dag.descendants(self, full_table_name)
- return [full_table_name] + nx.algorithms.dag.topological_sort(self, nodes)
diff --git a/datajoint/erd.py b/datajoint/erd.py
deleted file mode 100644
index 275006336..000000000
--- a/datajoint/erd.py
+++ /dev/null
@@ -1,308 +0,0 @@
-import networkx as nx
-import re
-import functools
-import io
-import warnings
-
-try:
- from matplotlib import pyplot as plt
- from networkx.drawing.nx_agraph import graphviz_layout
- erd_active = True
-except:
- erd_active = False
-
-from . import Manual, Imported, Computed, Lookup, Part, DataJointError
-from .base_relation import lookup_class_name
-
-
-user_relation_classes = (Manual, Lookup, Computed, Imported, Part)
-
-
-class _AliasNode:
- """
- special class to indicate aliased foreign keys
- """
- pass
-
-
-def _get_tier(table_name):
- if not table_name.startswith('`'):
- return _AliasNode
- else:
- try:
- return next(tier for tier in user_relation_classes
- if re.fullmatch(tier.tier_regexp, table_name.split('`')[-2]))
- except StopIteration:
- return None
-
-if not erd_active:
- class ERD:
- """
- Entity relationship diagram, currently disabled due to the lack of required packages: matplotlib and pygraphviz.
-
- To enable ERD feature, please install both matplotlib and pygraphviz. For instructions on how to install
- these two packages, refer to http://docs.datajoint.io/setup/Install-and-connect.html#python and
- http://tutorials.datajoint.io/setting-up/datajoint-python.html
- """
-
- def __init__(self, *args, **kwargs):
- warnings.warn('ERD functionality depends on matplotlib and pygraphviz. Please install both of these '
- 'libraries to enable the ERD feature.')
-else:
- class ERD(nx.DiGraph):
- """
- Entity relationship diagram.
-
- Usage:
-
- >>> erd = Erd(source)
-
- source can be a base relation object, a base relation class, a schema, or a module that has a schema.
-
- >>> erd.draw()
-
- draws the diagram using pyplot
-
- erd1 + erd2 - combines the two ERDs.
- erd + n - adds n levels of successors
- erd - n - adds n levels of predecessors
- Thus dj.ERD(schema.Table)+1-1 defines the diagram of immediate ancestors and descendants of schema.Table
-
- Note that erd + 1 - 1 may differ from erd - 1 + 1 and so forth.
- Only those tables that are loaded in the connection object are displayed
- """
- def __init__(self, source, context=None):
-
- if isinstance(source, ERD):
- # copy constructor
- self.nodes_to_show = set(source.nodes_to_show)
- self.context = source.context
- super().__init__(source)
- return
-
- # get the caller's locals()
- if context is None:
- import inspect
- frame = inspect.currentframe()
- try:
- context = frame.f_back.f_locals
- finally:
- del frame
- self.context = context
-
- # find connection in the source
- try:
- connection = source.connection
- except AttributeError:
- try:
- connection = source.schema.connection
- except AttributeError:
- raise DataJointError('Could not find database connection in %s' % repr(source[0]))
-
- # initialize graph from dependencies
- connection.dependencies.load()
- super().__init__(connection.dependencies)
-
- # Enumerate nodes from all the items in the list
- self.nodes_to_show = set()
- try:
- self.nodes_to_show.add(source.full_table_name)
- except AttributeError:
- try:
- database = source.database
- except AttributeError:
- try:
- database = source.schema.database
- except AttributeError:
- raise DataJointError('Cannot plot ERD for %s' % repr(source))
- for node in self:
- if node.startswith('`%s`' % database):
- self.nodes_to_show.add(node)
-
- @classmethod
- def from_sequence(cls, sequence):
- """
- The join ERD for all objects in sequence
- :param sequence: a sequence (e.g. list, tuple)
- :return: ERD(arg1) + ... + ERD(argn)
- """
- return functools.reduce(lambda x, y: x+y, map(ERD, sequence))
-
- def add_parts(self):
- """
- Adds to the diagram the part tables of tables already included in the diagram
- :return:
- """
- def is_part(part, master):
- """
- :param part: `database`.`table_name`
- :param master: `database`.`table_name`
- :return: True if part is part of master,
- """
- part = [s.strip('`') for s in part.split('.')]
- master = [s.strip('`') for s in master.split('.')]
- return master[0] == part[0] and master[1] + '__' == part[1][:len(master[1])+2]
-
- self = ERD(self) # copy
- self.nodes_to_show.update(n for n in self.nodes() if any(is_part(n, m) for m in self.nodes_to_show))
- return self
-
- def __add__(self, arg):
- """
- :param arg: either another ERD or a positive integer.
- :return: Union of the ERDs when arg is another ERD or an expansion downstream when arg is a positive integer.
- """
- self = ERD(self) # copy
- try:
- self.nodes_to_show.update(arg.nodes_to_show)
- except AttributeError:
- try:
- self.nodes_to_show.add(arg.full_table_name)
- except AttributeError:
- for i in range(arg):
- new = nx.algorithms.boundary.node_boundary(self, self.nodes_to_show)
- if not new:
- break
- self.nodes_to_show.update(new)
- return self
-
- def __sub__(self, arg):
- """
- :param arg: either another ERD or a positive integer.
- :return: Difference of the ERDs when arg is another ERD or an expansion upstream when arg is a positive integer.
- """
- self = ERD(self) # copy
- try:
- self.nodes_to_show.difference_update(arg.nodes_to_show)
- except AttributeError:
- try:
- self.nodes_to_show.remove(arg.full_table_name)
- except AttributeError:
- for i in range(arg):
- new = nx.algorithms.boundary.node_boundary(nx.DiGraph(self).reverse(), self.nodes_to_show)
- if not new:
- break
- self.nodes_to_show.update(new)
- return self
-
- def __mul__(self, arg):
- """
- Intersection of two ERDs
- :param arg: another ERD
- :return: a new ERD comprising nodes that are present in both operands.
- """
- self = ERD(self) # copy
- self.nodes_to_show.intersection_update(arg.nodes_to_show)
- return self
-
- def _make_graph(self):
- """
- Make the self.graph - a graph object ready for drawing
- """
- # include aliased nodes
- gaps = set(nx.algorithms.boundary.node_boundary(self, self.nodes_to_show)).intersection(
- nx.algorithms.boundary.node_boundary(nx.DiGraph(self).reverse(), self.nodes_to_show))
- nodes = self.nodes_to_show.union(a for a in gaps if a.isdigit)
- # construct subgraph and rename nodes to class names
- graph = nx.DiGraph(self).subgraph(nodes)
- nx.set_node_attributes(graph, 'node_type', {n: _get_tier(n) for n in graph})
- # relabel nodes to class names
- mapping = {node: (lookup_class_name(node, self.context) or node) for node in graph.nodes()}
- new_names = [mapping.values()]
- if len(new_names) > len(set(new_names)):
- raise DataJointError('Some classes have identical names. The ERD cannot be plotted.')
- nx.relabel_nodes(graph, mapping, copy=False)
- return graph
-
- def make_dot(self):
- import networkx as nx
-
- graph = self._make_graph()
- graph.nodes()
-
- scale = 1.2 # scaling factor for fonts and boxes
- label_props = { # http://matplotlib.org/examples/color/named_colors.html
- None: dict(shape='circle', color="#FFFF0040", fontcolor='yellow', fontsize=round(scale*8),
- size=0.4*scale, fixed=False),
- _AliasNode: dict(shape='circle', color="#FF880080", fontcolor='white', fontsize=round(scale*6),
- size=0.15*scale, fixed=True),
- Manual: dict(shape='box', color="#00FF0030", fontcolor='darkgreen', fontsize=round(scale*10),
- size=0.4*scale, fixed=False),
- Lookup: dict(shape='plaintext', color='#00000020', fontcolor='black', fontsize=round(scale*8),
- size=0.4*scale, fixed=False),
- Computed: dict(shape='circle', color='#FF000020', fontcolor='#7F0000A0', fontsize=round(scale*10),
- size=0.3*scale, fixed=True),
- Imported: dict(shape='ellipse', color='#00007F40', fontcolor='#00007FA0', fontsize=round(scale*10),
- size=0.4*scale, fixed=False),
- Part: dict(shape='plaintext', color='#0000000', fontcolor='black', fontsize=round(scale*8),
- size=0.1*scale, fixed=False)}
- node_props = {node: label_props[d['node_type']] for node, d in dict(graph.nodes(data=True)).items()}
-
- dot = nx.drawing.nx_pydot.to_pydot(graph)
- for node in dot.get_nodes():
- node.set_shape('circle')
- name = node.get_name().strip('"')
- props = node_props[name]
- node.set_fontsize(props['fontsize'])
- node.set_fontcolor(props['fontcolor'])
- node.set_shape(props['shape'])
- node.set_fontname('arial')
- node.set_fixedsize('shape' if props['fixed'] else False)
- node.set_width(props['size'])
- node.set_height(props['size'])
- node.set_label(name)
- # node.set_margin(0.05)
- node.set_color(props['color'])
- node.set_style('filled')
-
- for edge in dot.get_edges():
- # see http://www.graphviz.org/content/attrs
- src = edge.get_source().strip('"')
- dest = edge.get_destination().strip('"')
- props = graph.get_edge_data(src, dest)
- edge.set_color('#00000040')
- edge.set_style('solid' if props['primary'] else 'dashed')
- master_part = graph.node[dest]['node_type'] is Part and dest.startswith(src+'.')
- edge.set_weight(3 if master_part else 1)
- edge.set_arrowhead('none')
- edge.set_penwidth(.75 if props['multi'] else 2)
-
- return dot
-
- def make_svg(self):
- from IPython.display import SVG
- return SVG(self.make_dot().create_svg())
-
- def make_png(self):
- return io.BytesIO(self.make_dot().create_png())
-
- def make_image(self):
- return plt.imread(self.make_png())
-
- def _repr_svg_(self):
- return self.make_svg()._repr_svg_()
-
- def draw(self):
- plt.imshow(self.make_image())
- plt.gca().axis('off')
- plt.show()
-
- def save(self, filename, format=None):
- if format is None:
- if filename.lower().endswith('.png'):
- format = 'png'
- elif filename.lower().endswith('.svg'):
- format = 'svg'
- if format.lower() == 'png':
- with open(filename, 'wb') as f:
- f.write(self.make_png().getbuffer().tobytes())
- elif format.lower() == 'svg':
- with open(filename, 'w') as f:
- f.write(self.make_svg().data)
- else:
- raise DataJointError('Unsupported file format')
-
- @staticmethod
- def _layout(graph, **kwargs):
- return graphviz_layout(graph, prog='dot', **kwargs)
-
diff --git a/datajoint/fetch.py b/datajoint/fetch.py
deleted file mode 100644
index 5b5a428d6..000000000
--- a/datajoint/fetch.py
+++ /dev/null
@@ -1,349 +0,0 @@
-from collections import OrderedDict
-from collections.abc import Callable, Iterable
-from functools import partial
-import numpy as np
-from .blob import unpack
-from . import DataJointError
-from . import key as PRIMARY_KEY
-import warnings
-
-
-def update_dict(d1, d2):
- return {k: (d2[k] if k in d2 else d1[k]) for k in d1}
-
-
-class FetchBase:
- def __init__(self, arg):
- # prepare copy constructor
- if isinstance(arg, self.__class__):
- self.sql_behavior = dict(arg.sql_behavior)
- self.ext_behavior = dict(arg.ext_behavior)
- self._relation = arg._relation
- else:
- self._initialize_behavior()
- self._relation = arg
-
- def copy(self):
- """
- DEPRECATED
-
- Creates and returns a copy of this object
- :return: copy FetchBase derivatives
- """
- warnings.warn('Use of `copy` on `fetch` object is deprecated', stacklevel=2)
-
- return self.__class__(self)
-
- def _initialize_behavior(self):
- self.sql_behavior = {}
- self.ext_behavior = dict(squeeze=False)
-
- @property
- def squeeze(self):
- """
- DEPRECATED
-
- Changes the state of the fetch object to squeeze the returned values as much as possible.
- :return: a copy of the fetch object
- """
-
- warnings.warn('Use of `squeeze` on `fetch` object is deprecated. Please use `squeeze=True` keyword arguments '
- 'in the call to `fetch`/`keys` instead', stacklevel=2)
-
- ret = self.copy()
- ret.ext_behavior['squeeze'] = True
- return ret
-
- @staticmethod
- def _prepare_attributes(item):
- """
- Used by fetch.__getitem__ to deal with slices
- :param item: the item passed to __getitem__. Can be a string, a tuple, a list, or a slice.
- :return: a tuple of items to fetch, a list of the corresponding attributes
- :raise DataJointError: if item does not match one of the datatypes above
- """
- if isinstance(item, str) or item is PRIMARY_KEY:
- item = (item,)
- try:
- attributes = tuple(i for i in item if i is not PRIMARY_KEY)
- except TypeError:
- raise DataJointError("Index must be a sequence or a string.")
- return item, attributes
-
- def __len__(self):
- return len(self._relation)
-
-
-class Fetch(FetchBase, Callable, Iterable):
- """
- A fetch object that handles retrieving elements from the database table.
-
- :param relation: relation the fetch object fetches data from
- """
-
- def _initialize_behavior(self):
- super()._initialize_behavior()
- self.sql_behavior = dict(self.sql_behavior, offset=None, limit=None, order_by=None, as_dict=False)
-
- def order_by(self, *args):
- """
- DEPRECATED
-
- Changes the state of the fetch object to order the results by a particular attribute.
- The commands are handed down to mysql.
- :param args: the attributes to sort by. If DESC is passed after the name, then the order is descending.
- :return: a copy of the fetch object
- Example:
-
- >>> my_relation.fetch.order_by('language', 'name DESC')
-
- """
- warnings.warn('Use of `order_by` on `fetch` object is deprecated. Please use `order_by` keyword arguments in '
- 'the call to `fetch`/`keys` instead', stacklevel=2)
- self = Fetch(self)
- if len(args) > 0:
- self.sql_behavior['order_by'] = args
- return self
-
- @property
- def as_dict(self):
- """
- DEPRECATED
-
- Changes the state of the fetch object to return dictionaries.
- :return: a copy of the fetch object
- Example:
-
- >>> my_relation.fetch.as_dict()
-
- """
- warnings.warn('Use of `as_dict` on `fetch` object is deprecated. Please use `as_dict` keyword arguments in the '
- 'call to `fetch`/`keys` instead', stacklevel=2)
- ret = Fetch(self)
- ret.sql_behavior['as_dict'] = True
- return ret
-
- def limit(self, limit):
- """
- DEPRECATED
-
- Limits the number of items fetched.
-
- :param limit: limit on the number of items
- :return: a copy of the fetch object
- """
- warnings.warn('Use of `limit` on `fetch` object is deprecated. Please use `limit` keyword arguments in '
- 'the call to `fetch`/`keys` instead', stacklevel=2)
- ret = Fetch(self)
- ret.sql_behavior['limit'] = limit
- return ret
-
- def offset(self, offset):
- """
- DEPRECATED
-
- Offsets the number of itms fetched. Needs to be applied with limit.
-
- :param offset: offset
- :return: a copy of the fetch object
- """
-
- warnings.warn('Use of `offset` on `fetch` object is deprecated. Please use `offset` keyword arguments in '
- 'the call to `fetch`/`keys` instead', stacklevel=2)
- ret = Fetch(self)
- if ret.sql_behavior['limit'] is None:
- warnings.warn('Fetch offset should be used with a limit.')
- ret.sql_behavior['offset'] = offset
- return ret
-
- def __call__(self, *attrs, **kwargs):
- """
- Fetches the relation from the database table into an np.array and unpacks blob attributes.
-
- :param attrs: OPTIONAL. one or more attributes to fetch. If not provided, the call will return
- all attributes of this relation. If provided, returns tuples with an entry for each attribute.
- :param offset: the number of tuples to skip in the returned result
- :param limit: the maximum number of tuples to return
- :param order_by: the list of attributes to order the results. No ordering should be assumed if order_by=None.
- :param as_dict: returns a list of dictionaries instead of a record array
- :return: the contents of the relation in the form of a structured numpy.array
- """
- # if 'order_by' passed in a string, make into list
- if isinstance(kwargs.get('order_by'), str):
- kwargs['order_by'] = [kwargs['order_by']]
-
- sql_behavior = update_dict(self.sql_behavior, kwargs)
- ext_behavior = update_dict(self.ext_behavior, kwargs)
- total_behavior = dict(sql_behavior)
- total_behavior.update(ext_behavior)
-
- unpack_ = partial(unpack, squeeze=ext_behavior['squeeze'])
-
- if sql_behavior['limit'] is None and sql_behavior['offset'] is not None:
- warnings.warn('Offset set, but no limit. Setting limit to a large number. '
- 'Consider setting a limit explicitly.')
- sql_behavior['limit'] = 2 * len(self._relation)
-
- if len(attrs) == 0: # fetch all attributes
- cur = self._relation.cursor(**sql_behavior)
- heading = self._relation.heading
- if sql_behavior['as_dict']:
- ret = [OrderedDict((name, unpack_(d[name]) if heading[name].is_blob else d[name])
- for name in heading.names)
- for d in cur.fetchall()]
- else:
- ret = list(cur.fetchall())
- ret = np.array(ret, dtype=heading.as_dtype)
- for blob_name in heading.blobs:
- ret[blob_name] = list(map(unpack_, ret[blob_name]))
-
- else: # if list of attributes provided
- attributes = [a for a in attrs if a is not PRIMARY_KEY]
- result = self._relation.proj(*attributes).fetch(**total_behavior)
- return_values = [
- list(to_dicts(result[self._relation.primary_key]))
- if attribute is PRIMARY_KEY else result[attribute]
- for attribute in attrs]
- ret = return_values[0] if len(attrs) == 1 else return_values
-
- return ret
-
- def __iter__(self):
- """
- Iterator that returns the contents of the database.
- """
- sql_behavior = dict(self.sql_behavior)
- ext_behavior = dict(self.ext_behavior)
-
- unpack_ = partial(unpack, squeeze=ext_behavior['squeeze'])
-
- cur = self._relation.cursor(**sql_behavior)
-
- heading = self._relation.heading
- do_unpack = tuple(h in heading.blobs for h in heading.names)
- values = cur.fetchone()
- while values:
- if sql_behavior['as_dict']:
- yield OrderedDict(
- (field_name, unpack_(values[field_name])) if up
- else (field_name, values[field_name])
- for field_name, up in zip(heading.names, do_unpack))
- else:
- yield tuple(unpack_(value) if up else value for up, value in zip(do_unpack, values))
- values = cur.fetchone()
-
- def keys(self, **kwargs):
- """
- Iterator that returns primary keys as a sequence of dicts.
- """
- yield from self._relation.proj().fetch(**dict(self.sql_behavior, as_dict=True, **kwargs))
-
- def __getitem__(self, item):
- """
- DEPRECATED
-
- Fetch attributes as separate outputs.
- datajoint.key is a special value that requests the entire primary key
- :return: tuple with an entry for each element of item
-
- Examples:
- >>> a, b = relation['a', 'b']
- >>> a, b, key = relation['a', 'b', datajoint.key]
- """
-
- warnings.warn('Use of `rel.fetch[a, b]` notation is deprecated. Please use `rel.fetch(a, b) for equivalent '
- 'result', stacklevel=2)
-
- behavior = dict(self.sql_behavior)
- behavior.update(self.ext_behavior)
-
- single_output = isinstance(item, str) or item is PRIMARY_KEY or isinstance(item, int)
- item, attributes = self._prepare_attributes(item)
- result = self._relation.proj(*attributes).fetch(**behavior)
- return_values = [
- list(to_dicts(result[self._relation.primary_key]))
- if attribute is PRIMARY_KEY else result[attribute]
- for attribute in item]
- return return_values[0] if single_output else return_values
-
- def __repr__(self):
- repr_str = """Fetch object for {items} items on {name}\n""".format(name=self._relation.__class__.__name__,
- items=len(self._relation) )
- behavior = dict(self.sql_behavior)
- behavior.update(self.ext_behavior)
- repr_str += '\n'.join(
- ["\t{key}:\t{value}".format(key=k, value=str(v)) for k, v in behavior.items() if v is not None])
- return repr_str
-
-
-class Fetch1(FetchBase, Callable):
- """
- Fetch object for fetching exactly one row.
-
- :param relation: relation the fetch object fetches data from
- """
-
- def __call__(self, *attrs, **kwargs):
- """
- This version of fetch is called when self is expected to contain exactly one tuple.
- :return: the one tuple in the relation in the form of a dict
- """
- heading = self._relation.heading
- ext_behavior = update_dict(self.ext_behavior, kwargs)
- unpack_ = partial(unpack, squeeze=ext_behavior['squeeze'])
-
- if len(attrs) == 0: # fetch all attributes
- cur = self._relation.cursor(as_dict=True)
- ret = cur.fetchone()
- if not ret or cur.fetchone():
- raise DataJointError('fetch1 should only be used for relations with exactly one tuple')
- ret = OrderedDict((name, unpack_(ret[name]) if heading[name].is_blob else ret[name])
- for name in heading.names)
- else:
- attributes = [a for a in attrs if a is not PRIMARY_KEY]
- result = self._relation.proj(*attributes).fetch(**ext_behavior)
- if len(result) != 1:
- raise DataJointError('fetch1 should only return one tuple. %d tuples were found' % len(result))
- return_values = tuple(
- next(to_dicts(result[self._relation.primary_key]))
- if attribute is PRIMARY_KEY else result[attribute][0]
- for attribute in attrs)
- ret = return_values[0] if len(attrs) == 1 else return_values
-
- return ret
-
- def __getitem__(self, item):
- """
- DEPRECATED
-
- Fetch attributes as separate outputs.
- datajoint.key is a special value that requests the entire primary key
- :return: tuple with an entry for each element of item
-
- Examples:
-
- >>> a, b = relation['a', 'b']
- >>> a, b, key = relation['a', 'b', datajoint.key]
-
- """
- warnings.warn('Use of `rel.fetch[a, b]` notation is deprecated. Please use `rel.fetch(a, b) for equivalent '
- 'result', stacklevel=2)
-
- behavior = dict(self.sql_behavior)
- behavior.update(self.ext_behavior)
-
- single_output = isinstance(item, str) or item is PRIMARY_KEY
- item, attributes = self._prepare_attributes(item)
- result = self._relation.proj(*attributes).fetch(**behavior)
- if len(result) != 1:
- raise DataJointError('fetch1 should only return one tuple. %d tuples were found' % len(result))
- return_values = tuple(
- next(to_dicts(result[self._relation.primary_key]))
- if attribute is PRIMARY_KEY else result[attribute][0]
- for attribute in item)
- return return_values[0] if single_output else return_values
-
-
-def to_dicts(recarray):
- for rec in recarray:
- yield dict(zip(recarray.dtype.names, rec.tolist()))
diff --git a/datajoint/hash.py b/datajoint/hash.py
deleted file mode 100644
index c83f7a12e..000000000
--- a/datajoint/hash.py
+++ /dev/null
@@ -1,34 +0,0 @@
-import hashlib
-import base64
-
-
-def to_ascii(byte_string):
- """
- :param byte_string: a binary string
- :return: web-safe 64-bit ASCII encoding of binary strings
- """
- return base64.b64encode(byte_string, b'-_').decode()
-
-
-def long_hash(buffer):
- """
- :param buffer: a binary buffer (e.g. serialized blob)
- :return: 43-character base64 ASCII rendition SHA-256
- """
- return to_ascii(hashlib.sha256(buffer).digest())[0:43]
-
-
-def short_hash(buffer):
- """
- :param buffer: a binary buffer (e.g. serialized blob)
- :return: the first 8 characters of base64 ASCII rendition SHA-1
- """
- return to_ascii(hashlib.sha1(buffer).digest())[:8]
-
-
-# def filehash(filename):
-# s = hashlib.sha256()
-# with open(filename, 'rb') as f:
-# for block in iter(lambda: f.read(65536), b''):
-# s.update(block)
-# return to_ascii(s.digest())
diff --git a/datajoint/heading.py b/datajoint/heading.py
deleted file mode 100644
index 00f2101b9..000000000
--- a/datajoint/heading.py
+++ /dev/null
@@ -1,276 +0,0 @@
-import numpy as np
-from collections import namedtuple, OrderedDict
-import re
-import logging
-from . import DataJointError
-
-logger = logging.getLogger(__name__)
-
-default_attribute_properties = dict( # these default values are set in computed attributes
- name=None, type='expression', in_key=False, nullable=False, default=None, comment='calculated attribute',
- autoincrement=False, numeric=None, string=None, is_blob=False, sql_expression=None, dtype=object)
-
-
-class Attribute(namedtuple('_Attribute', default_attribute_properties.keys())):
- """
- Properties of a table column (attribute)
- """
- def todict(self):
- """Convert namedtuple to dict."""
- return OrderedDict((name, self[i]) for i, name in enumerate(self._fields))
-
- @property
- def sql(self):
- """
- Convert primary key attribute tuple into its SQL CREATE TABLE clause.
- Default values are not reflected.
- :return: SQL code
- """
- assert self.in_key and not self.nullable # primary key attributes are never nullable
- return '`{name}` {type} NOT NULL COMMENT "{comment}"'.format(
- name=self.name, type=self.type, comment=self.comment)
-
-
-class Heading:
- """
- Local class for relations' headings.
- Heading contains the property attributes, which is an OrderedDict in which the keys are
- the attribute names and the values are Attributes.
- """
-
- def __init__(self, arg=None):
- """
- :param arg: a list of dicts with the same keys as Attribute
- """
- assert not isinstance(arg, Heading), 'Headings cannot be copied'
- self.table_info = None
- self.attributes = None if arg is None else OrderedDict(
- (q['name'], Attribute(**q)) for q in arg)
-
- def __len__(self):
- return 0 if self.attributes is None else len(self.attributes)
-
- def __bool__(self):
- return self.attributes is not None
-
- @property
- def names(self):
- return [k for k in self.attributes]
-
- @property
- def primary_key(self):
- return [k for k, v in self.attributes.items() if v.in_key]
-
- @property
- def dependent_attributes(self):
- return [k for k, v in self.attributes.items() if not v.in_key]
-
- @property
- def blobs(self):
- return [k for k, v in self.attributes.items() if v.is_blob]
-
- @property
- def non_blobs(self):
- return [k for k, v in self.attributes.items() if not v.is_blob]
-
- @property
- def expressions(self):
- return [k for k, v in self.attributes.items() if v.sql_expression is not None]
-
- def __getitem__(self, name):
- """shortcut to the attribute"""
- return self.attributes[name]
-
- def __repr__(self):
- if self.attributes is None:
- return 'heading not loaded'
- in_key = True
- ret = ''
- if self.table_info:
- ret += '# ' + self.table_info['comment'] + '\n'
- for v in self.attributes.values():
- if in_key and not v.in_key:
- ret += '---\n'
- in_key = False
- ret += '%-20s : %-28s # %s\n' % (
- v.name if v.default is None else '%s=%s' % (v.name, v.default),
- '%s%s' % (v.type, 'auto_increment' if v.autoincrement else ''), v.comment)
- return ret
-
- @property
- def has_autoincrement(self):
- return any(e.autoincrement for e in self.attributes.values())
-
- @property
- def as_dtype(self):
- """
- represent the heading as a numpy dtype
- """
- return np.dtype(dict(
- names=self.names,
- formats=[v.dtype for v in self.attributes.values()]))
-
- @property
- def as_sql(self):
- """
- represent heading as SQL field list
- """
- return ','.join(['`%s`' % name
- if self.attributes[name].sql_expression is None
- else '%s as `%s`' % (self.attributes[name].sql_expression, name)
- for name in self.names])
-
- def __iter__(self):
- return iter(self.attributes)
-
- def init_from_database(self, conn, database, table_name):
- """
- initialize heading from a database table. The table must exist already.
- """
- info = conn.query('SHOW TABLE STATUS FROM `{database}` WHERE name="{table_name}"'.format(
- table_name=table_name, database=database), as_dict=True).fetchone()
- if info is None:
- if table_name == '~log':
- logger.warning('Could not create the ~log table')
- return
- else:
- raise DataJointError('The table `{database}`.`{table_name}` is not defined.'.format(
- table_name=table_name, database=database))
- self.table_info = {k.lower(): v for k, v in info.items()}
-
- cur = conn.query(
- 'SHOW FULL COLUMNS FROM `{table_name}` IN `{database}`'.format(
- table_name=table_name, database=database), as_dict=True)
-
- attributes = cur.fetchall()
-
- rename_map = {
- 'Field': 'name',
- 'Type': 'type',
- 'Null': 'nullable',
- 'Default': 'default',
- 'Key': 'in_key',
- 'Comment': 'comment'}
-
- fields_to_drop = ('Privileges', 'Collation')
-
- # rename and drop attributes
- attributes = [{rename_map[k] if k in rename_map else k: v
- for k, v in x.items() if k not in fields_to_drop}
- for x in attributes]
-
- numeric_types = {
- ('float', False): np.float64,
- ('float', True): np.float64,
- ('double', False): np.float64,
- ('double', True): np.float64,
- ('tinyint', False): np.int64,
- ('tinyint', True): np.int64,
- ('smallint', False): np.int64,
- ('smallint', True): np.int64,
- ('mediumint', False): np.int64,
- ('mediumint', True): np.int64,
- ('int', False): np.int64,
- ('int', True): np.int64,
- ('bigint', False): np.int64,
- ('bigint', True): np.uint64
- }
-
- sql_literals = ['CURRENT_TIMESTAMP']
-
- # additional attribute properties
- for attr in attributes:
- attr['nullable'] = (attr['nullable'] == 'YES')
- attr['in_key'] = (attr['in_key'] == 'PRI')
- attr['autoincrement'] = bool(re.search(r'auto_increment', attr['Extra'], flags=re.IGNORECASE))
- attr['type'] = re.sub(r'int\(\d+\)', 'int', attr['type'], count=1) # strip size off integers
- attr['numeric'] = bool(re.match(r'(tiny|small|medium|big)?int|decimal|double|float', attr['type']))
- attr['string'] = bool(re.match(r'(var)?char|enum|date|year|time|timestamp', attr['type']))
- attr['is_blob'] = bool(re.match(r'(tiny|medium|long)?blob', attr['type']))
-
- if attr['string'] and attr['default'] is not None and attr['default'] not in sql_literals:
- attr['default'] = '"%s"' % attr['default']
-
- if attr['nullable']: # nullable fields always default to null
- attr['default'] = 'null'
-
- attr['sql_expression'] = None
- if not (attr['numeric'] or attr['string'] or attr['is_blob']):
- raise DataJointError('Unsupported field type {field} in `{database}`.`{table_name}`'.format(
- field=attr['type'], database=database, table_name=table_name))
- attr.pop('Extra')
-
- # fill out dtype. All floats and non-nullable integers are turned into specific dtypes
- attr['dtype'] = object
- if attr['numeric']:
- is_integer = bool(re.match(r'(tiny|small|medium|big)?int', attr['type']))
- is_float = bool(re.match(r'(double|float)', attr['type']))
- if is_integer and not attr['nullable'] or is_float:
- is_unsigned = bool(re.match('\sunsigned', attr['type'], flags=re.IGNORECASE))
- t = attr['type']
- t = re.sub(r'\(.*\)', '', t) # remove parentheses
- t = re.sub(r' unsigned$', '', t) # remove unsigned
- assert (t, is_unsigned) in numeric_types, 'dtype not found for type %s' % t
- attr['dtype'] = numeric_types[(t, is_unsigned)]
- self.attributes = OrderedDict([(q['name'], Attribute(**q)) for q in attributes])
-
- def project(self, attribute_list, named_attributes=None, force_primary_key=None):
- """
- derive a new heading by selecting, renaming, or computing attributes.
- In relational algebra these operators are known as project, rename, and extend.
- :param attribute_list: the full list of existing attributes to include
- :param force_primary_key: attributes to force to be converted to primary
- :param named_attributes: dictionary of renamed attributes
- """
- try: # check for missing attributes
- raise DataJointError('Attribute `%s` is not found' % next(a for a in attribute_list if a not in self.names))
- except StopIteration:
- if named_attributes is None:
- named_attributes = {}
- if force_primary_key is None:
- force_primary_key = set()
- return Heading(
- [dict( # copied attributes
- self.attributes[k].todict(),
- in_key=self.attributes[k].in_key or k in force_primary_key)
- for k in attribute_list] +
- [dict( # renamed attributes
- self.attributes[sql_expression].todict(),
- name=new_name,
- sql_expression='`%s`' % sql_expression,
- in_key=self.attributes[sql_expression].in_key or sql_expression in force_primary_key)
- if sql_expression in self.names else
- dict( # computed attributes
- default_attribute_properties,
- name=new_name,
- sql_expression=sql_expression)
- for new_name, sql_expression in named_attributes.items()])
-
- def join(self, other):
- """
- Join two headings into a new one.
- It assumes that self and other are headings that share no common dependent attributes.
- """
- return Heading(
- [self.attributes[name].todict() for name in self.primary_key] +
- [other.attributes[name].todict() for name in other.primary_key if name not in self.primary_key] +
- [self.attributes[name].todict() for name in self.dependent_attributes if name not in other.primary_key] +
- [other.attributes[name].todict() for name in other.dependent_attributes if name not in self.primary_key])
-
- def make_subquery_heading(self):
- """
- Create a new heading with removed attribute sql_expressions.
- Used by subqueries, which resolve the sql_expressions.
- """
- return Heading(dict(v.todict(), sql_expression=None) for v in self.attributes.values())
-
- def extend_primary_key(self, new_attributes):
- """
- Create a new heading in which the primary key also includes new_attributes.
- :param new_attributes: new attributes to be added to the primary key.
- """
- try: # check for missing attributes
- raise DataJointError('Attribute `%s` is not found' % next(a for a in new_attributes if a not in self.names))
- except StopIteration:
- return Heading(dict(v.todict(), in_key=v.in_key or v.name in new_attributes)
- for v in self.attributes.values())
diff --git a/datajoint/jobs.py b/datajoint/jobs.py
deleted file mode 100644
index 5563125bc..000000000
--- a/datajoint/jobs.py
+++ /dev/null
@@ -1,135 +0,0 @@
-import hashlib
-import os
-import pymysql
-from .base_relation import BaseRelation
-
-ERROR_MESSAGE_LENGTH = 2047
-TRUNCATION_APPENDIX = '...truncated'
-
-
-def key_hash(key):
- """
- 32-byte hash used for lookup of primary keys of jobs
- """
- hashed = hashlib.md5()
- for k, v in sorted(key.items()):
- hashed.update(str(v).encode())
- return hashed.hexdigest()
-
-
-class JobTable(BaseRelation):
- """
- A base relation with no definition. Allows reserving jobs
- """
- def __init__(self, arg, database=None):
- if isinstance(arg, JobTable):
- super().__init__(arg)
- # copy constructor
- self.database = arg.database
- self._connection = arg._connection
- self._definition = arg._definition
- self._user = arg._user
- return
- super().__init__()
- self.database = database
- self._connection = arg
- self._definition = """ # job reservation table for `{database}`
- table_name :varchar(255) # className of the table
- key_hash :char(32) # key hash
- ---
- status :enum('reserved','error','ignore') # if tuple is missing, the job is available
- key=null :blob # structure containing the key
- error_message="" :varchar({error_message_length}) # error message returned if failed
- error_stack=null :blob # error stack if failed
- user="" :varchar(255) # database user
- host="" :varchar(255) # system hostname
- pid=0 :int unsigned # system process id
- connection_id = 0 : bigint unsigned # connection_id()
- timestamp=CURRENT_TIMESTAMP :timestamp # automatic timestamp
- """.format(database=database, error_message_length=ERROR_MESSAGE_LENGTH)
- if not self.is_declared:
- self.declare()
- self._user = self.connection.get_user()
-
- @property
- def definition(self):
- return self._definition
-
- @property
- def table_name(self):
- return '~jobs'
-
- def delete(self):
- """bypass interactive prompts and dependencies"""
- self.delete_quick()
-
- def drop(self):
- """bypass interactive prompts and dependencies"""
- self.drop_quick()
-
- def reserve(self, table_name, key):
- """
- Reserve a job for computation. When a job is reserved, the job table contains an entry for the
- job key, identified by its hash. When jobs are completed, the entry is removed.
- :param table_name: `database`.`table_name`
- :param key: the dict of the job's primary key
- :return: True if reserved job successfully. False = the jobs is already taken
- """
- job = dict(
- table_name=table_name,
- key_hash=key_hash(key),
- status='reserved',
- host=os.uname().nodename,
- pid=os.getpid(),
- connection_id=self.connection.connection_id,
- key=key,
- user=self._user)
- try:
- self.insert1(job, ignore_extra_fields=True)
- except pymysql.err.IntegrityError:
- return False
- return True
-
- def complete(self, table_name, key):
- """
- Log a completed job. When a job is completed, its reservation entry is deleted.
- :param table_name: `database`.`table_name`
- :param key: the dict of the job's primary key
- """
- job_key = dict(table_name=table_name, key_hash=key_hash(key))
- (self & job_key).delete_quick()
-
- def error(self, table_name, key, error_message):
- """
- Log an error message. The job reservation is replaced with an error entry.
- if an error occurs, leave an entry describing the problem
- :param table_name: `database`.`table_name`
- :param key: the dict of the job's primary key
- :param error_message: string error message
- """
- if len(error_message) > ERROR_MESSAGE_LENGTH:
- error_message = error_message[:ERROR_MESSAGE_LENGTH-len(TRUNCATION_APPENDIX)] + TRUNCATION_APPENDIX
- job_key = dict(table_name=table_name, key_hash=key_hash(key))
- self.insert1(
- dict(job_key,
- status="error",
- host=os.uname().nodename,
- pid=os.getpid(),
- connection_id=self.connection.connection_id,
- user=self._user,
- key=key,
- error_message=error_message), replace=True, ignore_extra_fields=True)
-
-
-class JobManager:
- """
- A container for all job tables (one job table per schema).
- """
- def __init__(self, connection):
- self.connection = connection
- self._jobs = {}
-
- def __getitem__(self, database):
- if database not in self._jobs:
- self._jobs[database] = JobTable(self.connection, database)
- return self._jobs[database]
diff --git a/datajoint/relational_operand.py b/datajoint/relational_operand.py
deleted file mode 100644
index 754258655..000000000
--- a/datajoint/relational_operand.py
+++ /dev/null
@@ -1,806 +0,0 @@
-import collections
-from itertools import zip_longest
-import logging
-import numpy as np
-import re
-import datetime
-import decimal
-from . import DataJointError, config
-from .fetch import Fetch, Fetch1
-
-logger = logging.getLogger(__name__)
-
-
-def equal_ignore_case(str1, str2):
- try:
- return str1.upper() == str2.upper()
- except AttributeError:
- return False
-
-
-def restricts_to_same(arg):
- """
- returns True if restriction with arg produces the same result as not restricting at all
- """
- return (isinstance(arg, U) or arg is True or equal_ignore_case(arg, "TRUE") or
- isinstance(arg, Not) and restricts_to_empty(arg.restriction))
-
-
-def restricts_to_empty(arg):
- """
- returns True if restriction with arg must produce the empty relation.
- """
- or_lists = (list, set, tuple, np.ndarray)
- return (arg is None or (isinstance(arg, AndList) and any(restricts_to_empty(r) for r in arg)) or
- arg is None or arg is False or equal_ignore_case(arg, "FALSE") or
- isinstance(arg, or_lists) and len(arg) == 0 or # empty OR-list equals FALSE
- isinstance(arg, Not) and restricts_to_same(arg.restriction))
-
-
-class AndList(list):
- """
- A list of restrictions to by applied to a relation. The restrictions are AND-ed.
- Each restriction can be a list or set or a relation whose elements are OR-ed.
- But the elements that are lists can contain other AndLists.
-
- Example:
- rel2 = rel & dj.AndList((cond1, cond2, cond3))
- is equivalent to
- rel2 = rel & cond1 & cond2 & cond3
- """
- pass
-
-
-class OrList(list):
- """
- A list of restrictions to by applied to a relation. The restrictions are OR-ed.
- If any restriction is .
- But the elements that are lists can contain other AndLists.
-
- Example:
- rel2 = rel & dj.ORList((cond1, cond2, cond3))
- is equivalent to
- rel2 = rel & [cond1, cond2, cond3]
-
- Since ORList is just an alias for list, it is not necessary and is only provided
- for consistency with AndList.
- """
- pass
-
-
-class RelationalOperand:
- """
- RelationalOperand implements the relational algebra.
- RelationalOperand objects link other relational operands with relational operators.
- The leaves of this tree of objects are base relations.
- When fetching data from the database, this tree of objects is compiled into an SQL expression.
- RelationalOperand operators are restrict, join, proj, and aggregate.
- """
-
- def __init__(self, arg=None):
- if arg is None: # initialize
- # initialize
- self._restrictions = AndList()
- self._distinct = False
- else: # copy
- assert isinstance(arg, RelationalOperand), 'Cannot make RelationalOperand from %s' % arg.__class__.__name__
- self._restrictions = AndList(arg._restrictions)
- self._distinct = arg.distinct
-
- @classmethod
- def create(cls): # pragma: no cover
- """abstract method for creating an instance"""
- assert False, "Abstract method `create` must be overridden in subclass."
-
- @property
- def connection(self):
- """
- :return: the dj.Connection object
- """
- return self._connection
-
- @property
- def heading(self):
- """
- :return: the dj.Heading object of the relation
- """
- return self._heading
-
- @property
- def distinct(self):
- """True if the DISTINCT modifier is required to turn the query into a relation"""
- return self._distinct
-
- @property
- def restrictions(self):
- """
- :return: The AndList of restrictions applied to the relation.
- """
- assert isinstance(self._restrictions, AndList)
- return self._restrictions
-
- @property
- def is_restricted(self):
- return len(self.restrictions) > 0
-
- @property
- def primary_key(self):
- return self.heading.primary_key
-
- @property
- def where_clause(self):
- """
- convert self.restrictions to the SQL WHERE clause
- """
-
- def make_condition(arg, _negate=False):
- if isinstance(arg, str):
- return arg, _negate
- elif isinstance(arg, AndList):
- return '(' + ' AND '.join([make_condition(element)[0] for element in arg]) + ')', _negate
- # semijoin or antijoin
- elif isinstance(arg, RelationalOperand):
- common_attributes = [q for q in self.heading.names if q in arg.heading.names]
- if not common_attributes:
- condition = 'FALSE' if _negate else 'TRUE'
- else:
- condition = '({fields}) {not_}in ({subquery})'.format(
- fields='`' + '`,`'.join(common_attributes) + '`',
- not_="not " if _negate else "",
- subquery=arg.make_sql(common_attributes))
- return condition, False # _negate is cleared
-
- # mappings are turned into ANDed equality conditions
- elif isinstance(arg, collections.abc.Mapping):
- condition = ['`%s`=%r' % (k, (v if not isinstance(v, (
- datetime.date, datetime.datetime, datetime.time, decimal.Decimal)) else str(v)))
- for k, v in arg.items() if k in self.heading]
- elif isinstance(arg, np.void):
- # element of a record array
- condition = [('`%s`='+('%s' if self.heading[k].numeric else '"%s"')) % (k, arg[k])
- for k in arg.dtype.fields if k in self.heading]
- else:
- raise DataJointError('Invalid restriction type')
- return ' AND '.join(condition) if condition else 'TRUE', _negate
-
- if not self.is_restricted:
- return ''
-
- # An empty or-list in the restrictions immediately causes an empty result
- if restricts_to_empty(self.restrictions):
- return ' WHERE FALSE'
-
- conditions = []
- for item in self.restrictions:
- negate = isinstance(item, Not)
- if negate:
- item = item.restriction # NOT is added below
- if isinstance(item, (list, tuple, set, np.ndarray)):
- item = '(' + ') OR ('.join(
- [make_condition(q)[0] for q in item if q is not restricts_to_empty(q)]) + ')'
- else:
- item, negate = make_condition(item, negate)
- conditions.append(('NOT (%s)' if negate else '(%s)') % item)
- return ' WHERE ' + ' AND '.join(conditions)
-
- def get_select_fields(self, select_fields=None):
- """
- :return: string specifying the attributes to return
- """
- return self.heading.as_sql if select_fields is None else self.heading.project(select_fields).as_sql
-
- # --------- relational operators -----------
-
- def __mul__(self, other):
- """
- natural join of relations self and other
- """
- return other * self if isinstance(other, U) else Join.create(self, other)
-
- def proj(self, *attributes, **named_attributes):
- """
- Relational projection operator.
- :param attributes: attributes to be included in the result. (The primary key is already included).
- :param named_attributes: new attributes computed or renamed from existing attributes.
- :return: the projected relation.
- Primary key attributes are always cannot be excluded but may be renamed.
- Thus self.proj() produces the relation with only the primary key of self.
- self.proj(a='id') renames the attribute 'id' into 'a' and includes 'a' in the projection.
- self.proj(a='expr') adds a new field a with the value computed with SQL expression.
- self.proj(a='(id)') adds a new computed field named 'a' that has the same value as id
- Each attribute can only be used once in attributes or named_attributes.
- """
- ret = Projection.create(self, attributes, named_attributes)
- return ret
-
- def aggregate(self, group, *attributes, keep_all_rows=False, **named_attributes):
- """
- Relational aggregation/projection operator
- :param group: relation whose tuples can be used in aggregation operators
- :param attributes: attributes of self to include in the resulting relation
- :param keep_all_rows: True = preserve the number of tuples in the result (equivalent of LEFT JOIN in SQL)
- :param named_attributes: renamings and computations on attributes of self and group
- :return: a relation representing the result of the aggregation/projection operator
- """
- return GroupBy.create(self, group, keep_all_rows=keep_all_rows,
- attributes=attributes, named_attributes=named_attributes)
-
- aggr = aggregate # shorthand
-
- def __iand__(self, restriction):
- """
- in-place restriction.
- A subquery is created if the argument has renamed attributes. Then the restriction is not in place.
-
- See relational_operand.restrict for more detail.
- """
- return (Subquery.create(self) if self.heading.expressions else self).restrict(restriction)
-
- def __and__(self, restriction):
- """
- relational restriction or semijoin
- :return: a restricted copy of the argument
- See relational_operand.restrict for more detail.
- """
- return (Subquery.create(self) # the HAVING clause in GroupBy can handle renamed attributes but WHERE cannot
- if self.heading.expressions and not isinstance(self, GroupBy)
- else self.__class__(self)).restrict(restriction)
-
- def __isub__(self, restriction):
- """
- in-place inverted restriction aka antijoin
-
- See relational_operand.restrict for more detail.
- """
- return self.restrict(Not(restriction))
-
- def __sub__(self, restriction):
- """
- inverted restriction aka antijoin
- :return: a restricted copy of the argument
-
- See relational_operand.restrict for more detail.
- """
- return self & Not(restriction)
-
- def restrict(self, restriction):
- """
- In-place restriction. Restricts the relation to a subset of its original tuples.
- rel.restrict(restriction) is equivalent to rel = rel & restriction or rel &= restriction
- rel.restrict(Not(restriction)) is equivalent to rel = rel - restriction or rel -= restriction
- The primary key of the result is unaffected.
- Successive restrictions are combined using the logical AND.
- The AndList class is provided to play the role of successive restrictions.
- Any relation, collection, or sequence other than an AndList are treated as OrLists.
- However, the class OrList is still provided for cases when explicitness is required.
- Inverse restriction is accomplished by either using the subtraction operator or the Not class.
-
- The expressions in each row equivalent:
-
- rel & True rel
- rel & False the empty relation
- rel & 'TRUE' rel
- rel & 'FALSE' the empty relation
- rel - cond rel & Not(cond)
- rel - 'TRUE' rel & False
- rel - 'FALSE' rel
- rel & AndList((cond1,cond2)) rel & cond1 & cond2
- rel & AndList() rel
- rel & [cond1, cond2] rel & OrList((cond1, cond2))
- rel & [] rel & False
- rel & None rel & False
- rel & any_empty_relation rel & False
- rel - AndList((cond1,cond2)) rel & [Not(cond1), Not(cond2)]
- rel - [cond1, cond2] rel & Not(cond1) & Not(cond2)
- rel - AndList() rel & False
- rel - [] rel
- rel - None rel
- rel - any_empty_relation rel
-
- When arg is another relation, the restrictions rel & arg and rel - arg become the relational semijoin and
- antijoin operators, respectively.
- Then, rel & arg restricts rel to tuples that match at least one tuple in arg (hence arg is treated as an OrList).
- Conversely, rel - arg restricts rel to tuples that do not match any tuples in arg.
- Two tuples match when their common attributes have equal values or when they have no common attributes.
- All shared attributes must be in the primary key of either rel or arg or both or an error will be raised.
-
- relational_operand.restrict is the only access point that modifies restrictions. All other operators must
- ultimately call restrict()
-
- :param restriction: a sequence or an array (treated as OR list), another relation, an SQL condition string, or
- an AndList.
- """
- if not restricts_to_same(restriction):
- assert not self.heading.expressions or isinstance(self, GroupBy), \
- "Cannot restrict in place a projection with renamed attributes."
- if isinstance(restriction, AndList):
- self.restrictions.extend(restriction)
- else:
- self.restrictions.append(restriction)
- return self
-
- @property
- def fetch1(self):
- return Fetch1(self)
-
- @property
- def fetch(self):
- return Fetch(self)
-
- def attributes_in_restriction(self):
- """
- :return: list of attributes that are probably used in the restrictions.
- The function errs on the side of false positives.
- For example, if the restriction is "val='id'", then the attribute 'id' would be flagged.
- This is used internally for optimizing SQL statements.
- """
- return set(name for name in self.heading.names
- if re.search(r'\b' + name + r'\b', self.where_clause))
-
- def __repr__(self):
- return super().__repr__() if config['loglevel'].lower() == 'debug' else self.preview()
-
- def preview(self, limit=None, width=None):
- """
- returns a preview of the contents of the relation.
- """
- rel = self.proj(*self.heading.non_blobs,
- **dict(zip_longest(self.heading.blobs, [], fillvalue="''"))) # replace blobs with
- if limit is None:
- limit = config['display.limit']
- if width is None:
- width = config['display.width']
- tuples = rel.fetch(limit=limit+1)
- has_more = len(tuples) > limit
- tuples = tuples[:limit]
- columns = rel.heading.names
- widths = {f: min(max([len(f)] + [len(str(e)) for e in tuples[f]]) + 4, width) for f in columns}
- templates = {f: '%%-%d.%ds' % (widths[f], widths[f]) for f in columns}
- return (
- ' '.join([templates[f] % ('*' + f if f in rel.primary_key else f) for f in columns]) + '\n' +
- ' '.join(['+' + '-' * (widths[column] - 2) + '+' for column in columns]) + '\n' +
- '\n'.join(' '.join(templates[f] % tup[f] for f in columns) for tup in tuples) +
- ('\n ...\n' if has_more else '\n') +
- (' (%d tuples)\n' % len(rel) if config['display.show_tuple_count'] else ''))
-
- def _repr_html_(self):
- rel = self.proj(*self.heading.non_blobs,
- **dict(zip_longest(self.heading.blobs, [], fillvalue="'=BLOB='"))) # replace blobs with =BLOB=
- info = self.heading.table_info
- tuples = rel.fetch(limit=config['display.limit']+1)
- has_more = len(tuples) > config['display.limit']
- tuples = tuples[0:config['display.limit']]
-
- css = """
-
- """
- head_template = """
-
{column}
- {comment}
-
"""
-
- return """
- {css}
- {title}
-
-
-
{head}
-
{body}
-
- {ellipsis}
- {count}
- """.format(
- css=css,
- title="" if info is None else "%s" % info['comment'],
- head='
'.join(
- head_template.format(column=c, comment=rel.heading.attributes[c].comment,
- primary='primary' if c in self.primary_key else 'nonprimary') for c in
- rel.heading.names),
- ellipsis='
...
' if has_more else '',
- body='
'.join(
- ['\n'.join(['
%s
' % column for column in tup])
- for tup in tuples]),
- count=('
%d tuples
' % len(rel)) if config['display.show_tuple_count'] else '')
-
- def make_sql(self, select_fields=None):
- return 'SELECT {fields} FROM {from_}{where}'.format(
- fields=("DISTINCT " if self.distinct else "") + self.get_select_fields(select_fields),
- from_=self.from_clause,
- where=self.where_clause)
-
- def __len__(self):
- """
- number of tuples in the relation.
- """
- return U().aggr(self, n='count(*)').fetch1('n')
-
- def __bool__(self):
- """
- :return: True if the relation is not empty. Equivalent to len(rel)>0 but may be more efficient.
- """
- return len(self) > 0
-
- def __contains__(self, item):
- """
- returns True if item is found in the relation.
- :param item: any restriction
- (item in relation) is equivalent to bool(self & item) but may be executed more efficiently.
- """
- return bool(self & item) # May be optimized e.g. using an EXISTS query
-
- def cursor(self, offset=0, limit=None, order_by=None, as_dict=False):
- """
- See Relation.fetch() for input description.
- :return: query cursor
- """
- if offset and limit is None:
- raise DataJointError('limit is required when offset is set')
- sql = self.make_sql()
- if order_by is not None:
- sql += ' ORDER BY ' + ', '.join(order_by)
- if limit is not None:
- sql += ' LIMIT %d' % limit + (' OFFSET %d' % offset if offset else "")
- logger.debug(sql)
- return self.connection.query(sql, as_dict=as_dict)
-
-
-class Not:
- """
- invert restriction
- """
-
- def __init__(self, restriction):
- self.restriction = True if isinstance(restriction, U) else restriction
-
-
-class Join(RelationalOperand):
- """
- Relational join.
- Join is a private DataJoint class not exposed to users.
- """
-
- def __init__(self, arg=None):
- super().__init__(arg)
- if arg is not None:
- assert isinstance(arg, Join), "Join copy constructor requires a Join object"
- self._connection = arg.connection
- self._heading = arg.heading
- self._arg1 = arg._arg1
- self._arg2 = arg._arg2
- self._left = arg._left
-
- @classmethod
- def create(cls, arg1, arg2, keep_all_rows=False):
- obj = cls()
- if not isinstance(arg1, RelationalOperand) or not isinstance(arg2, RelationalOperand):
- raise DataJointError('a relation can only be joined with another relation')
- if arg1.connection != arg2.connection:
- raise DataJointError("Cannot join relations from different connections.")
- obj._connection = arg1.connection
- obj._arg1 = cls.make_argument_subquery(arg1)
- obj._arg2 = cls.make_argument_subquery(arg2)
- obj._distinct = obj._arg1.distinct or obj._arg2.distinct
- obj._left = keep_all_rows
- try:
- # ensure no common dependent attributes
- raise DataJointError("Cannot join relations on dependent attribute `%s`" % next(r for r in set(
- obj._arg1.heading.dependent_attributes).intersection(obj._arg2.heading.dependent_attributes)))
- except StopIteration:
- obj._heading = obj._arg1.heading.join(obj._arg2.heading)
- obj.restrict(obj._arg1.restrictions)
- obj.restrict(obj._arg2.restrictions)
- return obj
-
- @staticmethod
- def make_argument_subquery(arg):
- """
- Decide when a Join argument needs to be wrapped in a subquery
- """
- return Subquery.create(arg) if isinstance(arg, (GroupBy, Projection)) else arg
-
- @property
- def from_clause(self):
- return '{from1} NATURAL{left} JOIN {from2}'.format(
- from1=self._arg1.from_clause,
- left=" LEFT" if self._left else "",
- from2=self._arg2.from_clause)
-
-
-class Projection(RelationalOperand):
- """
- Projection is an private DataJoint class that implements relational projection.
- See RelationalOperand.proj() for user interface.
- """
-
- def __init__(self, arg=None):
- super().__init__(arg)
- if arg is not None:
- assert isinstance(arg, Projection), "Projection copy constructor requires a Projection object."
- self._connection = arg.connection
- self._heading = arg.heading
- self._arg = arg._arg
-
- @classmethod
- def create(cls, arg, attributes=None, named_attributes=None, include_primary_key=True):
- """
- :param arg: A relation to be be projected
- :param attributes: attributes to be selected from
- :param named_attributes: new attributes to select or
- :param include_primary_key: True if the primary key must be included even if it's not in attributes.
- :return: the resulting Projection object
- """
- obj = cls()
- obj._connection = arg.connection
- named_attributes = {k: v.strip() for k, v in named_attributes.items()} # clean up values
- obj._distinct = arg.distinct
- if include_primary_key: # include primary key of relation
- attributes = (list(a for a in arg.primary_key if a not in named_attributes.values()) +
- list(a for a in attributes if a not in arg.primary_key))
- else:
- # make distinct if the primary key is not completely selected
- obj._distinct = obj._distinct or not set(arg.primary_key).issubset(
- set(attributes) | set(named_attributes.values()))
- if obj._distinct or cls._need_subquery(arg, attributes, named_attributes):
- obj._arg = Subquery.create(arg)
- obj._heading = obj._arg.heading.project(attributes, named_attributes)
- else:
- obj._arg = arg
- obj._heading = obj._arg.heading.project(attributes, named_attributes)
- obj &= arg.restrictions # copy restrictions when no subquery
- return obj
-
- @staticmethod
- def _need_subquery(arg, attributes, named_attributes):
- """
- Decide whether the projection argument needs to be wrapped in a subquery
- """
- if arg.heading.expressions or arg.distinct: # argument has any renamed (computed) attributes
- return True
- restricting_attributes = arg.attributes_in_restriction()
- return (not restricting_attributes.issubset(attributes) or # if any restricting attribute is projected out or
- any(v.strip() in restricting_attributes for v in named_attributes.values())) # or renamed
-
- @property
- def from_clause(self):
- return self._arg.from_clause
-
-
-class GroupBy(RelationalOperand):
- """
- GroupBy(rel, comp1='expr1', ..., compn='exprn') produces a relation with the primary key specified by rel.heading.
- The computed arguments comp1, ..., compn use aggregation operators on the attributes of rel.
- GroupBy is used RelationalOperand.aggregate and U.aggregate.
- GroupBy is a private class in DataJoint, not exposed to users.
- """
-
- def __init__(self, arg=None):
- super().__init__(arg)
- if arg is not None:
- # copy constructor
- assert isinstance(arg, GroupBy), "GroupBy copy constructor requires a GroupBy object"
- self._connection = arg.connection
- self._heading = arg.heading
- self._arg = arg._arg
- self._keep_all_rows = arg._keep_all_rows
-
- @classmethod
- def create(cls, arg, group, attributes=None, named_attributes=None, keep_all_rows=False):
- if not isinstance(group, RelationalOperand):
- raise DataJointError('a relation can only be joined with another relation')
- obj = cls()
- obj._keep_all_rows = keep_all_rows
- if not (set(group.primary_key) - set(arg.primary_key) or set(group.primary_key) == set(arg.primary_key)):
- raise DataJointError(
- 'The aggregated relation should have additional fields in its primary key for aggregation to work')
- obj._arg = (Join.make_argument_subquery(group) if isinstance(arg, U)
- else Join.create(arg, group, keep_all_rows=keep_all_rows))
- obj._connection = obj._arg.connection
- # always include primary key of arg
- attributes = (list(a for a in arg.primary_key if a not in named_attributes.values()) +
- list(a for a in attributes if a not in arg.primary_key))
- obj._heading = obj._arg.heading.project(
- attributes, named_attributes, force_primary_key=arg.primary_key)
- return obj
-
- def make_sql(self, select_fields=None):
- return 'SELECT {fields} FROM {from_}{where} GROUP BY `{group_by}`{having}'.format(
- fields=self.get_select_fields(select_fields),
- from_=self._arg.from_clause,
- where=self._arg.where_clause,
- group_by='`,`'.join(self.primary_key),
- having=re.sub(r'^ WHERE', ' HAVING', self.where_clause))
-
- def __len__(self):
- return len(Subquery.create(self))
-
-
-class Subquery(RelationalOperand):
- """
- A Subquery encapsulates its argument in a SELECT statement, enabling its use as a subquery.
- The attribute list and the WHERE clause are resolved. Thus, a subquery no longer has any renamed attributes.
- A subquery of a subquery is a just a copy of the subquery with no change in SQL.
- """
- __counter = 0
-
- def __init__(self, arg=None):
- super().__init__(arg)
- if arg is not None:
- # copy constructor
- assert isinstance(arg, Subquery)
- self._connection = arg.connection
- self._heading = arg.heading
- self._arg = arg._arg
-
- @classmethod
- def create(cls, arg):
- """
- construct a subquery from arg
- """
- obj = cls()
- obj._connection = arg.connection
- obj._heading = arg.heading.make_subquery_heading()
- obj._arg = arg
- return obj
-
- @property
- def counter(self):
- Subquery.__counter += 1
- return Subquery.__counter
-
- @property
- def from_clause(self):
- return '(' + self._arg.make_sql() + ') as `_s%x`' % self.counter
-
- def get_select_fields(self, select_fields=None):
- return '*' if select_fields is None else self.heading.project(select_fields).as_sql
-
-
-class U:
- """
- dj.U objects are special relations representing all possible values their attributes.
- dj.U objects cannot be queried on their own but are useful for forming some relational queries.
- dj.U('attr1', ..., 'attrn') represents a relation with the primary key attributes attr1 ... attrn.
- The body of the relation is filled with all possible combinations of values of the attributes.
- Without any attributes, dj.U() represents the relation with one tuple and no attributes.
- The Third Manifesto refers to dj.U() as TABLE_DEE.
-
- Relational restriction:
-
- dj.U can be used to enumerate unique combinations of values of attributes from other relations.
-
- The following expression produces a relation containing all unique combinations of contrast and brightness
- found in relation stimulus:
-
- >>> dj.U('contrast', 'brightness') & stimulus
-
- The following expression produces a relation containing all unique combinations of contrast and brightness that is
- contained in relation1 but not contained in relation 2.
-
- >>> (dj.U('contrast', 'brightness') & relation1) - relation2
-
- Relational aggregation:
-
- In aggregation, dj.U is used to compute aggregate expressions on the entire relation.
-
- The following expression produces a relation with one tuple and one attribute s containing the total number
- of tuples in relation:
-
- >>> dj.U().aggregate(relation, n='count(*)')
-
- The following expression produces a relation with one tuple containing the number n of distinct values of attr
- in relation.
-
- >>> dj.U().aggregate(relation, n='count(distinct attr)')
-
- The following expression produces a relation with one tuple and one attribute s containing the total sum of attr
- from relation:
-
- >>> dj.U().aggregate(relation, s='sum(attr)') # sum of attr from the entire relation
-
- The following expression produces a relation with the count n of tuples in relation containing each unique
- combination of values in attr1 and attr2.
-
- >>> dj.U(attr1,attr2).aggregate(relation, n='count(*)')
-
- Joins:
-
- If relation rel has attributes 'attr1' and 'attr2', then rel*dj.U('attr1','attr2') or produces a relation that is
- identical to rel except attr1 and attr2 are included in the primary key. This is useful for producing a join on
- non-primary key attributes.
- For example, if attr is in both rel1 and rel2 but not in their primary keys, then rel1*rel2 will throw an error
- because in most cases, it does not make sense to join on non-primary key attributes and users must first rename
- attr in one of the operands. The expression dj.U('attr')*rel1*rel2 overrides this constraint.
- Join is commutative.
- """
-
- def __init__(self, *primary_key):
- self._primary_key = primary_key
-
- @property
- def primary_key(self):
- return self._primary_key
-
- def __and__(self, relation):
- if not isinstance(relation, RelationalOperand):
- raise DataJointError('Relation U can only be restricted with another relation.')
- return Projection.create(relation, attributes=self.primary_key,
- named_attributes=dict(), include_primary_key=False)
-
- def __mul__(self, relation):
- """
- Joining relation U * relation has the effect of adding the attributes of U to the primary key of
- the other relation.
- :param relation: other relation
- :return: a copy of the other relation with the primary key extended.
- """
- if not isinstance(relation, RelationalOperand):
- raise DataJointError('Relation U can only be joined with another relation.')
- copy = relation.__class__(relation)
- copy._heading = copy.heading.extend_primary_key(self.primary_key)
- return copy
-
- def aggregate(self, group, **named_attributes):
- """
- Aggregation of the type U('attr1','attr2').aggregate(rel, computation="expression")
- has the primary key ('attr1','attr2') and performs aggregation computations for all matching tuples of relation.
- :param group: The other relation which will be aggregated
- :param named_attributes: computations of the form new_attribute="sql expression on attributes of group"
- :return: The new relation
- """
- return (
- GroupBy.create(self, group=group, keep_all_rows=False, attributes=(), named_attributes=named_attributes)
- if self.primary_key else
- Projection.create(group, attributes=(), named_attributes=named_attributes, include_primary_key=False))
-
- aggr = aggregate # shorthand
diff --git a/datajoint/schema.py b/datajoint/schema.py
deleted file mode 100644
index 9862408e9..000000000
--- a/datajoint/schema.py
+++ /dev/null
@@ -1,227 +0,0 @@
-import warnings
-import pymysql
-import logging
-import inspect
-import re
-from . import conn, DataJointError, config
-from .erd import ERD
-from .heading import Heading
-from .utils import user_choice, to_camel_case
-from .user_relations import Part, Computed, Imported, Manual, Lookup
-from .base_relation import lookup_class_name, Log
-
-logger = logging.getLogger(__name__)
-
-
-def ordered_dir(klass):
- """
- List (most) attributes of the class including inherited ones, similar to `dir` build-in function,
- but respects order of attribute declaration as much as possible.
- :param klass: class to list members for
- :return: a list of attributes declared in klass and its superclasses
- """
- m = []
- mro = klass.mro()
- for c in mro:
- if hasattr(c, '_ordered_class_members'):
- elements = c._ordered_class_members
- else:
- elements = c.__dict__.keys()
- m = [e for e in elements if e not in m] + m
- return m
-
-
-class Schema:
- """
- A schema object is a decorator for UserRelation classes that binds them to their database.
- It also specifies the namespace `context` in which other UserRelation classes are defined.
- """
-
- def __init__(self, database, context, connection=None, create_tables=True):
- """
- Associates the specified database with this schema object. If the target database does not exist
- already, will attempt on creating the database.
-
- :param database: name of the database to associate the decorated class with
- :param context: dictionary for looking up foreign keys references, usually set to locals()
- :param connection: Connection object. Defaults to datajoint.conn()
- """
- if connection is None:
- connection = conn()
- self._log = None
- self.database = database
- self.connection = connection
- self.context = context
- self.create_tables = create_tables
- if not self.exists:
- if not self.create_tables:
- raise DataJointError("Database named `{database}` was not defined. "
- "Set the create_tables flag to create it.".format(database=database))
- else:
- # create database
- logger.info("Database `{database}` could not be found. "
- "Attempting to create the database.".format(database=database))
- try:
- connection.query("CREATE DATABASE `{database}`".format(database=database))
- logger.info('Created database `{database}`.'.format(database=database))
- except pymysql.OperationalError:
- raise DataJointError("Database named `{database}` was not defined, and"
- " an attempt to create has failed. Check"
- " permissions.".format(database=database))
- else:
- self.log('created')
- self.log('connect')
- connection.register(self)
-
- @property
- def log(self):
- if self._log is None:
- self._log = Log(self.connection, self.database)
- return self._log
-
- def __repr__(self):
- return 'Schema database: `{database}` in module: {context}\n'.format(
- database=self.database,
- context=self.context['__name__'] if '__name__' in self.context else "__")
-
- @property
- def size_on_disk(self):
- """
- :return: size of the database in bytes
- """
- return int(self.connection.query(
- """
- SELECT Sum(data_length + index_length)
- FROM information_schema.tables WHERE table_schema='{db}'
- """.format(db=self.database)).fetchone()[0])
-
- def spawn_missing_classes(self):
- """
- Creates the appropriate python user relation classes from tables in the database and places them
- in the context.
- """
- tables = [
- row[0] for row in self.connection.query('SHOW TABLES in `%s`' % self.database)
- if lookup_class_name('`{db}`.`{tab}`'.format(db=self.database, tab=row[0]), self.context, 0) is None]
- master_classes = (Lookup, Manual, Imported, Computed)
- part_tables = []
- for table_name in tables:
- class_name = to_camel_case(table_name)
- if class_name not in self.context:
- try:
- cls = next(cls for cls in master_classes if re.fullmatch(cls.tier_regexp, table_name))
- except StopIteration:
- if re.fullmatch(Part.tier_regexp, table_name):
- part_tables.append(table_name)
- else:
- # declare and decorate master relation classes
- self.context[class_name] = self(type(class_name, (cls,), dict()))
-
- # attach parts to masters
- for table_name in part_tables:
- groups = re.fullmatch(Part.tier_regexp, table_name).groupdict()
- class_name = to_camel_case(groups['part'])
- try:
- master_class = self.context[to_camel_case(groups['master'])]
- except KeyError:
- raise DataJointError('The table %s does not follow DataJoint naming conventions' % table_name)
- part_class = type(class_name, (Part,), dict(definition=...))
- part_class._master = master_class
- self.process_relation_class(part_class, context=self.context, assert_declared=True)
- setattr(master_class, class_name, part_class)
-
- def drop(self, force=False):
- """
- Drop the associated database if it exists
- """
- if not self.exists:
- logger.info("Database named `{database}` does not exist. Doing nothing.".format(database=self.database))
- elif (not config['safemode'] or
- force or
- user_choice("Proceed to delete entire schema `%s`?" % self.database, default='no') == 'yes'):
- logger.info("Dropping `{database}`.".format(database=self.database))
- try:
- self.connection.query("DROP DATABASE `{database}`".format(database=self.database))
- logger.info("Database `{database}` was dropped successfully.".format(database=self.database))
- except pymysql.OperationalError:
- raise DataJointError("An attempt to drop database named `{database}` "
- "has failed. Check permissions.".format(database=self.database))
-
- @property
- def exists(self):
- """
- :return: true if the associated database exists on the server
- """
- cur = self.connection.query("SHOW DATABASES LIKE '{database}'".format(database=self.database))
- return cur.rowcount > 0
-
- def process_relation_class(self, relation_class, context, assert_declared=False):
- """
- assign schema properties to the relation class and declare the table
- """
- relation_class.database = self.database
- relation_class._connection = self.connection
- relation_class._heading = Heading()
- relation_class._context = context
- # instantiate the class, declare the table if not already
- instance = relation_class()
- if not instance.is_declared:
- if not self.create_tables or assert_declared:
- raise DataJointError('Table not declared %s' % instance.table_name)
- else:
- instance.declare()
-
- # fill values in Lookup tables from their contents property
- if instance.is_declared and hasattr(instance, 'contents') and isinstance(instance, Lookup):
- contents = list(instance.contents)
- if len(contents) > len(instance):
- if instance.heading.has_autoincrement:
- warnings.warn(
- 'Contents has changed but cannot be inserted because {table} has autoincrement.'.format(
- table=instance.__class__.__name__))
- else:
- instance.insert(contents, skip_duplicates=True)
-
- def __call__(self, cls):
- """
- Binds the passed in class object to a database. This is intended to be used as a decorator.
- :param cls: class to be decorated
- """
-
- if issubclass(cls, Part):
- raise DataJointError('The schema decorator should not be applied to Part relations')
- ext = {
- cls.__name__: cls,
- 'self': cls}
- self.process_relation_class(cls, context=dict(self.context, **ext))
-
- # Process part relations
- for part in ordered_dir(cls):
- if part[0].isupper():
- part = getattr(cls, part)
- if inspect.isclass(part) and issubclass(part, Part):
- part._master = cls
- # allow addressing master by name or keyword 'master'
- ext = {
- cls.__name__: cls,
- part.__name__: part,
- 'master': cls,
- 'self': part}
- self.process_relation_class(part, context=dict(self.context, **ext))
- return cls
-
- @property
- def jobs(self):
- """
- schema.jobs provides a view of the job reservation table for the schema
- :return: jobs relation
- """
- return self.connection.jobs[self.database]
-
- def erd(self):
- # get the caller's locals()
- import inspect
- frame = inspect.currentframe()
- context = frame.f_back.f_locals
- return ERD(self, context=context)
-
diff --git a/datajoint/settings.py b/datajoint/settings.py
deleted file mode 100644
index b7bc1a4e9..000000000
--- a/datajoint/settings.py
+++ /dev/null
@@ -1,179 +0,0 @@
-"""
-Settings for DataJoint.
-"""
-from contextlib import contextmanager
-import json
-import os
-import pprint
-from collections import OrderedDict
-import logging
-import collections
-from enum import Enum
-from . import DataJointError
-
-LOCALCONFIG = 'dj_local_conf.json'
-GLOBALCONFIG = '.datajoint_config.json'
-
-validators = collections.defaultdict(lambda: lambda value: True)
-validators['database.port'] = lambda a: isinstance(a, int)
-
-Role = Enum('Role', 'manual lookup imported computed job')
-role_to_prefix = {
- Role.manual: '',
- Role.lookup: '#',
- Role.imported: '_',
- Role.computed: '__',
- Role.job: '~'
-}
-prefix_to_role = dict(zip(role_to_prefix.values(), role_to_prefix.keys()))
-
-
-server_error_codes = {
- 'command denied': 1142,
- 'tables does not exist': 1146,
- 'syntax error': 1149
-}
-
-
-default = OrderedDict({
- 'database.host': 'localhost',
- 'database.password': None,
- 'database.user': None,
- 'database.port': 3306,
- 'connection.init_function': None,
- 'database.reconnect': False,
- 'loglevel': 'INFO',
- 'safemode': True,
- 'display.limit': 7,
- 'display.width': 14,
- 'display.show_tuple_count': True
-})
-
-logger = logging.getLogger(__name__)
-log_levels = {
- 'INFO': logging.INFO,
- 'WARNING': logging.WARNING,
- 'CRITICAL': logging.CRITICAL,
- 'DEBUG': logging.DEBUG,
- 'ERROR': logging.ERROR,
- None: logging.NOTSET
-}
-
-
-class Config(collections.MutableMapping):
-
- instance = None
-
- def __init__(self, *args, **kwargs):
- if not Config.instance:
- Config.instance = Config.__Config(*args, **kwargs)
- else:
- Config.instance._conf.update(dict(*args, **kwargs))
-
- def add_history(self, item):
- self.update({'history': self.get('history', []) + [item]})
-
- def __getattr__(self, name):
- return getattr(self.instance, name)
-
- def __getitem__(self, item):
- return self.instance.__getitem__(item)
-
- def __setitem__(self, item, value):
- self.instance.__setitem__(item, value)
-
- def __str__(self):
- return pprint.pformat(self.instance._conf, indent=4)
-
- def __repr__(self):
- return self.__str__()
-
- def __delitem__(self, key):
- del self.instance._conf[key]
-
- def __iter__(self):
- return iter(self.instance._conf)
-
- def __len__(self):
- return len(self.instance._conf)
-
- def save(self, filename):
- """
- Saves the settings in JSON format to the given file path.
- :param filename: filename of the local JSON settings file.
- """
- with open(filename, 'w') as fid:
- json.dump(self._conf, fid, indent=4)
-
- def load(self, filename):
- """
- Updates the setting from config file in JSON format.
- :param filename: filename of the local JSON settings file. If None, the local config file is used.
- """
- if filename is None:
- filename = LOCALCONFIG
- with open(filename, 'r') as fid:
- self._conf.update(json.load(fid))
- self.add_history('Updated from config file: %s' % filename)
-
- def save_local(self):
- """
- saves the settings in the local config file
- """
- self.save(LOCALCONFIG)
-
- def save_global(self):
- """
- saves the settings in the global config file
- """
- self.save(os.path.expanduser(os.path.join('~', GLOBALCONFIG)))
-
- @contextmanager
- def __call__(self, **kwargs):
- """
- The config object can also be used in a with statement to change the state of the configuration
- temporarily. kwargs to the context manager are the keys into config, where '.' is replaced by a
- double underscore '__'. The context manager yields the changed config object.
-
- Example:
- >>> import datajoint as dj
- >>> with dj.config(safemode=False, database__host="localhost") as cfg:
- >>> # do dangerous stuff here
- """
-
- try:
- backup = self.instance
- self.instance = Config.__Config(self.instance._conf)
- new = {k.replace('__', '.'): v for k, v in kwargs.items()}
- self.instance._conf.update(new)
- yield self
- except:
- self.instance = backup
- raise
- else:
- self.instance = backup
-
- class __Config:
- """
- Stores datajoint settings. Behaves like a dictionary, but applies validator functions
- when certain keys are set.
-
- The default parameters are stored in datajoint.settings.default . If a local config file
- exists, the settings specified in this file override the default settings.
- """
-
- def __init__(self, *args, **kwargs):
- self._conf = dict(default)
- self._conf.update(dict(*args, **kwargs)) # use the free update to set keys
-
- def __getitem__(self, key):
- return self._conf[key]
-
- def __setitem__(self, key, value):
- logger.log(logging.INFO, u"Setting {0:s} to {1:s}".format(str(key), str(value)))
- if isinstance(value, collections.Mapping):
- raise ValueError("Nested settings are not supported!")
- if validators[key](value):
- self._conf[key] = value
- else:
- raise DataJointError(u'Validator for {0:s} did not pass'.format(key, ))
\ No newline at end of file
diff --git a/datajoint/user_relations.py b/datajoint/user_relations.py
deleted file mode 100644
index 6f7074c80..000000000
--- a/datajoint/user_relations.py
+++ /dev/null
@@ -1,147 +0,0 @@
-"""
-Hosts the table tiers, user relations should be derived from.
-"""
-
-import collections
-from .base_relation import BaseRelation
-from .autopopulate import AutoPopulate
-from .utils import from_camel_case, ClassProperty
-from . import DataJointError
-
-_base_regexp = r'[a-z][a-z0-9]*(_[a-z][a-z0-9]*)*'
-
-
-class OrderedClass(type):
- """
- Class whose members are ordered
- See https://docs.python.org/3/reference/datamodel.html#metaclass-example
-
- TODO: In Python 3.6, this will no longer be necessary and should be removed (PEP 520)
- https://www.python.org/dev/peps/pep-0520/
- """
- @classmethod
- def __prepare__(metacls, name, bases, **kwds):
- return collections.OrderedDict()
-
- def __new__(cls, name, bases, namespace, **kwds):
- result = type.__new__(cls, name, bases, dict(namespace))
- result._ordered_class_members = list(namespace)
- return result
-
- def __setattr__(cls, name, value):
- if hasattr(cls, '_ordered_class_members'):
- cls._ordered_class_members.append(name)
- super().__setattr__(name, value)
-
-
-class UserRelation(BaseRelation, metaclass=OrderedClass):
- """
- A subclass of UserRelation is a dedicated class interfacing a base relation.
- UserRelation is initialized by the decorator generated by schema().
- """
- _connection = None
- _context = None
- _heading = None
- tier_regexp = None
- _prefix = None
-
- @property
- def definition(self):
- """
- :return: a string containing the table definition using the DataJoint DDL.
- """
- raise NotImplementedError('Subclasses of BaseRelation must implement the property "definition"')
-
- @ClassProperty
- def connection(cls):
- return cls._connection
-
- @ClassProperty
- def table_name(cls):
- """
- :returns: the table name of the table formatted for mysql.
- """
- if cls._prefix is None:
- raise AttributeError('Class prefix is not defined!')
- return cls._prefix + from_camel_case(cls.__name__)
-
- @ClassProperty
- def full_table_name(cls):
- if cls.database is None:
- raise DataJointError('Class %s is not properly declared (schema decorator not applied?)' % cls.__name__)
- return r"`{0:s}`.`{1:s}`".format(cls.database, cls.table_name)
-
-
-class Manual(UserRelation):
- """
- Inherit from this class if the table's values are entered manually.
- """
-
- _prefix = r''
- tier_regexp = r'(?P' + _prefix + _base_regexp + ')'
-
-
-class Lookup(UserRelation):
- """
- Inherit from this class if the table's values are for lookup. This is
- currently equivalent to defining the table as Manual and serves semantic
- purposes only.
- """
-
- _prefix = '#'
- tier_regexp = r'(?P' + _prefix + _base_regexp.replace('TIER', 'lookup') + ')'
-
-
-class Imported(UserRelation, AutoPopulate):
- """
- Inherit from this class if the table's values are imported from external data sources.
- The inherited class must at least provide the function `_make_tuples`.
- """
-
- _prefix = '_'
- tier_regexp = r'(?P' + _prefix + _base_regexp + ')'
-
-
-class Computed(UserRelation, AutoPopulate):
- """
- Inherit from this class if the table's values are computed from other relations in the schema.
- The inherited class must at least provide the function `_make_tuples`.
- """
-
- _prefix = '__'
- tier_regexp = r'(?P' + _prefix + _base_regexp + ')'
-
-
-class Part(UserRelation):
- """
- Inherit from this class if the table's values are details of an entry in another relation
- and if this table is populated by this relation. For example, the entries inheriting from
- dj.Part could be single entries of a matrix, while the parent table refers to the entire matrix.
- Part relations are implemented as classes inside classes.
- """
-
- _connection = None
- _context = None
- _heading = None
- _master = None
-
- tier_regexp = r'(?P' + '|'.join(
- [c.tier_regexp for c in (Manual, Lookup, Imported, Computed)]
- ) + r'){1,1}' + '__' + r'(?P' + _base_regexp + ')'
-
- @ClassProperty
- def connection(cls):
- return cls._connection
-
- @ClassProperty
- def full_table_name(cls):
- return None if cls.database is None or cls.table_name is None else r"`{0:s}`.`{1:s}`".format(
- cls.database, cls.table_name)
-
- @ClassProperty
- def master(cls):
- return cls._master
-
- @ClassProperty
- def table_name(cls):
- return None if cls.master is None else cls.master.table_name + '__' + from_camel_case(cls.__name__)
\ No newline at end of file
diff --git a/datajoint/utils.py b/datajoint/utils.py
deleted file mode 100644
index c202c232e..000000000
--- a/datajoint/utils.py
+++ /dev/null
@@ -1,68 +0,0 @@
-import re
-from datajoint import DataJointError
-
-class ClassProperty:
- def __init__(self, f):
- self.f = f
-
- def __get__(self, obj, owner):
- return self.f(owner)
-
-
-def user_choice(prompt, choices=("yes", "no"), default=None):
- """
- Prompts the user for confirmation. The default value, if any, is capitalized.
-
- :param prompt: Information to display to the user.
- :param choices: an iterable of possible choices.
- :param default: default choice
- :return: the user's choice
- """
- choice_list = ', '.join((choice.title() if choice == default else choice for choice in choices))
- valid = False
- while not valid:
- response = input(prompt + ' [' + choice_list + ']: ')
- response = response.lower() if response else default
- valid = response in choices
- return response
-
-
-def to_camel_case(s):
- """
- Convert names with under score (_) separation into camel case names.
-
- :param s: string in under_score notation
- :returns: string in CamelCase notation
-
- Example:
-
- >>> to_camel_case("table_name") # yields "TableName"
-
- """
-
- def to_upper(match):
- return match.group(0)[-1].upper()
-
- return re.sub('(^|[_\W])+[a-zA-Z]', to_upper, s)
-
-
-def from_camel_case(s):
- """
- Convert names in camel case into underscore (_) separated names
-
- :param s: string in CamelCase notation
- :returns: string in under_score notation
-
- Example:
-
- >>> from_camel_case("TableName") # yields "table_name"
-
- """
-
- def convert(match):
- return ('_' if match.groups()[0] else '') + match.group(0).lower()
-
- if not re.match(r'[A-Z][a-zA-Z0-9]*', s):
- raise DataJointError(
- 'ClassName must be alphanumeric in CamelCase, begin with a capital letter')
- return re.sub(r'(\B[A-Z])|(\b[A-Z])', convert, s)
diff --git a/datajoint/version.py b/datajoint/version.py
deleted file mode 100644
index 777f190df..000000000
--- a/datajoint/version.py
+++ /dev/null
@@ -1 +0,0 @@
-__version__ = "0.8.0"
diff --git a/docker-compose.yaml b/docker-compose.yaml
new file mode 100644
index 000000000..23fd773c1
--- /dev/null
+++ b/docker-compose.yaml
@@ -0,0 +1,104 @@
+# Development environment with MySQL and MinIO services
+#
+# NOTE: docker-compose is OPTIONAL for running tests.
+# Tests use testcontainers to automatically manage containers.
+# Just run: pytest tests/
+#
+# Use docker-compose for development/debugging when you want
+# persistent containers that survive test runs:
+# docker compose up -d db minio # Start services manually
+# pytest tests/ # Tests will use these containers
+#
+# Full Docker testing (CI):
+# docker compose --profile test up djtest --build
+services:
+ db:
+ image: datajoint/mysql:${MYSQL_VER:-8.0}
+ environment:
+ - MYSQL_ROOT_PASSWORD=${DJ_PASS:-password}
+ command: mysqld --default-authentication-plugin=mysql_native_password
+ ports:
+ - "3306:3306"
+ healthcheck:
+ test: [ "CMD", "mysqladmin", "ping", "-h", "localhost" ]
+ timeout: 30s
+ retries: 5
+ interval: 15s
+ postgres:
+ image: postgres:${POSTGRES_VER:-15}
+ environment:
+ - POSTGRES_PASSWORD=${PG_PASS:-password}
+ - POSTGRES_USER=${PG_USER:-postgres}
+ - POSTGRES_DB=${PG_DB:-test}
+ ports:
+ - "5432:5432"
+ healthcheck:
+ test: [ "CMD-SHELL", "pg_isready -U postgres" ]
+ timeout: 30s
+ retries: 5
+ interval: 15s
+ minio:
+ image: minio/minio:${MINIO_VER:-RELEASE.2025-02-28T09-55-16Z}
+ environment:
+ - MINIO_ACCESS_KEY=datajoint
+ - MINIO_SECRET_KEY=datajoint
+ ports:
+ - "9000:9000"
+ command: server --address ":9000" /data
+ healthcheck:
+ test:
+ - "CMD"
+ - "curl"
+ - "--fail"
+ - "http://localhost:9000/minio/health/live"
+ timeout: 30s
+ retries: 5
+ interval: 15s
+ app:
+ image: datajoint/datajoint:${DJ_VERSION:-latest}
+ build:
+ context: .
+ dockerfile: Dockerfile
+ args:
+ PY_VER: ${PY_VER:-3.10}
+ HOST_UID: ${HOST_UID:-1000}
+ depends_on:
+ db:
+ condition: service_healthy
+ postgres:
+ condition: service_healthy
+ minio:
+ condition: service_healthy
+ environment:
+ - DJ_HOST=db
+ - DJ_USER=root
+ - DJ_PASS=password
+ - DJ_TEST_HOST=db
+ - DJ_TEST_USER=datajoint
+ - DJ_TEST_PASSWORD=datajoint
+ - DJ_PG_HOST=postgres
+ - DJ_PG_USER=postgres
+ - DJ_PG_PASS=password
+ - DJ_PG_PORT=5432
+ - S3_ENDPOINT=minio:9000
+ - S3_ACCESS_KEY=datajoint
+ - S3_SECRET_KEY=datajoint
+ - S3_BUCKET=datajoint.test
+ - PYTHON_USER=dja
+ - JUPYTER_PASSWORD=datajoint
+ working_dir: /src
+ user: ${HOST_UID:-1000}:mambauser
+ volumes:
+ - .:/src
+ djtest:
+ extends:
+ service: app
+ profiles: ["test"]
+ command:
+ - sh
+ - -c
+ - |
+ set -e
+ pip install -q -e ".[test]"
+ pip freeze | grep datajoint
+ pytest --cov-report term-missing --cov=datajoint tests
diff --git a/docker-compose.yml b/docker-compose.yml
deleted file mode 100644
index 929e8a2c5..000000000
--- a/docker-compose.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-version: '3'
-services:
- datajoint:
- build: .
- environment:
- - DJ_HOST=db
- - DJ_USER=root
- - DJ_PASS=simple
- volumes:
- - .:/src
- links:
- - db
- ports:
- - "8888:8888"
- db:
- image: datajoint/mysql
- environment:
- - MYSQL_ROOT_PASSWORD=simple
-
-
diff --git a/images/pipeline.png b/images/pipeline.png
new file mode 100644
index 000000000..48f5f3ecd
Binary files /dev/null and b/images/pipeline.png differ
diff --git a/images/pipeline.svg b/images/pipeline.svg
new file mode 100644
index 000000000..94154a0c7
--- /dev/null
+++ b/images/pipeline.svg
@@ -0,0 +1,118 @@
+
diff --git a/pixi.lock b/pixi.lock
new file mode 100644
index 000000000..0421929da
--- /dev/null
+++ b/pixi.lock
@@ -0,0 +1,6805 @@
+version: 6
+environments:
+ default:
+ channels:
+ - url: https://conda.anaconda.org/conda-forge/
+ indexes:
+ - https://pypi.org/simple
+ options:
+ pypi-prerelease-mode: if-necessary-or-explicit
+ packages:
+ linux-64:
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/adwaita-icon-theme-48.1-unix_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-atk-2.38.0-h0630a04_3.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-core-2.40.3-h0630a04_0.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-h04ea711_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_8.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/cairo-1.18.4-h3394656_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/dbus-1.16.2-h3c4dab8_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/epoxy-1.5.10-h166bdaf_1.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-h77eed37_3.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-ecosystem-1-0.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/noarch/fonts-conda-forge-1-0.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/freetype-2.14.1-ha770c72_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/fribidi-1.0.16-hb03c661_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/gdk-pixbuf-2.44.1-h2b0a6b4_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/glib-tools-2.86.0-hf516916_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.14-hecca717_2.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/graphviz-13.1.2-h87b6fe6_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/gtk3-3.24.43-h0c6a113_5.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/gts-0.7.6-h977cf35_4.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/harfbuzz-11.5.0-h15599e2_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/hicolor-icon-theme-0.17-ha770c72_2.tar.bz2
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/icu-75.1-he02047a_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/keyutils-1.6.3-hb9d3cd8_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h0aef613_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libcups-2.3.3-hb8b1518_5.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.24-h86f0d12_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libedit-3.1.20250104-pl5321h7949ede_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.7.1-hecca717_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype-2.14.1-ha770c72_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libfreetype6-2.14.1-h73754d4_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.1.0-h767d61c_5.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_5.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libgd-2.3.3-h6f5c62b_11.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libglib-2.86.0-h1fed272_0.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.1.0-h767d61c_5.conda
+ - conda: https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.18-h3b78370_2.conda
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+ sha256: 7c6b9461a2a8b47c65eef63bb1c76a4f1c119618ffa99ea79bc5bb1e46c5821b
+ requires_dist:
+ - idna>=2.0
+ - multidict>=4.0
+ - propcache>=0.2.1
+ requires_python: '>=3.10'
+- pypi: https://files.pythonhosted.org/packages/c4/f4/4e30b250927ffdab4db70da08b9b8d2194d7c7b400167b8fbeca1e4701ca/yarl-1.23.0-cp313-cp313-manylinux2014_aarch64.manylinux_2_17_aarch64.manylinux_2_28_aarch64.whl
+ name: yarl
+ version: 1.23.0
+ sha256: 2569b67d616eab450d262ca7cb9f9e19d2f718c70a8b88712859359d0ab17035
+ requires_dist:
+ - idna>=2.0
+ - multidict>=4.0
+ - propcache>=0.2.1
+ requires_python: '>=3.10'
+- conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
+ sha256: a4166e3d8ff4e35932510aaff7aa90772f84b4d07e9f6f83c614cba7ceefe0eb
+ md5: 6432cb5d4ac0046c3ac0a8a0f95842f9
+ depends:
+ - __glibc >=2.17,<3.0.a0
+ - libgcc >=13
+ - libstdcxx >=13
+ - libzlib >=1.3.1,<2.0a0
+ license: BSD-3-Clause
+ license_family: BSD
+ purls: []
+ size: 567578
+ timestamp: 1742433379869
+- conda: https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-hbcf94c1_2.conda
+ sha256: 0812e7b45f087cfdd288690ada718ce5e13e8263312e03b643dd7aa50d08b51b
+ md5: 5be90c5a3e4b43c53e38f50a85e11527
+ depends:
+ - libgcc >=13
+ - libstdcxx >=13
+ - libzlib >=1.3.1,<2.0a0
+ license: BSD-3-Clause
+ license_family: BSD
+ purls: []
+ size: 551176
+ timestamp: 1742433378347
+- conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.7-h6491c7d_2.conda
+ sha256: 0d02046f57f7a1a3feae3e9d1aa2113788311f3cf37a3244c71e61a93177ba67
+ md5: e6f69c7bcccdefa417f056fa593b40f0
+ depends:
+ - __osx >=11.0
+ - libzlib >=1.3.1,<2.0a0
+ license: BSD-3-Clause
+ license_family: BSD
+ purls: []
+ size: 399979
+ timestamp: 1742433432699
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 000000000..d5c361658
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,272 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "datajoint"
+dynamic = ["version"]
+dependencies = [
+ "numpy",
+ "pymysql>=0.7.2",
+ "deepdiff",
+ "pyparsing",
+ "pandas",
+ "tqdm",
+ "networkx",
+ "pydot",
+ "fsspec>=2023.1.0",
+ "pydantic-settings>=2.0.0",
+ "packaging",
+]
+
+requires-python = ">=3.10,<3.14"
+authors = [
+ {name = "Dimitri Yatsenko", email = "dimitri@datajoint.com"},
+ {name = "Thinh Nguyen", email = "thinh@datajoint.com"},
+ {name = "Raphael Guzman"},
+ {name = "Edgar Walker"},
+ {name = "DataJoint Contributors", email = "support@datajoint.com"},
+]
+maintainers = [
+ {name = "Dimitri Yatsenko", email = "dimitri@datajoint.com"},
+ {name = "DataJoint Contributors", email = "support@datajoint.com"},
+]
+# manually sync here: https://docs.datajoint.com/core/datajoint-python/latest/#welcome-to-datajoint-for-python
+description = "DataJoint for Python is a framework for scientific workflow management based on relational principles. DataJoint is built on the foundation of the relational data model and prescribes a consistent method for organizing, populating, computing, and querying data."
+readme = "README.md"
+license = {file = "LICENSE"}
+keywords = [
+ "datajoint",
+ "data-pipelines",
+ "workflow-management",
+ "data-engineering",
+ "scientific-computing",
+ "neuroscience",
+ "research-software",
+ "data-integrity",
+ "reproducibility",
+ "declarative",
+ "etl",
+ "object-storage",
+ "schema-management",
+ "data-lineage",
+ "relational-model",
+ "mysql",
+ "postgresql",
+]
+# https://pypi.org/classifiers/
+classifiers = [
+ "Programming Language :: Python",
+ "Development Status :: 5 - Production/Stable",
+ "Intended Audience :: Science/Research",
+ "Intended Audience :: Healthcare Industry",
+ "License :: OSI Approved :: Apache Software License",
+ "Topic :: Software Development :: Libraries :: Python Modules",
+ "Topic :: Scientific/Engineering",
+ "Topic :: Scientific/Engineering :: Bio-Informatics",
+ "Topic :: Scientific/Engineering :: Artificial Intelligence",
+]
+
+[project.urls]
+Homepage = "https://docs.datajoint.com/"
+Documentation = "https://docs.datajoint.com/"
+Repository = "https://github.com/datajoint/datajoint-python"
+"Bug Tracker" = "https://github.com/datajoint/datajoint-python/issues"
+"Release Notes" = "https://github.com/datajoint/datajoint-python/releases"
+
+[project.scripts]
+dj = "datajoint.cli:cli"
+datajoint = "datajoint.cli:cli"
+
+[dependency-groups]
+test = [
+ "pytest",
+ "pytest-cov",
+ "requests",
+ "faker",
+ "matplotlib",
+ "ipython",
+ "graphviz",
+ "testcontainers[mysql,minio,postgres]>=4.0",
+ "polars>=0.20.0",
+ "pyarrow>=14.0.0",
+]
+
+[project.optional-dependencies]
+s3 = ["s3fs>=2023.1.0"]
+gcs = ["gcsfs>=2023.1.0"]
+azure = ["adlfs>=2023.1.0"]
+postgres = ["psycopg2-binary>=2.9.0"]
+polars = ["polars>=0.20.0"]
+arrow = ["pyarrow>=14.0.0"]
+viz = ["matplotlib", "ipython"]
+test = [
+ "pytest",
+ "pytest-cov",
+ "requests",
+ "faker",
+ "matplotlib",
+ "ipython",
+ "s3fs>=2023.1.0",
+ "testcontainers[mysql,minio,postgres]>=4.0",
+ "psycopg2-binary>=2.9.0",
+ "polars>=0.20.0",
+ "pyarrow>=14.0.0",
+]
+dev = [
+ "pre-commit",
+ "ruff",
+ "codespell",
+ # including test
+ "pytest",
+ "pytest-cov",
+ "polars>=0.20.0",
+ "pyarrow>=14.0.0",
+]
+
+[tool.ruff]
+# Equivalent to flake8 configuration
+line-length = 127
+target-version = "py310"
+
+[tool.ruff.lint]
+# Enable specific rule sets equivalent to flake8 configuration
+select = [
+ "E", # pycodestyle errors
+ "W", # pycodestyle warnings
+ "F", # pyflakes
+ "C90", # mccabe complexity
+]
+
+# Ignore specific rules (equivalent to flake8 --ignore)
+ignore = [
+ "E203", # whitespace before ':'
+ "E722", # bare except
+]
+
+# Per-file ignores (equivalent to flake8 --per-file-ignores)
+[tool.ruff.lint.per-file-ignores]
+"datajoint/diagram.py" = ["C901"] # function too complex
+"tests/integration/test_blob_matlab.py" = ["E501"] # SQL hex strings cannot be broken across lines
+
+[tool.ruff.lint.mccabe]
+# Maximum complexity (equivalent to flake8 --max-complexity)
+max-complexity = 62
+
+[tool.ruff.format]
+# Use black-compatible formatting
+quote-style = "double"
+indent-style = "space"
+line-ending = "auto"
+
+[tool.mypy]
+python_version = "3.10"
+ignore_missing_imports = true
+# Start with lenient settings, gradually enable stricter checks
+warn_return_any = false
+warn_unused_ignores = false
+disallow_untyped_defs = false
+disallow_incomplete_defs = false
+check_untyped_defs = true
+
+# Modules with complete type coverage - strict checking enabled
+[[tool.mypy.overrides]]
+module = [
+ "datajoint.hash_registry",
+ "datajoint.errors",
+ "datajoint.hash",
+]
+disallow_untyped_defs = true
+disallow_incomplete_defs = true
+warn_return_any = true
+
+# Modules excluded from type checking until fully typed
+[[tool.mypy.overrides]]
+module = [
+ "datajoint.admin",
+ "datajoint.autopopulate",
+ "datajoint.blob",
+ "datajoint.builtin_codecs",
+ "datajoint.cli",
+ "datajoint.codecs",
+ "datajoint.condition",
+ "datajoint.connection",
+ "datajoint.declare",
+ "datajoint.dependencies",
+ "datajoint.diagram",
+ "datajoint.expression",
+ "datajoint.gc",
+ "datajoint.heading",
+ "datajoint.jobs",
+ "datajoint.lineage",
+ "datajoint.logging",
+ "datajoint.migrate",
+ "datajoint.objectref",
+ "datajoint.preview",
+ "datajoint.schemas",
+ "datajoint.settings",
+ "datajoint.staged_insert",
+ "datajoint.storage",
+ "datajoint.table",
+ "datajoint.user_tables",
+ "datajoint.utils",
+]
+ignore_errors = true
+
+[tool.hatch.version]
+path = "src/datajoint/version.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/datajoint"]
+
+[tool.codespell]
+skip = ".git,*.pdf,*.svg,*.csv,*.ipynb,*.drawio"
+# Rever -- nobody knows
+# numer -- numerator variable
+# astroid -- Python library name (not "asteroid")
+ignore-words-list = "rever,numer,astroid"
+
+[tool.pytest.ini_options]
+markers = [
+ "requires_mysql: marks tests as requiring MySQL database (deselect with '-m \"not requires_mysql\"')",
+ "requires_minio: marks tests as requiring MinIO object storage (deselect with '-m \"not requires_minio\"')",
+ "mysql: marks tests that run on MySQL backend (select with '-m mysql')",
+ "postgresql: marks tests that run on PostgreSQL backend (select with '-m postgresql')",
+ "backend_agnostic: marks tests that should pass on all backends (auto-marked for parameterized tests)",
+]
+
+
+
+[tool.pixi.workspace]
+channels = ["conda-forge"]
+platforms = ["linux-64", "osx-arm64", "linux-aarch64"]
+
+[tool.pixi.pypi-dependencies]
+datajoint = { path = ".", editable = true }
+
+[tool.pixi.feature.test.pypi-dependencies]
+datajoint = { path = ".", editable = true, extras = ["test"] }
+
+[tool.pixi.feature.dev.pypi-dependencies]
+datajoint = { path = ".", editable = true, extras = ["dev", "test"] }
+
+[tool.pixi.environments]
+default = { solve-group = "default" }
+dev = { features = ["dev"], solve-group = "default" }
+test = { features = ["test"], solve-group = "default" }
+
+[tool.pixi.tasks]
+# Tests use testcontainers - no manual setup required
+test = "pytest tests/"
+test-cov = "pytest --cov-report term-missing --cov=datajoint tests/"
+# Optional: use external containers (docker-compose) instead of testcontainers
+services-up = "docker compose up -d db minio"
+services-down = "docker compose down"
+test-external = { cmd = "DJ_USE_EXTERNAL_CONTAINERS=1 pytest tests/", depends-on = ["services-up"] }
+
+[tool.pixi.dependencies]
+python = ">=3.10,<3.14"
+graphviz = ">=13.1.2,<14"
+
+[tool.pixi.activation]
+scripts=["activate.sh"]
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 88a246fe7..000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-numpy
-pymysql>=0.7.2
-pyparsing
-ipython
-networkx
-pydotplus
diff --git a/setup.py b/setup.py
deleted file mode 100644
index bd916c260..000000000
--- a/setup.py
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env python
-from setuptools import setup, find_packages
-from os import path
-import sys
-
-if sys.version_info < (3,4):
- sys.exit('DataJoint is only supported on Python 3.4 or higher')
-
-here = path.abspath(path.dirname(__file__))
-
-long_description = "An object-relational mapping and relational algebra to facilitate data definition and data manipulation in MySQL databases."
-
-# read in version number
-with open(path.join(here, 'datajoint', 'version.py')) as f:
- exec(f.read())
-
-with open(path.join(here, 'requirements.txt')) as f:
- requirements = f.read().split()
-
-setup(
- name='datajoint',
- version=__version__,
- description="An ORM with closed relational algebra",
- long_description=long_description,
- author='Dimitri Yatsenko',
- author_email='Dimitri.Yatsenko@gmail.com',
- license="GNU LGPL",
- url='https://github.com/datajoint/datajoint-python',
- keywords='database organization',
- packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
- install_requires=requirements,
-)
diff --git a/src/datajoint/__init__.py b/src/datajoint/__init__.py
new file mode 100644
index 000000000..2e242ce84
--- /dev/null
+++ b/src/datajoint/__init__.py
@@ -0,0 +1,306 @@
+"""
+DataJoint for Python — a framework for scientific data pipelines.
+
+DataJoint introduces the Relational Workflow Model, where your database schema
+is an executable specification of your workflow. Tables represent workflow steps,
+foreign keys encode dependencies, and computations are declarative.
+
+Documentation: https://docs.datajoint.com
+Source: https://github.com/datajoint/datajoint-python
+
+Copyright 2014-2026 DataJoint Inc. and contributors.
+Licensed under the Apache License, Version 2.0.
+
+If DataJoint contributes to a publication, please cite:
+https://doi.org/10.1101/031658
+"""
+
+__author__ = "DataJoint Contributors"
+__date__ = "November 7, 2020"
+__all__ = [
+ "__author__",
+ "__version__",
+ "config",
+ "conn",
+ "Connection",
+ "Instance",
+ "Schema",
+ "VirtualModule",
+ "virtual_schema",
+ "list_schemas",
+ "Table",
+ "FreeTable",
+ "AutoPopulate",
+ "Job",
+ "Manual",
+ "Lookup",
+ "Imported",
+ "Computed",
+ "Part",
+ "Not",
+ "AndList",
+ "Top",
+ "U",
+ "Diagram",
+ "MatCell",
+ "MatStruct",
+ # Codec API
+ "Codec",
+ "SchemaCodec",
+ "list_codecs",
+ "get_codec",
+ "ObjectRef",
+ "NpyRef",
+ # SparkAdapter Codec Protocol
+ "SparkAdapter",
+ # Storage Adapter API
+ "StorageAdapter",
+ "get_storage_adapter",
+ # Other
+ "errors",
+ "migrate",
+ "deploy",
+ "DataJointError",
+ "ThreadSafetyError",
+ "logger",
+ "cli",
+ "ValidationResult",
+]
+
+# =============================================================================
+# Eager imports — core functionality needed immediately
+# =============================================================================
+from . import errors
+from . import migrate
+from . import deploy
+from .codecs import (
+ Codec,
+ get_codec,
+ list_codecs,
+)
+from .builtin_codecs import (
+ SchemaCodec,
+ NpyRef,
+)
+from .blob import MatCell, MatStruct
+from .connection import Connection
+from .errors import DataJointError, ThreadSafetyError
+from .expression import AndList, Not, Top, U
+from .instance import Instance, _ConfigProxy, _get_singleton_connection, _global_config, _check_thread_safe
+from .logging import logger
+from .objectref import ObjectRef
+from .spark import SparkAdapter
+from .storage_adapter import StorageAdapter, get_storage_adapter
+from .schemas import _Schema, VirtualModule, list_schemas, virtual_schema
+from .autopopulate import AutoPopulate
+from .jobs import Job
+from .table import FreeTable as _FreeTable, Table, ValidationResult
+from .user_tables import Computed, Imported, Lookup, Manual, Part
+from .version import __version__
+
+# =============================================================================
+# Singleton-aware API
+# =============================================================================
+# config is a proxy that delegates to the singleton instance's config
+config = _ConfigProxy()
+
+
+def conn(
+ host: str | None = None,
+ user: str | None = None,
+ password: str | None = None,
+ *,
+ reset: bool = False,
+ use_tls: bool | dict | None = None,
+) -> Connection:
+ """
+ Return a persistent connection object.
+
+ When called without arguments, returns the singleton connection using
+ credentials from dj.config. When connection parameters are provided,
+ updates the singleton connection with the new credentials.
+
+ Parameters
+ ----------
+ host : str, optional
+ Database hostname. If provided, updates singleton.
+ user : str, optional
+ Database username. If provided, updates singleton.
+ password : str, optional
+ Database password. If provided, updates singleton.
+ reset : bool, optional
+ If True, reset existing connection. Default False.
+ use_tls : bool or dict, optional
+ TLS encryption option.
+
+ Returns
+ -------
+ Connection
+ Database connection.
+
+ Raises
+ ------
+ ThreadSafetyError
+ If thread_safe mode is enabled.
+ """
+ import datajoint.instance as instance_module
+ from pydantic import SecretStr
+
+ _check_thread_safe()
+
+ # If reset requested, always recreate
+ # If credentials provided and no singleton exists, create one
+ # If credentials provided and singleton exists, return existing singleton
+ if reset or (
+ instance_module._singleton_connection is None and (host is not None or user is not None or password is not None)
+ ):
+ # Use provided values or fall back to config
+ host = host if host is not None else _global_config.database.host
+ user = user if user is not None else _global_config.database.user
+ raw_password = password if password is not None else _global_config.database.password
+ password = raw_password.get_secret_value() if isinstance(raw_password, SecretStr) else raw_password
+ port = _global_config.database.port
+ use_tls = use_tls if use_tls is not None else _global_config.database.use_tls
+
+ if user is None:
+ from .errors import DataJointError
+
+ raise DataJointError("Database user not configured. Set dj.config['database.user'] or pass user= argument.")
+ if password is None:
+ from .errors import DataJointError
+
+ raise DataJointError(
+ "Database password not configured. Set dj.config['database.password'] or pass password= argument."
+ )
+
+ instance_module._singleton_connection = Connection(host, user, password, port, use_tls, config_override=_global_config)
+
+ return _get_singleton_connection()
+
+
+class Schema(_Schema):
+ """
+ Decorator that binds table classes to a database schema.
+
+ When connection is not provided, uses the singleton connection.
+ In thread-safe mode (``DJ_THREAD_SAFE=true``), a connection must be
+ provided explicitly or use ``dj.Instance().Schema()`` instead.
+
+ Parameters
+ ----------
+ schema_name : str, optional
+ Database schema name. If omitted, call ``activate()`` later.
+ context : dict, optional
+ Namespace for foreign key lookup. None uses caller's context.
+ connection : Connection, optional
+ Database connection. Defaults to singleton connection.
+ create_schema : bool, optional
+ If False, raise error if schema doesn't exist. Default True.
+ create_tables : bool, optional
+ If False, raise error when accessing missing tables.
+ add_objects : dict, optional
+ Additional objects for declaration context.
+
+ Raises
+ ------
+ ThreadSafetyError
+ If thread_safe mode is enabled and no connection is provided.
+
+ Examples
+ --------
+ >>> schema = dj.Schema('my_schema')
+ >>> @schema
+ ... class Session(dj.Manual):
+ ... definition = '''
+ ... session_id : int
+ ... '''
+ """
+
+ def __init__(
+ self,
+ schema_name: str | None = None,
+ context: dict | None = None,
+ *,
+ connection: Connection | None = None,
+ create_schema: bool = True,
+ create_tables: bool | None = None,
+ add_objects: dict | None = None,
+ ) -> None:
+ if connection is None:
+ _check_thread_safe()
+ super().__init__(
+ schema_name,
+ context=context,
+ connection=connection,
+ create_schema=create_schema,
+ create_tables=create_tables,
+ add_objects=add_objects,
+ )
+
+
+def FreeTable(conn_or_name, full_table_name: str | None = None) -> _FreeTable:
+ """
+ Create a FreeTable for accessing a table without a dedicated class.
+
+ Can be called in two ways:
+ - ``FreeTable("schema.table")`` - uses singleton connection
+ - ``FreeTable(connection, "schema.table")`` - uses provided connection
+
+ Parameters
+ ----------
+ conn_or_name : Connection or str
+ Either a Connection object, or the full table name if using singleton.
+ full_table_name : str, optional
+ Full table name when first argument is a connection.
+
+ Returns
+ -------
+ FreeTable
+ A FreeTable instance for the specified table.
+
+ Raises
+ ------
+ ThreadSafetyError
+ If thread_safe mode is enabled and using singleton.
+ """
+ if full_table_name is None:
+ # Called as FreeTable("db.table") - use singleton connection
+ _check_thread_safe()
+ return _FreeTable(_get_singleton_connection(), conn_or_name)
+ else:
+ # Called as FreeTable(conn, "db.table") - use provided connection
+ return _FreeTable(conn_or_name, full_table_name)
+
+
+# =============================================================================
+# Lazy imports — heavy dependencies loaded on first access
+# =============================================================================
+# These modules import heavy dependencies (networkx, matplotlib, click, pymysql)
+# that slow down `import datajoint`. They are loaded on demand.
+
+_lazy_modules = {
+ # Diagram imports networkx and matplotlib
+ "Diagram": (".diagram", "Diagram"),
+ "diagram": (".diagram", None), # Return the module itself
+ # cli imports click
+ "cli": (".cli", "cli"),
+ # gc — exposed lazily so `dj.gc.scan(...)` works as documented in gc.py
+ # and in the user docs (how-to/garbage-collection.md).
+ "gc": (".gc", None), # Return the module itself
+}
+
+
+def __getattr__(name: str):
+ """Lazy import for heavy dependencies."""
+ if name in _lazy_modules:
+ module_path, attr_name = _lazy_modules[name]
+ import importlib
+
+ module = importlib.import_module(module_path, __package__)
+ # If attr_name is None, return the module itself
+ attr = module if attr_name is None else getattr(module, attr_name)
+ # Cache in module __dict__ to avoid repeated __getattr__ calls
+ # and to override the submodule that importlib adds automatically
+ globals()[name] = attr
+ return attr
+ raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
diff --git a/src/datajoint/adapters/__init__.py b/src/datajoint/adapters/__init__.py
new file mode 100644
index 000000000..5115a982a
--- /dev/null
+++ b/src/datajoint/adapters/__init__.py
@@ -0,0 +1,54 @@
+"""
+Database adapter registry for DataJoint.
+
+This module provides the adapter factory function and exports all adapters.
+"""
+
+from __future__ import annotations
+
+from .base import DatabaseAdapter
+from .mysql import MySQLAdapter
+from .postgres import PostgreSQLAdapter
+
+__all__ = ["DatabaseAdapter", "MySQLAdapter", "PostgreSQLAdapter", "get_adapter"]
+
+# Adapter registry mapping backend names to adapter classes
+ADAPTERS: dict[str, type[DatabaseAdapter]] = {
+ "mysql": MySQLAdapter,
+ "postgresql": PostgreSQLAdapter,
+ "postgres": PostgreSQLAdapter, # Alias for postgresql
+}
+
+
+def get_adapter(backend: str) -> DatabaseAdapter:
+ """
+ Get adapter instance for the specified database backend.
+
+ Parameters
+ ----------
+ backend : str
+ Backend name: 'mysql', 'postgresql', or 'postgres'.
+
+ Returns
+ -------
+ DatabaseAdapter
+ Adapter instance for the specified backend.
+
+ Raises
+ ------
+ ValueError
+ If the backend is not supported.
+
+ Examples
+ --------
+ >>> from datajoint.adapters import get_adapter
+ >>> mysql_adapter = get_adapter('mysql')
+ >>> postgres_adapter = get_adapter('postgresql')
+ """
+ backend_lower = backend.lower()
+
+ if backend_lower not in ADAPTERS:
+ supported = sorted(set(ADAPTERS.keys()))
+ raise ValueError(f"Unknown database backend: {backend}. " f"Supported backends: {', '.join(supported)}")
+
+ return ADAPTERS[backend_lower]()
diff --git a/src/datajoint/adapters/base.py b/src/datajoint/adapters/base.py
new file mode 100644
index 000000000..e79a5d4df
--- /dev/null
+++ b/src/datajoint/adapters/base.py
@@ -0,0 +1,1332 @@
+"""
+Abstract base class for database backend adapters.
+
+This module defines the interface that all database adapters must implement
+to support multiple database backends (MySQL, PostgreSQL, etc.) in DataJoint.
+"""
+
+from __future__ import annotations
+
+from abc import ABC, abstractmethod
+from typing import Any
+
+
+class DatabaseAdapter(ABC):
+ """
+ Abstract base class for database backend adapters.
+
+ Adapters provide database-specific implementations for SQL generation,
+ type mapping, error translation, and connection management.
+ """
+
+ # =========================================================================
+ # Connection Management
+ # =========================================================================
+
+ @abstractmethod
+ def connect(
+ self,
+ host: str,
+ port: int,
+ user: str,
+ password: str,
+ **kwargs: Any,
+ ) -> Any:
+ """
+ Establish database connection.
+
+ Parameters
+ ----------
+ host : str
+ Database server hostname.
+ port : int
+ Database server port.
+ user : str
+ Username for authentication.
+ password : str
+ Password for authentication.
+ **kwargs : Any
+ Additional backend-specific connection parameters.
+
+ Returns
+ -------
+ Any
+ Database connection object (backend-specific).
+ """
+ ...
+
+ @abstractmethod
+ def close(self, connection: Any) -> None:
+ """
+ Close the database connection.
+
+ Parameters
+ ----------
+ connection : Any
+ Database connection object to close.
+ """
+ ...
+
+ @abstractmethod
+ def ping(self, connection: Any) -> bool:
+ """
+ Check if connection is alive.
+
+ Parameters
+ ----------
+ connection : Any
+ Database connection object to check.
+
+ Returns
+ -------
+ bool
+ True if connection is alive, False otherwise.
+ """
+ ...
+
+ @abstractmethod
+ def get_connection_id(self, connection: Any) -> int:
+ """
+ Get the current connection/backend process ID.
+
+ Parameters
+ ----------
+ connection : Any
+ Database connection object.
+
+ Returns
+ -------
+ int
+ Connection or process ID.
+ """
+ ...
+
+ @property
+ @abstractmethod
+ def default_port(self) -> int:
+ """
+ Default port for this database backend.
+
+ Returns
+ -------
+ int
+ Default port number (3306 for MySQL, 5432 for PostgreSQL).
+ """
+ ...
+
+ @property
+ @abstractmethod
+ def backend(self) -> str:
+ """
+ Backend identifier string.
+
+ Returns
+ -------
+ str
+ Backend name: 'mysql' or 'postgresql'.
+ """
+ ...
+
+ @abstractmethod
+ def get_cursor(self, connection: Any, as_dict: bool = False) -> Any:
+ """
+ Get a cursor from the database connection.
+
+ Parameters
+ ----------
+ connection : Any
+ Database connection object.
+ as_dict : bool, optional
+ If True, return cursor that yields rows as dictionaries.
+ If False, return cursor that yields rows as tuples.
+ Default False.
+
+ Returns
+ -------
+ Any
+ Database cursor object (backend-specific).
+ """
+ ...
+
+ # =========================================================================
+ # SQL Syntax
+ # =========================================================================
+
+ @abstractmethod
+ def quote_identifier(self, name: str) -> str:
+ """
+ Quote an identifier (table/column name) for this backend.
+
+ Parameters
+ ----------
+ name : str
+ Identifier to quote.
+
+ Returns
+ -------
+ str
+ Quoted identifier (e.g., `name` for MySQL, "name" for PostgreSQL).
+ """
+ ...
+
+ @abstractmethod
+ def split_full_table_name(self, full_table_name: str) -> tuple[str, str]:
+ """
+ Split a fully-qualified table name into schema and table components.
+
+ Inverse of quoting: strips backend-specific identifier quotes
+ and splits into (schema, table).
+
+ Parameters
+ ----------
+ full_table_name : str
+ Quoted full table name (e.g., ```\\`schema\\`.\\`table\\` ``` or
+ ``"schema"."table"``).
+
+ Returns
+ -------
+ tuple[str, str]
+ (schema_name, table_name) with quotes stripped.
+ """
+ ...
+
+ @abstractmethod
+ def quote_string(self, value: str) -> str:
+ """
+ Quote a string literal for this backend.
+
+ Parameters
+ ----------
+ value : str
+ String value to quote.
+
+ Returns
+ -------
+ str
+ Quoted string literal with proper escaping.
+ """
+ ...
+
+ @abstractmethod
+ def get_master_table_name(self, part_table: str) -> str | None:
+ """
+ Extract master table name from a part table name.
+
+ Parameters
+ ----------
+ part_table : str
+ Full table name (e.g., `schema`.`master__part` for MySQL,
+ "schema"."master__part" for PostgreSQL).
+
+ Returns
+ -------
+ str or None
+ Master table name if part_table is a part table, None otherwise.
+ """
+ ...
+
+ @property
+ @abstractmethod
+ def parameter_placeholder(self) -> str:
+ """
+ Parameter placeholder style for this backend.
+
+ Returns
+ -------
+ str
+ Placeholder string (e.g., '%s' for MySQL/psycopg2, '?' for SQLite).
+ """
+ ...
+
+ def make_full_table_name(self, database: str, table_name: str) -> str:
+ """
+ Construct a fully-qualified table name for this backend.
+
+ Default implementation produces a two-part name (``schema.table``).
+ Backends that require additional namespace levels can override.
+
+ Parameters
+ ----------
+ database : str
+ Schema/database name.
+ table_name : str
+ Table name (including tier prefix).
+
+ Returns
+ -------
+ str
+ Fully-qualified, quoted table name.
+ """
+ return f"{self.quote_identifier(database)}.{self.quote_identifier(table_name)}"
+
+ @property
+ def max_table_name_length(self) -> int:
+ """
+ Maximum length of a table name for this backend.
+
+ Returns
+ -------
+ int
+ Maximum allowed characters in a table identifier.
+ """
+ return 64 # safe default (MySQL limit)
+
+ # =========================================================================
+ # Type Mapping
+ # =========================================================================
+
+ @abstractmethod
+ def core_type_to_sql(self, core_type: str) -> str:
+ """
+ Convert a DataJoint core type to backend SQL type.
+
+ Parameters
+ ----------
+ core_type : str
+ DataJoint core type (e.g., 'int64', 'float32', 'uuid').
+
+ Returns
+ -------
+ str
+ Backend SQL type (e.g., 'bigint', 'float', 'binary(16)').
+
+ Raises
+ ------
+ ValueError
+ If core_type is not a valid DataJoint core type.
+ """
+ ...
+
+ @abstractmethod
+ def sql_type_to_core(self, sql_type: str) -> str | None:
+ """
+ Convert a backend SQL type to DataJoint core type (if mappable).
+
+ Parameters
+ ----------
+ sql_type : str
+ Backend SQL type.
+
+ Returns
+ -------
+ str or None
+ DataJoint core type if mappable, None otherwise.
+ """
+ ...
+
+ # =========================================================================
+ # DDL Generation
+ # =========================================================================
+
+ @abstractmethod
+ def create_schema_sql(self, schema_name: str) -> str:
+ """
+ Generate CREATE SCHEMA/DATABASE statement.
+
+ Parameters
+ ----------
+ schema_name : str
+ Name of schema/database to create.
+
+ Returns
+ -------
+ str
+ CREATE SCHEMA/DATABASE SQL statement.
+ """
+ ...
+
+ @abstractmethod
+ def drop_schema_sql(self, schema_name: str, if_exists: bool = True) -> str:
+ """
+ Generate DROP SCHEMA/DATABASE statement.
+
+ Parameters
+ ----------
+ schema_name : str
+ Name of schema/database to drop.
+ if_exists : bool, optional
+ Include IF EXISTS clause. Default True.
+
+ Returns
+ -------
+ str
+ DROP SCHEMA/DATABASE SQL statement.
+ """
+ ...
+
+ @abstractmethod
+ def create_table_sql(
+ self,
+ table_name: str,
+ columns: list[dict[str, Any]],
+ primary_key: list[str],
+ foreign_keys: list[dict[str, Any]],
+ indexes: list[dict[str, Any]],
+ comment: str | None = None,
+ ) -> str:
+ """
+ Generate CREATE TABLE statement.
+
+ Parameters
+ ----------
+ table_name : str
+ Name of table to create.
+ columns : list[dict]
+ Column definitions with keys: name, type, nullable, default, comment.
+ primary_key : list[str]
+ List of primary key column names.
+ foreign_keys : list[dict]
+ Foreign key definitions with keys: columns, ref_table, ref_columns.
+ indexes : list[dict]
+ Index definitions with keys: columns, unique.
+ comment : str, optional
+ Table comment.
+
+ Returns
+ -------
+ str
+ CREATE TABLE SQL statement.
+ """
+ ...
+
+ @abstractmethod
+ def drop_table_sql(self, table_name: str, if_exists: bool = True) -> str:
+ """
+ Generate DROP TABLE statement.
+
+ Parameters
+ ----------
+ table_name : str
+ Name of table to drop.
+ if_exists : bool, optional
+ Include IF EXISTS clause. Default True.
+
+ Returns
+ -------
+ str
+ DROP TABLE SQL statement.
+ """
+ ...
+
+ @abstractmethod
+ def alter_table_sql(
+ self,
+ table_name: str,
+ add_columns: list[dict[str, Any]] | None = None,
+ drop_columns: list[str] | None = None,
+ modify_columns: list[dict[str, Any]] | None = None,
+ ) -> str:
+ """
+ Generate ALTER TABLE statement.
+
+ Parameters
+ ----------
+ table_name : str
+ Name of table to alter.
+ add_columns : list[dict], optional
+ Columns to add with keys: name, type, nullable, default, comment.
+ drop_columns : list[str], optional
+ Column names to drop.
+ modify_columns : list[dict], optional
+ Columns to modify with keys: name, type, nullable, default, comment.
+
+ Returns
+ -------
+ str
+ ALTER TABLE SQL statement.
+ """
+ ...
+
+ @abstractmethod
+ def add_comment_sql(
+ self,
+ object_type: str,
+ object_name: str,
+ comment: str,
+ ) -> str | None:
+ """
+ Generate comment statement (may be None if embedded in CREATE).
+
+ Parameters
+ ----------
+ object_type : str
+ Type of object ('table', 'column').
+ object_name : str
+ Fully qualified object name.
+ comment : str
+ Comment text.
+
+ Returns
+ -------
+ str or None
+ COMMENT statement, or None if comments are inline in CREATE.
+ """
+ ...
+
+ # =========================================================================
+ # DML Generation
+ # =========================================================================
+
+ @abstractmethod
+ def insert_sql(
+ self,
+ table_name: str,
+ columns: list[str],
+ on_duplicate: str | None = None,
+ ) -> str:
+ """
+ Generate INSERT statement.
+
+ Parameters
+ ----------
+ table_name : str
+ Name of table to insert into.
+ columns : list[str]
+ Column names to insert.
+ on_duplicate : str, optional
+ Duplicate handling: 'ignore', 'replace', 'update', or None.
+
+ Returns
+ -------
+ str
+ INSERT SQL statement with parameter placeholders.
+ """
+ ...
+
+ @abstractmethod
+ def update_sql(
+ self,
+ table_name: str,
+ set_columns: list[str],
+ where_columns: list[str],
+ ) -> str:
+ """
+ Generate UPDATE statement.
+
+ Parameters
+ ----------
+ table_name : str
+ Name of table to update.
+ set_columns : list[str]
+ Column names to set.
+ where_columns : list[str]
+ Column names for WHERE clause.
+
+ Returns
+ -------
+ str
+ UPDATE SQL statement with parameter placeholders.
+ """
+ ...
+
+ @abstractmethod
+ def delete_sql(self, table_name: str) -> str:
+ """
+ Generate DELETE statement (WHERE clause added separately).
+
+ Parameters
+ ----------
+ table_name : str
+ Name of table to delete from.
+
+ Returns
+ -------
+ str
+ DELETE SQL statement without WHERE clause.
+ """
+ ...
+
+ @abstractmethod
+ def upsert_on_duplicate_sql(
+ self,
+ table_name: str,
+ columns: list[str],
+ primary_key: list[str],
+ num_rows: int,
+ ) -> str:
+ """
+ Generate INSERT ... ON DUPLICATE KEY UPDATE (MySQL) or
+ INSERT ... ON CONFLICT ... DO UPDATE (PostgreSQL) statement.
+
+ Parameters
+ ----------
+ table_name : str
+ Fully qualified table name (with quotes).
+ columns : list[str]
+ Column names to insert (unquoted).
+ primary_key : list[str]
+ Primary key column names (unquoted) for conflict detection.
+ num_rows : int
+ Number of rows to insert (for generating placeholders).
+
+ Returns
+ -------
+ str
+ Upsert SQL statement with placeholders.
+
+ Examples
+ --------
+ MySQL:
+ INSERT INTO `table` (a, b, c) VALUES (%s, %s, %s), (%s, %s, %s)
+ ON DUPLICATE KEY UPDATE a = VALUES(a), b = VALUES(b), c = VALUES(c)
+
+ PostgreSQL:
+ INSERT INTO "table" (a, b, c) VALUES (%s, %s, %s), (%s, %s, %s)
+ ON CONFLICT (a) DO UPDATE SET b = EXCLUDED.b, c = EXCLUDED.c
+ """
+ ...
+
+ @abstractmethod
+ def skip_duplicates_clause(
+ self,
+ full_table_name: str,
+ primary_key: list[str],
+ ) -> str:
+ """
+ Generate clause to skip duplicate key insertions.
+
+ For MySQL: ON DUPLICATE KEY UPDATE pk=table.pk (no-op update)
+ For PostgreSQL: ON CONFLICT (pk_cols) DO NOTHING
+
+ Parameters
+ ----------
+ full_table_name : str
+ Fully qualified table name (with quotes).
+ primary_key : list[str]
+ Primary key column names (unquoted).
+
+ Returns
+ -------
+ str
+ SQL clause to append to INSERT statement.
+ """
+ ...
+
+ @property
+ def supports_inline_indexes(self) -> bool:
+ """
+ Whether this backend supports inline INDEX in CREATE TABLE.
+
+ MySQL supports inline index definitions in CREATE TABLE.
+ PostgreSQL requires separate CREATE INDEX statements.
+
+ Returns
+ -------
+ bool
+ True for MySQL, False for PostgreSQL.
+ """
+ return True # Default for MySQL, override in PostgreSQL
+
+ def create_index_ddl(
+ self,
+ full_table_name: str,
+ columns: list[str],
+ unique: bool = False,
+ index_name: str | None = None,
+ ) -> str:
+ """
+ Generate CREATE INDEX statement.
+
+ Parameters
+ ----------
+ full_table_name : str
+ Fully qualified table name (with quotes).
+ columns : list[str]
+ Column names to index (unquoted).
+ unique : bool, optional
+ If True, create a unique index.
+ index_name : str, optional
+ Custom index name. If None, auto-generate from table/columns.
+
+ Returns
+ -------
+ str
+ CREATE INDEX SQL statement.
+ """
+ quoted_cols = ", ".join(self.quote_identifier(col) for col in columns)
+ # Generate index name from table and columns if not provided
+ if index_name is None:
+ # Extract table name from full_table_name for index naming
+ _, table_part = self.split_full_table_name(full_table_name)
+ col_part = "_".join(columns)[:30] # Truncate for long column lists
+ index_name = f"idx_{table_part}_{col_part}"
+ unique_clause = "UNIQUE " if unique else ""
+ return f"CREATE {unique_clause}INDEX {self.quote_identifier(index_name)} ON {full_table_name} ({quoted_cols})"
+
+ # =========================================================================
+ # Introspection
+ # =========================================================================
+
+ @abstractmethod
+ def list_schemas_sql(self) -> str:
+ """
+ Generate query to list all schemas/databases.
+
+ Returns
+ -------
+ str
+ SQL query to list schemas.
+ """
+ ...
+
+ @abstractmethod
+ def schema_exists_sql(self, schema_name: str) -> str:
+ """
+ Generate query to check if a schema exists.
+
+ Parameters
+ ----------
+ schema_name : str
+ Name of schema to check.
+
+ Returns
+ -------
+ str
+ SQL query that returns a row if the schema exists.
+ """
+ ...
+
+ @abstractmethod
+ def list_tables_sql(self, schema_name: str, pattern: str | None = None) -> str:
+ """
+ Generate query to list tables in a schema.
+
+ Parameters
+ ----------
+ schema_name : str
+ Name of schema to list tables from.
+ pattern : str, optional
+ LIKE pattern to filter table names. Use %% for % in SQL.
+
+ Returns
+ -------
+ str
+ SQL query to list tables.
+ """
+ ...
+
+ @abstractmethod
+ def get_table_info_sql(self, schema_name: str, table_name: str) -> str:
+ """
+ Generate query to get table metadata (comment, engine, etc.).
+
+ Parameters
+ ----------
+ schema_name : str
+ Schema name.
+ table_name : str
+ Table name.
+
+ Returns
+ -------
+ str
+ SQL query to get table info.
+ """
+ ...
+
+ @abstractmethod
+ def get_columns_sql(self, schema_name: str, table_name: str) -> str:
+ """
+ Generate query to get column definitions.
+
+ Parameters
+ ----------
+ schema_name : str
+ Schema name.
+ table_name : str
+ Table name.
+
+ Returns
+ -------
+ str
+ SQL query to get column definitions.
+ """
+ ...
+
+ @abstractmethod
+ def get_primary_key_sql(self, schema_name: str, table_name: str) -> str:
+ """
+ Generate query to get primary key columns.
+
+ Parameters
+ ----------
+ schema_name : str
+ Schema name.
+ table_name : str
+ Table name.
+
+ Returns
+ -------
+ str
+ SQL query to get primary key columns.
+ """
+ ...
+
+ @abstractmethod
+ def get_foreign_keys_sql(self, schema_name: str, table_name: str) -> str:
+ """
+ Generate query to get foreign key constraints.
+
+ Parameters
+ ----------
+ schema_name : str
+ Schema name.
+ table_name : str
+ Table name.
+
+ Returns
+ -------
+ str
+ SQL query to get foreign key constraints.
+ """
+ ...
+
+ @abstractmethod
+ def load_primary_keys_sql(self, schemas_list: str, like_pattern: str) -> str:
+ """
+ Generate query to load primary key columns for all tables across schemas.
+
+ Used by the dependency graph to build the schema graph.
+
+ Parameters
+ ----------
+ schemas_list : str
+ Comma-separated, quoted schema names for an IN clause.
+ like_pattern : str
+ SQL LIKE pattern to exclude (e.g., "'~%%'" for internal tables).
+
+ Returns
+ -------
+ str
+ SQL query returning rows with columns:
+ - tab: fully qualified table name (quoted)
+ - column_name: primary key column name
+ """
+ ...
+
+ @abstractmethod
+ def load_foreign_keys_sql(self, schemas_list: str, like_pattern: str) -> str:
+ """
+ Generate query to load foreign key relationships across schemas.
+
+ Used by the dependency graph to build the schema graph.
+
+ Parameters
+ ----------
+ schemas_list : str
+ Comma-separated, quoted schema names for an IN clause.
+ like_pattern : str
+ SQL LIKE pattern to exclude (e.g., "'~%%'" for internal tables).
+
+ Returns
+ -------
+ str
+ SQL query returning rows (as dicts) with columns:
+ - constraint_name: FK constraint name
+ - referencing_table: fully qualified child table name (quoted)
+ - referenced_table: fully qualified parent table name (quoted)
+ - column_name: FK column in child table
+ - referenced_column_name: referenced column in parent table
+ """
+ ...
+
+ def find_downstream_schemas_sql(self, schemas_list: str) -> str:
+ """
+ Generate query to find schemas with FK references to the given schemas.
+
+ Used to discover unloaded schemas that depend on loaded ones.
+
+ Parameters
+ ----------
+ schemas_list : str
+ Comma-separated, quoted schema names for an IN clause.
+
+ Returns
+ -------
+ str
+ SQL query returning rows with a single column ``schema_name``
+ containing distinct schema names that reference the given schemas.
+ """
+ raise NotImplementedError
+ ...
+
+ def find_upstream_schemas_sql(self, schemas_list: str) -> str:
+ """
+ Generate query to find schemas that the given schemas reference via FK.
+
+ Used to discover unloaded schemas that the loaded ones depend on
+ (the upstream / ancestor direction). Symmetric to
+ :meth:`find_downstream_schemas_sql`.
+
+ Parameters
+ ----------
+ schemas_list : str
+ Comma-separated, quoted schema names for an IN clause.
+
+ Returns
+ -------
+ str
+ SQL query returning rows with a single column ``schema_name``
+ containing distinct schema names that are referenced by the
+ given schemas.
+ """
+ raise NotImplementedError
+ ...
+
+ @abstractmethod
+ def get_constraint_info_sql(self, constraint_name: str, schema_name: str, table_name: str) -> str:
+ """
+ Generate query to get foreign key constraint details from information_schema.
+
+ Used during cascade delete to determine FK columns when error message
+ doesn't provide full details.
+
+ Parameters
+ ----------
+ constraint_name : str
+ Name of the foreign key constraint.
+ schema_name : str
+ Schema/database name of the child table.
+ table_name : str
+ Name of the child table.
+
+ Returns
+ -------
+ str
+ SQL query that returns rows with columns:
+ - fk_attrs: foreign key column name in child table
+ - parent: parent table name (quoted, with schema)
+ - pk_attrs: referenced column name in parent table
+ """
+ ...
+
+ @abstractmethod
+ def parse_foreign_key_error(self, error_message: str) -> dict[str, str | list[str] | None] | None:
+ """
+ Parse a foreign key violation error message to extract constraint details.
+
+ Used during cascade delete to identify which child table is preventing
+ deletion and what columns are involved.
+
+ Parameters
+ ----------
+ error_message : str
+ The error message from a foreign key constraint violation.
+
+ Returns
+ -------
+ dict or None
+ Dictionary with keys if successfully parsed:
+ - child: child table name (quoted with schema if available)
+ - name: constraint name (quoted)
+ - fk_attrs: list of foreign key column names (may be None if not in message)
+ - parent: parent table name (quoted, may be None if not in message)
+ - pk_attrs: list of parent key column names (may be None if not in message)
+
+ Returns None if error message doesn't match FK violation pattern.
+
+ Examples
+ --------
+ MySQL error:
+ "Cannot delete or update a parent row: a foreign key constraint fails
+ (`schema`.`child`, CONSTRAINT `fk_name` FOREIGN KEY (`child_col`)
+ REFERENCES `parent` (`parent_col`))"
+
+ PostgreSQL error:
+ "update or delete on table \"parent\" violates foreign key constraint
+ \"child_parent_id_fkey\" on table \"child\"
+ DETAIL: Key (parent_id)=(1) is still referenced from table \"child\"."
+ """
+ ...
+
+ @abstractmethod
+ def get_indexes_sql(self, schema_name: str, table_name: str) -> str:
+ """
+ Generate query to get index definitions.
+
+ Parameters
+ ----------
+ schema_name : str
+ Schema name.
+ table_name : str
+ Table name.
+
+ Returns
+ -------
+ str
+ SQL query to get index definitions.
+ """
+ ...
+
+ @abstractmethod
+ def parse_column_info(self, row: dict[str, Any]) -> dict[str, Any]:
+ """
+ Parse a column info row into standardized format.
+
+ Parameters
+ ----------
+ row : dict
+ Raw column info row from database introspection query.
+
+ Returns
+ -------
+ dict
+ Standardized column info with keys: name, type, nullable,
+ default, comment, etc.
+ """
+ ...
+
+ # =========================================================================
+ # Transactions
+ # =========================================================================
+
+ @abstractmethod
+ def start_transaction_sql(self, isolation_level: str | None = None) -> str:
+ """
+ Generate START TRANSACTION statement.
+
+ Parameters
+ ----------
+ isolation_level : str, optional
+ Transaction isolation level.
+
+ Returns
+ -------
+ str
+ START TRANSACTION SQL statement.
+ """
+ ...
+
+ @abstractmethod
+ def commit_sql(self) -> str:
+ """
+ Generate COMMIT statement.
+
+ Returns
+ -------
+ str
+ COMMIT SQL statement.
+ """
+ ...
+
+ @abstractmethod
+ def rollback_sql(self) -> str:
+ """
+ Generate ROLLBACK statement.
+
+ Returns
+ -------
+ str
+ ROLLBACK SQL statement.
+ """
+ ...
+
+ # =========================================================================
+ # Functions and Expressions
+ # =========================================================================
+
+ @abstractmethod
+ def current_timestamp_expr(self, precision: int | None = None) -> str:
+ """
+ Expression for current timestamp.
+
+ Parameters
+ ----------
+ precision : int, optional
+ Fractional seconds precision (0-6).
+
+ Returns
+ -------
+ str
+ SQL expression for current timestamp.
+ """
+ ...
+
+ @abstractmethod
+ def interval_expr(self, value: int, unit: str) -> str:
+ """
+ Expression for time interval.
+
+ Parameters
+ ----------
+ value : int
+ Interval value.
+ unit : str
+ Time unit ('second', 'minute', 'hour', 'day', etc.).
+
+ Returns
+ -------
+ str
+ SQL expression for interval (e.g., 'INTERVAL 5 SECOND' for MySQL,
+ "INTERVAL '5 seconds'" for PostgreSQL).
+ """
+ ...
+
+ @abstractmethod
+ def current_user_expr(self) -> str:
+ """
+ SQL expression to get the current user.
+
+ Returns
+ -------
+ str
+ SQL expression for current user (e.g., 'user()' for MySQL,
+ 'current_user' for PostgreSQL).
+ """
+ ...
+
+ @abstractmethod
+ def json_path_expr(self, column: str, path: str, return_type: str | None = None) -> str:
+ """
+ Generate JSON path extraction expression.
+
+ Parameters
+ ----------
+ column : str
+ Column name containing JSON data.
+ path : str
+ JSON path (e.g., 'field' or 'nested.field').
+ return_type : str, optional
+ Return type specification (MySQL-specific).
+
+ Returns
+ -------
+ str
+ Database-specific JSON extraction SQL expression.
+
+ Examples
+ --------
+ MySQL: json_value(`column`, _utf8mb4'$.path' returning type)
+ PostgreSQL: jsonb_extract_path_text("column", 'path_part1', 'path_part2')
+ """
+ ...
+
+ def translate_expression(self, expr: str) -> str:
+ """
+ Translate SQL expression for backend compatibility.
+
+ Converts database-specific function calls to the equivalent syntax
+ for the current backend. This enables portable DataJoint code that
+ uses common aggregate functions.
+
+ Translations performed:
+ - GROUP_CONCAT(col) ↔ STRING_AGG(col, ',')
+
+ Parameters
+ ----------
+ expr : str
+ SQL expression that may contain function calls.
+
+ Returns
+ -------
+ str
+ Translated expression for the current backend.
+
+ Notes
+ -----
+ The base implementation returns the expression unchanged.
+ Subclasses override to provide backend-specific translations.
+ """
+ return expr
+
+ # =========================================================================
+ # DDL Generation
+ # =========================================================================
+
+ @abstractmethod
+ def format_column_definition(
+ self,
+ name: str,
+ sql_type: str,
+ nullable: bool = False,
+ default: str | None = None,
+ comment: str | None = None,
+ ) -> str:
+ """
+ Format a column definition for DDL.
+
+ Parameters
+ ----------
+ name : str
+ Column name.
+ sql_type : str
+ SQL type (already backend-specific, e.g., 'bigint', 'varchar(255)').
+ nullable : bool, optional
+ Whether column is nullable. Default False.
+ default : str | None, optional
+ Default value expression (e.g., 'NULL', '"value"', 'CURRENT_TIMESTAMP').
+ comment : str | None, optional
+ Column comment.
+
+ Returns
+ -------
+ str
+ Formatted column definition (without trailing comma).
+
+ Examples
+ --------
+ MySQL: `name` bigint NOT NULL COMMENT "user ID"
+ PostgreSQL: "name" bigint NOT NULL
+ """
+ ...
+
+ @abstractmethod
+ def table_options_clause(self, comment: str | None = None) -> str:
+ """
+ Generate table options clause (ENGINE, etc.) for CREATE TABLE.
+
+ Parameters
+ ----------
+ comment : str | None, optional
+ Table-level comment.
+
+ Returns
+ -------
+ str
+ Table options clause (e.g., 'ENGINE=InnoDB, COMMENT "..."' for MySQL).
+
+ Examples
+ --------
+ MySQL: ENGINE=InnoDB, COMMENT "experiment sessions"
+ PostgreSQL: (empty string, comments handled separately)
+ """
+ ...
+
+ @abstractmethod
+ def table_comment_ddl(self, full_table_name: str, comment: str) -> str | None:
+ """
+ Generate DDL for table-level comment (if separate from CREATE TABLE).
+
+ Parameters
+ ----------
+ full_table_name : str
+ Fully qualified table name (quoted).
+ comment : str
+ Table comment.
+
+ Returns
+ -------
+ str or None
+ DDL statement for table comment, or None if handled inline.
+
+ Examples
+ --------
+ MySQL: None (inline)
+ PostgreSQL: COMMENT ON TABLE "schema"."table" IS 'comment text'
+ """
+ ...
+
+ @abstractmethod
+ def column_comment_ddl(self, full_table_name: str, column_name: str, comment: str) -> str | None:
+ """
+ Generate DDL for column-level comment (if separate from CREATE TABLE).
+
+ Parameters
+ ----------
+ full_table_name : str
+ Fully qualified table name (quoted).
+ column_name : str
+ Column name (unquoted).
+ comment : str
+ Column comment.
+
+ Returns
+ -------
+ str or None
+ DDL statement for column comment, or None if handled inline.
+
+ Examples
+ --------
+ MySQL: None (inline)
+ PostgreSQL: COMMENT ON COLUMN "schema"."table"."column" IS 'comment text'
+ """
+ ...
+
+ @abstractmethod
+ def enum_type_ddl(self, type_name: str, values: list[str]) -> str | None:
+ """
+ Generate DDL for enum type definition (if needed before CREATE TABLE).
+
+ Parameters
+ ----------
+ type_name : str
+ Enum type name.
+ values : list[str]
+ Enum values.
+
+ Returns
+ -------
+ str or None
+ DDL statement for enum type, or None if handled inline.
+
+ Examples
+ --------
+ MySQL: None (inline enum('val1', 'val2'))
+ PostgreSQL: CREATE TYPE "type_name" AS ENUM ('val1', 'val2')
+ """
+ ...
+
+ @abstractmethod
+ def job_metadata_columns(self) -> list[str]:
+ """
+ Return job metadata column definitions for Computed/Imported tables.
+
+ Returns
+ -------
+ list[str]
+ List of column definition strings (fully formatted with quotes).
+
+ Examples
+ --------
+ MySQL:
+ ["`_job_start_time` datetime(3) DEFAULT NULL",
+ "`_job_duration` float DEFAULT NULL",
+ "`_job_version` varchar(64) DEFAULT ''"]
+ PostgreSQL:
+ ['"_job_start_time" timestamp DEFAULT NULL',
+ '"_job_duration" real DEFAULT NULL',
+ '"_job_version" varchar(64) DEFAULT \'\'']
+ """
+ ...
+
+ # =========================================================================
+ # Error Translation
+ # =========================================================================
+
+ @abstractmethod
+ def translate_error(self, error: Exception, query: str = "") -> Exception:
+ """
+ Translate backend-specific error to DataJoint error.
+
+ Parameters
+ ----------
+ error : Exception
+ Backend-specific exception.
+
+ Returns
+ -------
+ Exception
+ DataJoint exception or original error if no mapping exists.
+ """
+ ...
+
+ # =========================================================================
+ # Native Type Validation
+ # =========================================================================
+
+ @abstractmethod
+ def validate_native_type(self, type_str: str) -> bool:
+ """
+ Check if a native type string is valid for this backend.
+
+ Parameters
+ ----------
+ type_str : str
+ Native type string to validate.
+
+ Returns
+ -------
+ bool
+ True if valid for this backend, False otherwise.
+ """
+ ...
diff --git a/src/datajoint/adapters/mysql.py b/src/datajoint/adapters/mysql.py
new file mode 100644
index 000000000..4d2d4ca73
--- /dev/null
+++ b/src/datajoint/adapters/mysql.py
@@ -0,0 +1,1141 @@
+"""
+MySQL database adapter for DataJoint.
+
+This module provides MySQL-specific implementations for SQL generation,
+type mapping, error translation, and connection management.
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+import pymysql as client
+
+from .. import errors
+from .base import DatabaseAdapter
+
+# Core type mapping: DataJoint core types → MySQL types
+CORE_TYPE_MAP = {
+ "int64": "bigint",
+ "int32": "int",
+ "int16": "smallint",
+ "int8": "tinyint",
+ "float32": "float",
+ "float64": "double",
+ "bool": "tinyint",
+ "uuid": "binary(16)",
+ "bytes": "longblob",
+ "json": "json",
+ "date": "date",
+ # datetime, char, varchar, decimal, enum require parameters - handled in method
+}
+
+# Reverse mapping: MySQL types → DataJoint core types (for introspection)
+SQL_TO_CORE_MAP = {
+ "bigint": "int64",
+ "int": "int32",
+ "smallint": "int16",
+ "tinyint": "int8", # Could be bool, need context
+ "float": "float32",
+ "double": "float64",
+ "binary(16)": "uuid",
+ "longblob": "bytes",
+ "json": "json",
+ "date": "date",
+}
+
+
+class MySQLAdapter(DatabaseAdapter):
+ """MySQL database adapter implementation."""
+
+ # =========================================================================
+ # Connection Management
+ # =========================================================================
+
+ def connect(
+ self,
+ host: str,
+ port: int,
+ user: str,
+ password: str,
+ **kwargs: Any,
+ ) -> Any:
+ """
+ Establish MySQL connection.
+
+ Parameters
+ ----------
+ host : str
+ MySQL server hostname.
+ port : int
+ MySQL server port.
+ user : str
+ Username for authentication.
+ password : str
+ Password for authentication.
+ **kwargs : Any
+ Additional MySQL-specific parameters:
+ - ssl: TLS/SSL configuration dict (deprecated, use use_tls)
+ - use_tls: bool or dict - DataJoint's SSL parameter (preferred)
+ - charset: Character set (default from kwargs)
+
+ Returns
+ -------
+ pymysql.Connection
+ MySQL connection object.
+ """
+ # Handle both ssl (old) and use_tls (new) parameter names
+ ssl_config = kwargs.get("use_tls", kwargs.get("ssl"))
+ # Convert boolean True to dict for PyMySQL (PyMySQL expects dict or SSLContext)
+ if ssl_config is True:
+ ssl_config = {} # Enable SSL with default settings
+ charset = kwargs.get("charset", "")
+
+ # Prepare connection parameters
+ conn_params = {
+ "host": host,
+ "port": port,
+ "user": user,
+ "passwd": password,
+ "sql_mode": "NO_ZERO_DATE,NO_ZERO_IN_DATE,ERROR_FOR_DIVISION_BY_ZERO,"
+ "STRICT_ALL_TABLES,NO_ENGINE_SUBSTITUTION,ONLY_FULL_GROUP_BY",
+ "charset": charset,
+ "autocommit": True, # DataJoint manages transactions explicitly
+ }
+
+ # Handle SSL configuration
+ if ssl_config is False:
+ # Explicitly disable SSL
+ conn_params["ssl_disabled"] = True
+ elif ssl_config is not None:
+ # Enable SSL with config dict (can be empty for defaults)
+ conn_params["ssl"] = ssl_config
+ # Explicitly enable SSL by setting ssl_disabled=False
+ conn_params["ssl_disabled"] = False
+
+ return client.connect(**conn_params)
+
+ def close(self, connection: Any) -> None:
+ """Close the MySQL connection."""
+ connection.close()
+
+ def ping(self, connection: Any) -> bool:
+ """
+ Check if MySQL connection is alive.
+
+ Returns
+ -------
+ bool
+ True if connection is alive.
+ """
+ try:
+ connection.ping(reconnect=False)
+ return True
+ except Exception:
+ return False
+
+ def get_connection_id(self, connection: Any) -> int:
+ """
+ Get MySQL connection ID.
+
+ Returns
+ -------
+ int
+ MySQL connection_id().
+ """
+ cursor = connection.cursor()
+ cursor.execute("SELECT connection_id()")
+ return cursor.fetchone()[0]
+
+ @property
+ def default_port(self) -> int:
+ """MySQL default port 3306."""
+ return 3306
+
+ @property
+ def backend(self) -> str:
+ """Backend identifier: 'mysql'."""
+ return "mysql"
+
+ def get_cursor(self, connection: Any, as_dict: bool = False) -> Any:
+ """
+ Get a cursor from MySQL connection.
+
+ Parameters
+ ----------
+ connection : Any
+ pymysql connection object.
+ as_dict : bool, optional
+ If True, return DictCursor that yields rows as dictionaries.
+ If False, return standard Cursor that yields rows as tuples.
+ Default False.
+
+ Returns
+ -------
+ Any
+ pymysql cursor object.
+ """
+ import pymysql
+
+ cursor_class = pymysql.cursors.DictCursor if as_dict else pymysql.cursors.Cursor
+ return connection.cursor(cursor=cursor_class)
+
+ # =========================================================================
+ # SQL Syntax
+ # =========================================================================
+
+ def quote_identifier(self, name: str) -> str:
+ """
+ Quote identifier with backticks for MySQL.
+
+ Parameters
+ ----------
+ name : str
+ Identifier to quote.
+
+ Returns
+ -------
+ str
+ Backtick-quoted identifier: `name`
+ """
+ return f"`{name}`"
+
+ def split_full_table_name(self, full_table_name: str) -> tuple[str, str]:
+ """Split ```\\`schema\\`.\\`table\\` ``` into ``('schema', 'table')``."""
+ schema, table = full_table_name.replace("`", "").split(".")
+ return schema, table
+
+ def quote_string(self, value: str) -> str:
+ """
+ Quote string literal for MySQL with escaping.
+
+ Parameters
+ ----------
+ value : str
+ String value to quote.
+
+ Returns
+ -------
+ str
+ Quoted and escaped string literal.
+ """
+ # Use pymysql's escape_string for proper escaping
+ escaped = client.converters.escape_string(value)
+ return f"'{escaped}'"
+
+ def get_master_table_name(self, part_table: str) -> str | None:
+ """Extract master table name from part table (MySQL backtick format)."""
+ import re
+
+ # MySQL format: `schema`.`master__part`
+ match = re.match(r"(?P`\w+`.`#?\w+)__\w+`", part_table)
+ return match["master"] + "`" if match else None
+
+ @property
+ def parameter_placeholder(self) -> str:
+ """MySQL/pymysql uses %s placeholders."""
+ return "%s"
+
+ # =========================================================================
+ # Type Mapping
+ # =========================================================================
+
+ def core_type_to_sql(self, core_type: str) -> str:
+ """
+ Convert DataJoint core type to MySQL type.
+
+ Parameters
+ ----------
+ core_type : str
+ DataJoint core type, possibly with parameters:
+ - int64, float32, bool, uuid, bytes, json, date
+ - datetime or datetime(n)
+ - char(n), varchar(n)
+ - decimal(p,s)
+ - enum('a','b','c')
+
+ Returns
+ -------
+ str
+ MySQL SQL type.
+
+ Raises
+ ------
+ ValueError
+ If core_type is not recognized.
+ """
+ # Handle simple types without parameters
+ if core_type in CORE_TYPE_MAP:
+ return CORE_TYPE_MAP[core_type]
+
+ # Handle parametrized types
+ if core_type.startswith("datetime"):
+ # datetime or datetime(precision)
+ return core_type # MySQL supports datetime(n) directly
+
+ if core_type.startswith("char("):
+ # char(n)
+ return core_type
+
+ if core_type.startswith("varchar("):
+ # varchar(n)
+ return core_type
+
+ if core_type.startswith("decimal("):
+ # decimal(precision, scale)
+ return core_type
+
+ if core_type.startswith("enum("):
+ # enum('value1', 'value2', ...)
+ return core_type
+
+ raise ValueError(f"Unknown core type: {core_type}")
+
+ def sql_type_to_core(self, sql_type: str) -> str | None:
+ """
+ Convert MySQL type to DataJoint core type (if mappable).
+
+ Parameters
+ ----------
+ sql_type : str
+ MySQL SQL type.
+
+ Returns
+ -------
+ str or None
+ DataJoint core type if mappable, None otherwise.
+ """
+ # Normalize type string (lowercase, strip spaces)
+ sql_type_lower = sql_type.lower().strip()
+
+ # Direct mapping
+ if sql_type_lower in SQL_TO_CORE_MAP:
+ return SQL_TO_CORE_MAP[sql_type_lower]
+
+ # Handle parametrized types
+ if sql_type_lower.startswith("datetime"):
+ return sql_type # Keep precision
+
+ if sql_type_lower.startswith("char("):
+ return sql_type # Keep size
+
+ if sql_type_lower.startswith("varchar("):
+ return sql_type # Keep size
+
+ if sql_type_lower.startswith("decimal("):
+ return sql_type # Keep precision/scale
+
+ if sql_type_lower.startswith("enum("):
+ return sql_type # Keep values
+
+ # Not a mappable core type
+ return None
+
+ # =========================================================================
+ # DDL Generation
+ # =========================================================================
+
+ def create_schema_sql(self, schema_name: str) -> str:
+ """
+ Generate CREATE DATABASE statement for MySQL.
+
+ Parameters
+ ----------
+ schema_name : str
+ Database name.
+
+ Returns
+ -------
+ str
+ CREATE DATABASE SQL.
+ """
+ return f"CREATE DATABASE {self.quote_identifier(schema_name)}"
+
+ def drop_schema_sql(self, schema_name: str, if_exists: bool = True) -> str:
+ """
+ Generate DROP DATABASE statement for MySQL.
+
+ Parameters
+ ----------
+ schema_name : str
+ Database name.
+ if_exists : bool
+ Include IF EXISTS clause.
+
+ Returns
+ -------
+ str
+ DROP DATABASE SQL.
+ """
+ if_exists_clause = "IF EXISTS " if if_exists else ""
+ return f"DROP DATABASE {if_exists_clause}{self.quote_identifier(schema_name)}"
+
+ def create_table_sql(
+ self,
+ table_name: str,
+ columns: list[dict[str, Any]],
+ primary_key: list[str],
+ foreign_keys: list[dict[str, Any]],
+ indexes: list[dict[str, Any]],
+ comment: str | None = None,
+ ) -> str:
+ """
+ Generate CREATE TABLE statement for MySQL.
+
+ Parameters
+ ----------
+ table_name : str
+ Fully qualified table name (schema.table).
+ columns : list[dict]
+ Column defs: [{name, type, nullable, default, comment}, ...]
+ primary_key : list[str]
+ Primary key column names.
+ foreign_keys : list[dict]
+ FK defs: [{columns, ref_table, ref_columns}, ...]
+ indexes : list[dict]
+ Index defs: [{columns, unique}, ...]
+ comment : str, optional
+ Table comment.
+
+ Returns
+ -------
+ str
+ CREATE TABLE SQL statement.
+ """
+ lines = []
+
+ # Column definitions
+ for col in columns:
+ col_name = self.quote_identifier(col["name"])
+ col_type = col["type"]
+ nullable = "NULL" if col.get("nullable", False) else "NOT NULL"
+ default = f" DEFAULT {col['default']}" if "default" in col else ""
+ col_comment = f" COMMENT {self.quote_string(col['comment'])}" if "comment" in col else ""
+ lines.append(f"{col_name} {col_type} {nullable}{default}{col_comment}")
+
+ # Primary key
+ if primary_key:
+ pk_cols = ", ".join(self.quote_identifier(col) for col in primary_key)
+ lines.append(f"PRIMARY KEY ({pk_cols})")
+
+ # Foreign keys
+ for fk in foreign_keys:
+ fk_cols = ", ".join(self.quote_identifier(col) for col in fk["columns"])
+ ref_cols = ", ".join(self.quote_identifier(col) for col in fk["ref_columns"])
+ lines.append(
+ f"FOREIGN KEY ({fk_cols}) REFERENCES {fk['ref_table']} ({ref_cols}) ON UPDATE CASCADE ON DELETE RESTRICT"
+ )
+
+ # Indexes
+ for idx in indexes:
+ unique = "UNIQUE " if idx.get("unique", False) else ""
+ idx_cols = ", ".join(self.quote_identifier(col) for col in idx["columns"])
+ lines.append(f"{unique}INDEX ({idx_cols})")
+
+ # Assemble CREATE TABLE
+ table_def = ",\n ".join(lines)
+ comment_clause = f" COMMENT={self.quote_string(comment)}" if comment else ""
+ return f"CREATE TABLE IF NOT EXISTS {table_name} (\n {table_def}\n) ENGINE=InnoDB{comment_clause}"
+
+ def drop_table_sql(self, table_name: str, if_exists: bool = True) -> str:
+ """Generate DROP TABLE statement for MySQL."""
+ if_exists_clause = "IF EXISTS " if if_exists else ""
+ return f"DROP TABLE {if_exists_clause}{table_name}"
+
+ def alter_table_sql(
+ self,
+ table_name: str,
+ add_columns: list[dict[str, Any]] | None = None,
+ drop_columns: list[str] | None = None,
+ modify_columns: list[dict[str, Any]] | None = None,
+ ) -> str:
+ """
+ Generate ALTER TABLE statement for MySQL.
+
+ Parameters
+ ----------
+ table_name : str
+ Table name.
+ add_columns : list[dict], optional
+ Columns to add.
+ drop_columns : list[str], optional
+ Column names to drop.
+ modify_columns : list[dict], optional
+ Columns to modify.
+
+ Returns
+ -------
+ str
+ ALTER TABLE SQL statement.
+ """
+ clauses = []
+
+ if add_columns:
+ for col in add_columns:
+ col_name = self.quote_identifier(col["name"])
+ col_type = col["type"]
+ nullable = "NULL" if col.get("nullable", False) else "NOT NULL"
+ clauses.append(f"ADD {col_name} {col_type} {nullable}")
+
+ if drop_columns:
+ for col_name in drop_columns:
+ clauses.append(f"DROP {self.quote_identifier(col_name)}")
+
+ if modify_columns:
+ for col in modify_columns:
+ col_name = self.quote_identifier(col["name"])
+ col_type = col["type"]
+ nullable = "NULL" if col.get("nullable", False) else "NOT NULL"
+ clauses.append(f"MODIFY {col_name} {col_type} {nullable}")
+
+ return f"ALTER TABLE {table_name} {', '.join(clauses)}"
+
+ def add_comment_sql(
+ self,
+ object_type: str,
+ object_name: str,
+ comment: str,
+ ) -> str | None:
+ """
+ MySQL embeds comments in CREATE/ALTER, not separate statements.
+
+ Returns None since comments are inline.
+ """
+ return None
+
+ # =========================================================================
+ # DML Generation
+ # =========================================================================
+
+ def insert_sql(
+ self,
+ table_name: str,
+ columns: list[str],
+ on_duplicate: str | None = None,
+ ) -> str:
+ """
+ Generate INSERT statement for MySQL.
+
+ Parameters
+ ----------
+ table_name : str
+ Table name.
+ columns : list[str]
+ Column names.
+ on_duplicate : str, optional
+ 'ignore', 'replace', or 'update'.
+
+ Returns
+ -------
+ str
+ INSERT SQL with placeholders.
+ """
+ cols = ", ".join(self.quote_identifier(col) for col in columns)
+ placeholders = ", ".join([self.parameter_placeholder] * len(columns))
+
+ if on_duplicate == "ignore":
+ return f"INSERT IGNORE INTO {table_name} ({cols}) VALUES ({placeholders})"
+ elif on_duplicate == "replace":
+ return f"REPLACE INTO {table_name} ({cols}) VALUES ({placeholders})"
+ elif on_duplicate == "update":
+ # ON DUPLICATE KEY UPDATE col=VALUES(col)
+ updates = ", ".join(f"{self.quote_identifier(col)}=VALUES({self.quote_identifier(col)})" for col in columns)
+ return f"INSERT INTO {table_name} ({cols}) VALUES ({placeholders}) ON DUPLICATE KEY UPDATE {updates}"
+ else:
+ return f"INSERT INTO {table_name} ({cols}) VALUES ({placeholders})"
+
+ def update_sql(
+ self,
+ table_name: str,
+ set_columns: list[str],
+ where_columns: list[str],
+ ) -> str:
+ """Generate UPDATE statement for MySQL."""
+ set_clause = ", ".join(f"{self.quote_identifier(col)} = {self.parameter_placeholder}" for col in set_columns)
+ where_clause = " AND ".join(f"{self.quote_identifier(col)} = {self.parameter_placeholder}" for col in where_columns)
+ return f"UPDATE {table_name} SET {set_clause} WHERE {where_clause}"
+
+ def delete_sql(self, table_name: str) -> str:
+ """Generate DELETE statement for MySQL (WHERE added separately)."""
+ return f"DELETE FROM {table_name}"
+
+ def upsert_on_duplicate_sql(
+ self,
+ table_name: str,
+ columns: list[str],
+ primary_key: list[str],
+ num_rows: int,
+ ) -> str:
+ """Generate INSERT ... ON DUPLICATE KEY UPDATE statement for MySQL."""
+ # Build column list
+ col_list = ", ".join(columns)
+
+ # Build placeholders for VALUES
+ placeholders = ", ".join(["(%s)" % ", ".join(["%s"] * len(columns))] * num_rows)
+
+ # Build UPDATE clause (all columns)
+ update_clauses = ", ".join(f"{col} = VALUES({col})" for col in columns)
+
+ return f"""
+ INSERT INTO {table_name} ({col_list})
+ VALUES {placeholders}
+ ON DUPLICATE KEY UPDATE {update_clauses}
+ """
+
+ def skip_duplicates_clause(
+ self,
+ full_table_name: str,
+ primary_key: list[str],
+ ) -> str:
+ """
+ Generate clause to skip duplicate key insertions for MySQL.
+
+ Uses ON DUPLICATE KEY UPDATE with a no-op update (pk=pk) to effectively
+ skip duplicates without raising an error.
+
+ Parameters
+ ----------
+ full_table_name : str
+ Fully qualified table name (with quotes).
+ primary_key : list[str]
+ Primary key column names (unquoted).
+
+ Returns
+ -------
+ str
+ MySQL ON DUPLICATE KEY UPDATE clause.
+ """
+ quoted_pk = self.quote_identifier(primary_key[0])
+ return f" ON DUPLICATE KEY UPDATE {quoted_pk}={full_table_name}.{quoted_pk}"
+
+ # =========================================================================
+ # Introspection
+ # =========================================================================
+
+ def list_schemas_sql(self) -> str:
+ """Query to list all databases in MySQL."""
+ return "SELECT schema_name FROM information_schema.schemata"
+
+ def schema_exists_sql(self, schema_name: str) -> str:
+ """Query to check if a database exists in MySQL."""
+ return f"SELECT schema_name FROM information_schema.schemata WHERE schema_name = {self.quote_string(schema_name)}"
+
+ def list_tables_sql(self, schema_name: str, pattern: str | None = None) -> str:
+ """Query to list tables in a database."""
+ sql = f"SHOW TABLES IN {self.quote_identifier(schema_name)}"
+ if pattern:
+ sql += f" LIKE '{pattern}'"
+ return sql
+
+ def get_table_info_sql(self, schema_name: str, table_name: str) -> str:
+ """Query to get table metadata (comment, engine, etc.)."""
+ return (
+ f"SELECT * FROM information_schema.tables "
+ f"WHERE table_schema = {self.quote_string(schema_name)} "
+ f"AND table_name = {self.quote_string(table_name)}"
+ )
+
+ def get_columns_sql(self, schema_name: str, table_name: str) -> str:
+ """Query to get column definitions."""
+ return f"SHOW FULL COLUMNS FROM {self.quote_identifier(table_name)} IN {self.quote_identifier(schema_name)}"
+
+ def get_primary_key_sql(self, schema_name: str, table_name: str) -> str:
+ """Query to get primary key columns."""
+ return (
+ f"SELECT COLUMN_NAME as column_name FROM information_schema.key_column_usage "
+ f"WHERE table_schema = {self.quote_string(schema_name)} "
+ f"AND table_name = {self.quote_string(table_name)} "
+ f"AND constraint_name = 'PRIMARY' "
+ f"ORDER BY ordinal_position"
+ )
+
+ def get_foreign_keys_sql(self, schema_name: str, table_name: str) -> str:
+ """Query to get foreign key constraints."""
+ return (
+ f"SELECT CONSTRAINT_NAME as constraint_name, COLUMN_NAME as column_name, "
+ f"REFERENCED_TABLE_NAME as referenced_table_name, REFERENCED_COLUMN_NAME as referenced_column_name "
+ f"FROM information_schema.key_column_usage "
+ f"WHERE table_schema = {self.quote_string(schema_name)} "
+ f"AND table_name = {self.quote_string(table_name)} "
+ f"AND referenced_table_name IS NOT NULL "
+ f"ORDER BY constraint_name, ordinal_position"
+ )
+
+ def load_primary_keys_sql(self, schemas_list: str, like_pattern: str) -> str:
+ """Query to load all primary key columns across schemas."""
+ tab_expr = "concat('`', table_schema, '`.`', table_name, '`')"
+ return (
+ f"SELECT {tab_expr} as tab, column_name "
+ f"FROM information_schema.key_column_usage "
+ f"WHERE table_name NOT LIKE {like_pattern} "
+ f"AND table_schema in ({schemas_list}) "
+ f"AND constraint_name='PRIMARY'"
+ )
+
+ def load_foreign_keys_sql(self, schemas_list: str, like_pattern: str) -> str:
+ """Query to load all foreign key relationships across schemas."""
+ tab_expr = "concat('`', table_schema, '`.`', table_name, '`')"
+ ref_tab_expr = "concat('`', referenced_table_schema, '`.`', referenced_table_name, '`')"
+ return (
+ f"SELECT constraint_name, "
+ f"{tab_expr} as referencing_table, "
+ f"{ref_tab_expr} as referenced_table, "
+ f"column_name, referenced_column_name "
+ f"FROM information_schema.key_column_usage "
+ f"WHERE referenced_table_name NOT LIKE {like_pattern} "
+ f"AND (referenced_table_schema in ({schemas_list}) "
+ f"OR referenced_table_schema is not NULL AND table_schema in ({schemas_list}))"
+ )
+
+ def find_downstream_schemas_sql(self, schemas_list: str) -> str:
+ """Find schemas with FK references to the given schemas."""
+ return (
+ f"SELECT DISTINCT table_schema as schema_name "
+ f"FROM information_schema.key_column_usage "
+ f"WHERE referenced_table_schema IN ({schemas_list}) "
+ f"AND table_schema NOT IN ({schemas_list})"
+ )
+
+ def find_upstream_schemas_sql(self, schemas_list: str) -> str:
+ """Find schemas that the given schemas reference via FK."""
+ return (
+ f"SELECT DISTINCT referenced_table_schema as schema_name "
+ f"FROM information_schema.key_column_usage "
+ f"WHERE table_schema IN ({schemas_list}) "
+ f"AND referenced_table_schema IS NOT NULL "
+ f"AND referenced_table_schema NOT IN ({schemas_list})"
+ )
+
+ def get_constraint_info_sql(self, constraint_name: str, schema_name: str, table_name: str) -> str:
+ """Query to get FK constraint details from information_schema."""
+ return (
+ "SELECT "
+ " COLUMN_NAME as fk_attrs, "
+ " CONCAT('`', REFERENCED_TABLE_SCHEMA, '`.`', REFERENCED_TABLE_NAME, '`') as parent, "
+ " REFERENCED_COLUMN_NAME as pk_attrs "
+ "FROM INFORMATION_SCHEMA.KEY_COLUMN_USAGE "
+ "WHERE CONSTRAINT_NAME = %s AND TABLE_SCHEMA = %s AND TABLE_NAME = %s"
+ )
+
+ def parse_foreign_key_error(self, error_message: str) -> dict[str, str | list[str] | None] | None:
+ """Parse MySQL foreign key violation error message."""
+ import re
+
+ # MySQL FK error pattern with backticks
+ pattern = re.compile(
+ r"[\w\s:]*\((?P`[^`]+`.`[^`]+`), "
+ r"CONSTRAINT (?P`[^`]+`) "
+ r"(FOREIGN KEY \((?P[^)]+)\) "
+ r"REFERENCES (?P`[^`]+`(\.`[^`]+`)?) \((?P[^)]+)\)[\s\w]+\))?"
+ )
+
+ match = pattern.match(error_message)
+ if not match:
+ return None
+
+ result = match.groupdict()
+
+ # Parse comma-separated FK attrs if present
+ if result.get("fk_attrs"):
+ result["fk_attrs"] = [col.strip("`") for col in result["fk_attrs"].split(",")]
+ # Parse comma-separated PK attrs if present
+ if result.get("pk_attrs"):
+ result["pk_attrs"] = [col.strip("`") for col in result["pk_attrs"].split(",")]
+
+ return result
+
+ def get_indexes_sql(self, schema_name: str, table_name: str) -> str:
+ """Query to get index definitions. Functional indexes (NULL COLUMN_NAME) are skipped downstream."""
+ return (
+ f"SELECT INDEX_NAME as index_name, "
+ f"COLUMN_NAME as column_name, "
+ f"NON_UNIQUE as non_unique, SEQ_IN_INDEX as seq_in_index "
+ f"FROM information_schema.statistics "
+ f"WHERE table_schema = {self.quote_string(schema_name)} "
+ f"AND table_name = {self.quote_string(table_name)} "
+ f"AND index_name != 'PRIMARY' "
+ f"ORDER BY index_name, seq_in_index"
+ )
+
+ def parse_column_info(self, row: dict[str, Any]) -> dict[str, Any]:
+ """
+ Parse MySQL SHOW FULL COLUMNS output into standardized format.
+
+ Parameters
+ ----------
+ row : dict
+ Row from SHOW FULL COLUMNS query.
+
+ Returns
+ -------
+ dict
+ Standardized column info with keys:
+ name, type, nullable, default, comment, key, extra
+ """
+ return {
+ "name": row["Field"],
+ "type": row["Type"],
+ "nullable": row["Null"] == "YES",
+ "default": row["Default"],
+ "comment": row["Comment"],
+ "key": row["Key"], # PRI, UNI, MUL
+ "extra": row["Extra"], # auto_increment, etc.
+ }
+
+ # =========================================================================
+ # Transactions
+ # =========================================================================
+
+ def start_transaction_sql(self, isolation_level: str | None = None) -> str:
+ """Generate START TRANSACTION statement."""
+ if isolation_level:
+ return f"START TRANSACTION WITH CONSISTENT SNAPSHOT, {isolation_level}"
+ return "START TRANSACTION WITH CONSISTENT SNAPSHOT"
+
+ def commit_sql(self) -> str:
+ """Generate COMMIT statement."""
+ return "COMMIT"
+
+ def rollback_sql(self) -> str:
+ """Generate ROLLBACK statement."""
+ return "ROLLBACK"
+
+ # =========================================================================
+ # Functions and Expressions
+ # =========================================================================
+
+ def current_timestamp_expr(self, precision: int | None = None) -> str:
+ """
+ CURRENT_TIMESTAMP expression for MySQL.
+
+ Parameters
+ ----------
+ precision : int, optional
+ Fractional seconds precision (0-6).
+
+ Returns
+ -------
+ str
+ CURRENT_TIMESTAMP or CURRENT_TIMESTAMP(n).
+ """
+ if precision is not None:
+ return f"CURRENT_TIMESTAMP({precision})"
+ return "CURRENT_TIMESTAMP"
+
+ def interval_expr(self, value: int, unit: str) -> str:
+ """
+ INTERVAL expression for MySQL.
+
+ Parameters
+ ----------
+ value : int
+ Interval value.
+ unit : str
+ Time unit (singular: 'second', 'minute', 'hour', 'day').
+
+ Returns
+ -------
+ str
+ INTERVAL n UNIT (e.g., 'INTERVAL 5 SECOND').
+ """
+ # MySQL uses singular unit names
+ return f"INTERVAL {value} {unit.upper()}"
+
+ def current_user_expr(self) -> str:
+ """MySQL current user expression."""
+ return "user()"
+
+ def json_path_expr(self, column: str, path: str, return_type: str | None = None) -> str:
+ """
+ Generate MySQL json_value() expression.
+
+ Parameters
+ ----------
+ column : str
+ Column name containing JSON data.
+ path : str
+ JSON path (e.g., 'field' or 'nested.field').
+ return_type : str, optional
+ Return type specification (e.g., 'decimal(10,2)').
+
+ Returns
+ -------
+ str
+ MySQL json_value() expression.
+
+ Examples
+ --------
+ >>> adapter.json_path_expr('data', 'field')
+ "json_value(`data`, _utf8mb4'$.field')"
+ >>> adapter.json_path_expr('data', 'value', 'decimal(10,2)')
+ "json_value(`data`, _utf8mb4'$.value' returning decimal(10,2))"
+ """
+ quoted_col = self.quote_identifier(column)
+ return_clause = f" returning {return_type}" if return_type else ""
+ return f"json_value({quoted_col}, _utf8mb4'$.{path}'{return_clause})"
+
+ def translate_expression(self, expr: str) -> str:
+ """
+ Translate SQL expression for MySQL compatibility.
+
+ Converts PostgreSQL-specific functions to MySQL equivalents:
+ - STRING_AGG(col, 'sep') → GROUP_CONCAT(col SEPARATOR 'sep')
+ - STRING_AGG(col, ',') → GROUP_CONCAT(col)
+
+ Parameters
+ ----------
+ expr : str
+ SQL expression that may contain function calls.
+
+ Returns
+ -------
+ str
+ Translated expression for MySQL.
+ """
+ import re
+
+ # STRING_AGG(col, 'sep') → GROUP_CONCAT(col SEPARATOR 'sep')
+ def replace_string_agg(match):
+ inner = match.group(1).strip()
+ # Parse arguments: col, 'separator'
+ # Handle both single and double quoted separators
+ arg_match = re.match(r"(.+?)\s*,\s*(['\"])(.+?)\2", inner)
+ if arg_match:
+ col = arg_match.group(1).strip()
+ sep = arg_match.group(3)
+ # Remove ::text cast if present (PostgreSQL-specific)
+ col = re.sub(r"::text$", "", col)
+ if sep == ",":
+ return f"GROUP_CONCAT({col})"
+ else:
+ return f"GROUP_CONCAT({col} SEPARATOR '{sep}')"
+ else:
+ # No separator found, just use the expression
+ col = re.sub(r"::text$", "", inner)
+ return f"GROUP_CONCAT({col})"
+
+ expr = re.sub(r"STRING_AGG\s*\((.+?)\)", replace_string_agg, expr, flags=re.IGNORECASE)
+
+ return expr
+
+ # =========================================================================
+ # DDL Generation
+ # =========================================================================
+
+ def format_column_definition(
+ self,
+ name: str,
+ sql_type: str,
+ nullable: bool = False,
+ default: str | None = None,
+ comment: str | None = None,
+ ) -> str:
+ """
+ Format a column definition for MySQL DDL.
+
+ Examples
+ --------
+ >>> adapter.format_column_definition('user_id', 'bigint', nullable=False, comment='user ID')
+ "`user_id` bigint NOT NULL COMMENT \\"user ID\\""
+ """
+ parts = [self.quote_identifier(name), sql_type]
+ if default:
+ parts.append(default) # e.g., "DEFAULT NULL" or "NOT NULL DEFAULT 5"
+ elif not nullable:
+ parts.append("NOT NULL")
+ if comment:
+ parts.append(f'COMMENT "{comment}"')
+ return " ".join(parts)
+
+ def table_options_clause(self, comment: str | None = None) -> str:
+ """
+ Generate MySQL table options clause.
+
+ Examples
+ --------
+ >>> adapter.table_options_clause('test table')
+ 'ENGINE=InnoDB, COMMENT "test table"'
+ >>> adapter.table_options_clause()
+ 'ENGINE=InnoDB'
+ """
+ clause = "ENGINE=InnoDB"
+ if comment:
+ clause += f', COMMENT "{comment}"'
+ return clause
+
+ def table_comment_ddl(self, full_table_name: str, comment: str) -> str | None:
+ """
+ MySQL uses inline COMMENT in CREATE TABLE, so no separate DDL needed.
+
+ Examples
+ --------
+ >>> adapter.table_comment_ddl('`schema`.`table`', 'test comment')
+ None
+ """
+ return None # MySQL uses inline COMMENT
+
+ def column_comment_ddl(self, full_table_name: str, column_name: str, comment: str) -> str | None:
+ """
+ MySQL uses inline COMMENT in column definitions, so no separate DDL needed.
+
+ Examples
+ --------
+ >>> adapter.column_comment_ddl('`schema`.`table`', 'column', 'test comment')
+ None
+ """
+ return None # MySQL uses inline COMMENT
+
+ def enum_type_ddl(self, type_name: str, values: list[str]) -> str | None:
+ """
+ MySQL uses inline enum type in column definition, so no separate DDL needed.
+
+ Examples
+ --------
+ >>> adapter.enum_type_ddl('status_type', ['active', 'inactive'])
+ None
+ """
+ return None # MySQL uses inline enum
+
+ def job_metadata_columns(self) -> list[str]:
+ """
+ Return MySQL-specific job metadata column definitions.
+
+ Examples
+ --------
+ >>> adapter.job_metadata_columns()
+ ["`_job_start_time` datetime(3) DEFAULT NULL",
+ "`_job_duration` float DEFAULT NULL",
+ "`_job_version` varchar(64) DEFAULT ''"]
+ """
+ return [
+ "`_job_start_time` datetime(3) DEFAULT NULL",
+ "`_job_duration` float DEFAULT NULL",
+ "`_job_version` varchar(64) DEFAULT ''",
+ ]
+
+ # =========================================================================
+ # Error Translation
+ # =========================================================================
+
+ def translate_error(self, error: Exception, query: str = "") -> Exception:
+ """
+ Translate MySQL error to DataJoint exception.
+
+ Parameters
+ ----------
+ error : Exception
+ MySQL exception (typically pymysql error).
+
+ Returns
+ -------
+ Exception
+ DataJoint exception or original error.
+ """
+ if not hasattr(error, "args") or len(error.args) == 0:
+ return error
+
+ err, *args = error.args
+
+ match err:
+ # Loss of connection errors
+ case 0 | "(0, '')":
+ return errors.LostConnectionError("Server connection lost due to an interface error.", *args)
+ case 2006:
+ return errors.LostConnectionError("Connection timed out", *args)
+ case 2013:
+ return errors.LostConnectionError("Server connection lost", *args)
+
+ # Access errors
+ case 1044 | 1142:
+ query = args[0] if args else ""
+ return errors.AccessError("Insufficient privileges.", args[0] if args else "", query)
+
+ # Integrity errors
+ case 1062:
+ return errors.DuplicateError(*args)
+ case 1217 | 1451 | 1452 | 3730:
+ return errors.IntegrityError(*args)
+
+ # Syntax errors
+ case 1064:
+ query = args[0] if args else ""
+ return errors.QuerySyntaxError(args[0] if args else "", query)
+
+ # Existence errors
+ case 1146:
+ query = args[0] if args else ""
+ return errors.MissingTableError(args[0] if args else "", query)
+ case 1364:
+ return errors.MissingAttributeError(*args)
+ case 1054:
+ return errors.UnknownAttributeError(*args)
+
+ # All other errors pass through unchanged
+ case _:
+ return error
+
+ # =========================================================================
+ # Native Type Validation
+ # =========================================================================
+
+ def validate_native_type(self, type_str: str) -> bool:
+ """
+ Check if a native MySQL type string is valid.
+
+ Parameters
+ ----------
+ type_str : str
+ Type string to validate.
+
+ Returns
+ -------
+ bool
+ True if valid MySQL type.
+ """
+ type_lower = type_str.lower().strip()
+
+ # MySQL native types (simplified validation)
+ valid_types = {
+ # Integer types
+ "tinyint",
+ "smallint",
+ "mediumint",
+ "int",
+ "integer",
+ "bigint",
+ # Floating point
+ "float",
+ "double",
+ "real",
+ "decimal",
+ "numeric",
+ # String types
+ "char",
+ "varchar",
+ "binary",
+ "varbinary",
+ "tinyblob",
+ "blob",
+ "mediumblob",
+ "longblob",
+ "tinytext",
+ "text",
+ "mediumtext",
+ "longtext",
+ # Temporal types
+ "date",
+ "time",
+ "datetime",
+ "timestamp",
+ "year",
+ # Other
+ "enum",
+ "set",
+ "json",
+ "geometry",
+ }
+
+ # Extract base type (before parentheses)
+ base_type = type_lower.split("(")[0].strip()
+
+ return base_type in valid_types
diff --git a/src/datajoint/adapters/postgres.py b/src/datajoint/adapters/postgres.py
new file mode 100644
index 000000000..07e0732a4
--- /dev/null
+++ b/src/datajoint/adapters/postgres.py
@@ -0,0 +1,1615 @@
+"""
+PostgreSQL database adapter for DataJoint.
+
+This module provides PostgreSQL-specific implementations for SQL generation,
+type mapping, error translation, and connection management.
+"""
+
+from __future__ import annotations
+
+import re
+from typing import Any
+
+try:
+ import psycopg2 as client
+ from psycopg2 import sql
+except ImportError:
+ client = None # type: ignore
+ sql = None # type: ignore
+
+from .. import errors
+from .base import DatabaseAdapter
+
+# Core type mapping: DataJoint core types → PostgreSQL types
+CORE_TYPE_MAP = {
+ "int64": "bigint",
+ "int32": "integer",
+ "int16": "smallint",
+ "int8": "smallint", # PostgreSQL lacks tinyint; semantically equivalent
+ "float32": "real",
+ "float64": "double precision",
+ "bool": "boolean",
+ "uuid": "uuid", # Native UUID support
+ "bytes": "bytea",
+ "json": "jsonb", # Using jsonb for better performance
+ "date": "date",
+ # datetime, char, varchar, decimal, enum require parameters - handled in method
+}
+
+# Reverse mapping: PostgreSQL types → DataJoint core types (for introspection)
+SQL_TO_CORE_MAP = {
+ "bigint": "int64",
+ "integer": "int32",
+ "smallint": "int16",
+ "real": "float32",
+ "double precision": "float64",
+ "boolean": "bool",
+ "uuid": "uuid",
+ "bytea": "bytes",
+ "jsonb": "json",
+ "json": "json",
+ "date": "date",
+}
+
+
+class PostgreSQLAdapter(DatabaseAdapter):
+ """PostgreSQL database adapter implementation."""
+
+ def __init__(self) -> None:
+ """Initialize PostgreSQL adapter."""
+ if client is None:
+ raise ImportError(
+ "psycopg2 is required for PostgreSQL support. " "Install it with: pip install 'datajoint[postgres]'"
+ )
+
+ # =========================================================================
+ # Connection Management
+ # =========================================================================
+
+ def connect(
+ self,
+ host: str,
+ port: int,
+ user: str,
+ password: str,
+ **kwargs: Any,
+ ) -> Any:
+ """
+ Establish PostgreSQL connection.
+
+ Parameters
+ ----------
+ host : str
+ PostgreSQL server hostname.
+ port : int
+ PostgreSQL server port.
+ user : str
+ Username for authentication.
+ password : str
+ Password for authentication.
+ **kwargs : Any
+ Additional PostgreSQL-specific parameters:
+ - dbname: Database name
+ - sslmode: SSL mode ('disable', 'allow', 'prefer', 'require')
+ - use_tls: bool or dict - DataJoint's SSL parameter (converted to sslmode)
+ - connect_timeout: Connection timeout in seconds
+
+ Returns
+ -------
+ psycopg2.connection
+ PostgreSQL connection object.
+ """
+ dbname = kwargs.get("dbname", "postgres") # Default to postgres database
+ connect_timeout = kwargs.get("connect_timeout", 10)
+
+ # Handle use_tls parameter (from DataJoint Connection)
+ # Convert to PostgreSQL's sslmode
+ use_tls = kwargs.get("use_tls")
+ if "sslmode" in kwargs:
+ # Explicit sslmode takes precedence
+ sslmode = kwargs["sslmode"]
+ elif use_tls is False:
+ # use_tls=False → disable SSL
+ sslmode = "disable"
+ elif use_tls is True or isinstance(use_tls, dict):
+ # use_tls=True or dict → require SSL
+ sslmode = "require"
+ else:
+ # use_tls=None (default) → prefer SSL but allow fallback
+ sslmode = "prefer"
+
+ conn = client.connect(
+ host=host,
+ port=port,
+ user=user,
+ password=password,
+ dbname=dbname,
+ sslmode=sslmode,
+ connect_timeout=connect_timeout,
+ )
+ # DataJoint manages transactions explicitly via start_transaction()
+ # Set autocommit=True to avoid implicit transactions
+ conn.autocommit = True
+
+ # Register numpy type adapters so numpy types can be used directly in queries
+ self._register_numpy_adapters()
+
+ return conn
+
+ def _register_numpy_adapters(self) -> None:
+ """
+ Register psycopg2 adapters for numpy types.
+
+ This allows numpy scalar types (bool_, int64, float64, etc.) to be used
+ directly in queries without explicit conversion to Python native types.
+ """
+ try:
+ import numpy as np
+ from psycopg2.extensions import register_adapter, AsIs
+
+ # Numpy bool type
+ register_adapter(np.bool_, lambda x: AsIs(str(bool(x)).upper()))
+
+ # Numpy integer types
+ for np_type in (np.int8, np.int16, np.int32, np.int64, np.uint8, np.uint16, np.uint32, np.uint64):
+ register_adapter(np_type, lambda x: AsIs(int(x)))
+
+ # Numpy float types
+ for np_ftype in (np.float16, np.float32, np.float64):
+ register_adapter(np_ftype, lambda x: AsIs(repr(float(x))))
+
+ except ImportError:
+ pass # numpy not available
+
+ def close(self, connection: Any) -> None:
+ """Close the PostgreSQL connection."""
+ connection.close()
+
+ def ping(self, connection: Any) -> bool:
+ """
+ Check if PostgreSQL connection is alive.
+
+ Returns
+ -------
+ bool
+ True if connection is alive.
+ """
+ try:
+ cursor = connection.cursor()
+ cursor.execute("SELECT 1")
+ cursor.close()
+ return True
+ except Exception:
+ return False
+
+ def get_connection_id(self, connection: Any) -> int:
+ """
+ Get PostgreSQL backend process ID.
+
+ Returns
+ -------
+ int
+ PostgreSQL pg_backend_pid().
+ """
+ cursor = connection.cursor()
+ cursor.execute("SELECT pg_backend_pid()")
+ return cursor.fetchone()[0]
+
+ @property
+ def default_port(self) -> int:
+ """PostgreSQL default port 5432."""
+ return 5432
+
+ @property
+ def backend(self) -> str:
+ """Backend identifier: 'postgresql'."""
+ return "postgresql"
+
+ def get_cursor(self, connection: Any, as_dict: bool = False) -> Any:
+ """
+ Get a cursor from PostgreSQL connection.
+
+ Parameters
+ ----------
+ connection : Any
+ psycopg2 connection object.
+ as_dict : bool, optional
+ If True, return Real DictCursor that yields rows as dictionaries.
+ If False, return standard cursor that yields rows as tuples.
+ Default False.
+
+ Returns
+ -------
+ Any
+ psycopg2 cursor object.
+ """
+ import psycopg2.extras
+
+ if as_dict:
+ return connection.cursor(cursor_factory=psycopg2.extras.RealDictCursor)
+ return connection.cursor()
+
+ # =========================================================================
+ # SQL Syntax
+ # =========================================================================
+
+ def quote_identifier(self, name: str) -> str:
+ """
+ Quote identifier with double quotes for PostgreSQL.
+
+ Parameters
+ ----------
+ name : str
+ Identifier to quote.
+
+ Returns
+ -------
+ str
+ Double-quoted identifier: "name"
+ """
+ return f'"{name}"'
+
+ @property
+ def max_table_name_length(self) -> int:
+ """PostgreSQL NAMEDATALEN-1 = 63."""
+ return 63
+
+ def split_full_table_name(self, full_table_name: str) -> tuple[str, str]:
+ """Split ``"schema"."table"`` into ``('schema', 'table')``."""
+ schema, table = full_table_name.replace('"', "").split(".")
+ return schema, table
+
+ def quote_string(self, value: str) -> str:
+ """
+ Quote string literal for PostgreSQL with escaping.
+
+ Parameters
+ ----------
+ value : str
+ String value to quote.
+
+ Returns
+ -------
+ str
+ Quoted and escaped string literal.
+ """
+ # Escape single quotes by doubling them (PostgreSQL standard)
+ escaped = value.replace("'", "''")
+ return f"'{escaped}'"
+
+ def get_master_table_name(self, part_table: str) -> str | None:
+ """Extract master table name from part table (PostgreSQL double-quote format)."""
+ import re
+
+ # PostgreSQL format: "schema"."master__part"
+ match = re.match(r'(?P"\w+"."#?\w+)__\w+"', part_table)
+ return match["master"] + '"' if match else None
+
+ @property
+ def parameter_placeholder(self) -> str:
+ """PostgreSQL/psycopg2 uses %s placeholders."""
+ return "%s"
+
+ # =========================================================================
+ # Type Mapping
+ # =========================================================================
+
+ def core_type_to_sql(self, core_type: str) -> str:
+ """
+ Convert DataJoint core type to PostgreSQL type.
+
+ Parameters
+ ----------
+ core_type : str
+ DataJoint core type, possibly with parameters:
+ - int64, float32, bool, uuid, bytes, json, date
+ - datetime or datetime(n) → timestamp(n)
+ - char(n), varchar(n)
+ - decimal(p,s) → numeric(p,s)
+ - enum('a','b','c') → requires CREATE TYPE
+
+ Returns
+ -------
+ str
+ PostgreSQL SQL type.
+
+ Raises
+ ------
+ ValueError
+ If core_type is not recognized.
+ """
+ # Handle simple types without parameters
+ if core_type in CORE_TYPE_MAP:
+ return CORE_TYPE_MAP[core_type]
+
+ # Handle parametrized types
+ if core_type.startswith("datetime"):
+ # datetime or datetime(precision) → timestamp or timestamp(precision)
+ if "(" in core_type:
+ # Extract precision: datetime(3) → timestamp(3)
+ precision = core_type[core_type.index("(") : core_type.index(")") + 1]
+ return f"timestamp{precision}"
+ return "timestamp"
+
+ if core_type.startswith("char("):
+ # char(n)
+ return core_type
+
+ if core_type.startswith("varchar("):
+ # varchar(n)
+ return core_type
+
+ if core_type.startswith("decimal("):
+ # decimal(precision, scale) → numeric(precision, scale)
+ params = core_type[7:] # Remove "decimal"
+ return f"numeric{params}"
+
+ if core_type.startswith("enum("):
+ # PostgreSQL requires CREATE TYPE for enums
+ # Extract enum values and generate a deterministic type name
+ enum_match = re.match(r"enum\s*\((.+)\)", core_type, re.I)
+ if enum_match:
+ # Parse enum values: enum('M','F') -> ['M', 'F']
+ values_str = enum_match.group(1)
+ # Split by comma, handling quoted values
+ values = [v.strip().strip("'\"") for v in values_str.split(",")]
+ # Generate a deterministic type name based on values
+ # Use a hash to keep name reasonable length
+ import hashlib
+
+ value_hash = hashlib.md5("_".join(sorted(values)).encode()).hexdigest()[:8]
+ type_name = f"enum_{value_hash}"
+ # Track this enum type for CREATE TYPE DDL
+ if not hasattr(self, "_pending_enum_types"):
+ self._pending_enum_types = {}
+ self._pending_enum_types[type_name] = values
+ # Return schema-qualified type reference using placeholder
+ # {database} will be replaced with actual schema name in table.py
+ return '"{database}".' + self.quote_identifier(type_name)
+ return "text" # Fallback if parsing fails
+
+ raise ValueError(f"Unknown core type: {core_type}")
+
+ def sql_type_to_core(self, sql_type: str) -> str | None:
+ """
+ Convert PostgreSQL type to DataJoint core type (if mappable).
+
+ Parameters
+ ----------
+ sql_type : str
+ PostgreSQL SQL type.
+
+ Returns
+ -------
+ str or None
+ DataJoint core type if mappable, None otherwise.
+ """
+ # Normalize type string (lowercase, strip spaces)
+ sql_type_lower = sql_type.lower().strip()
+
+ # Direct mapping
+ if sql_type_lower in SQL_TO_CORE_MAP:
+ return SQL_TO_CORE_MAP[sql_type_lower]
+
+ # Handle parametrized types
+ if sql_type_lower.startswith("timestamp"):
+ # timestamp(n) → datetime(n)
+ if "(" in sql_type_lower:
+ precision = sql_type_lower[sql_type_lower.index("(") : sql_type_lower.index(")") + 1]
+ return f"datetime{precision}"
+ return "datetime"
+
+ if sql_type_lower.startswith("char("):
+ return sql_type # Keep size
+
+ if sql_type_lower.startswith("varchar("):
+ return sql_type # Keep size
+
+ if sql_type_lower.startswith("numeric("):
+ # numeric(p,s) → decimal(p,s)
+ params = sql_type_lower[7:] # Remove "numeric"
+ return f"decimal{params}"
+
+ # Not a mappable core type
+ return None
+
+ # =========================================================================
+ # DDL Generation
+ # =========================================================================
+
+ def create_schema_sql(self, schema_name: str) -> str:
+ """
+ Generate CREATE SCHEMA statement for PostgreSQL.
+
+ Parameters
+ ----------
+ schema_name : str
+ Schema name.
+
+ Returns
+ -------
+ str
+ CREATE SCHEMA SQL.
+ """
+ return f"CREATE SCHEMA {self.quote_identifier(schema_name)}"
+
+ def drop_schema_sql(self, schema_name: str, if_exists: bool = True) -> str:
+ """
+ Generate DROP SCHEMA statement for PostgreSQL.
+
+ Parameters
+ ----------
+ schema_name : str
+ Schema name.
+ if_exists : bool
+ Include IF EXISTS clause.
+
+ Returns
+ -------
+ str
+ DROP SCHEMA SQL.
+ """
+ if_exists_clause = "IF EXISTS " if if_exists else ""
+ return f"DROP SCHEMA {if_exists_clause}{self.quote_identifier(schema_name)} CASCADE"
+
+ def create_table_sql(
+ self,
+ table_name: str,
+ columns: list[dict[str, Any]],
+ primary_key: list[str],
+ foreign_keys: list[dict[str, Any]],
+ indexes: list[dict[str, Any]],
+ comment: str | None = None,
+ ) -> str:
+ """
+ Generate CREATE TABLE statement for PostgreSQL.
+
+ Parameters
+ ----------
+ table_name : str
+ Fully qualified table name (schema.table).
+ columns : list[dict]
+ Column defs: [{name, type, nullable, default, comment}, ...]
+ primary_key : list[str]
+ Primary key column names.
+ foreign_keys : list[dict]
+ FK defs: [{columns, ref_table, ref_columns}, ...]
+ indexes : list[dict]
+ Index defs: [{columns, unique}, ...]
+ comment : str, optional
+ Table comment (added via separate COMMENT ON statement).
+
+ Returns
+ -------
+ str
+ CREATE TABLE SQL statement (comments via separate COMMENT ON).
+ """
+ lines = []
+
+ # Column definitions
+ for col in columns:
+ col_name = self.quote_identifier(col["name"])
+ col_type = col["type"]
+ nullable = "NULL" if col.get("nullable", False) else "NOT NULL"
+ default = f" DEFAULT {col['default']}" if "default" in col else ""
+ # PostgreSQL comments are via COMMENT ON, not inline
+ lines.append(f"{col_name} {col_type} {nullable}{default}")
+
+ # Primary key
+ if primary_key:
+ pk_cols = ", ".join(self.quote_identifier(col) for col in primary_key)
+ lines.append(f"PRIMARY KEY ({pk_cols})")
+
+ # Foreign keys
+ for fk in foreign_keys:
+ fk_cols = ", ".join(self.quote_identifier(col) for col in fk["columns"])
+ ref_cols = ", ".join(self.quote_identifier(col) for col in fk["ref_columns"])
+ lines.append(
+ f"FOREIGN KEY ({fk_cols}) REFERENCES {fk['ref_table']} ({ref_cols}) " f"ON UPDATE CASCADE ON DELETE RESTRICT"
+ )
+
+ # Indexes - PostgreSQL creates indexes separately via CREATE INDEX
+ # (handled by caller after table creation)
+
+ # Assemble CREATE TABLE (no ENGINE in PostgreSQL)
+ table_def = ",\n ".join(lines)
+ return f"CREATE TABLE IF NOT EXISTS {table_name} (\n {table_def}\n)"
+
+ def drop_table_sql(self, table_name: str, if_exists: bool = True) -> str:
+ """Generate DROP TABLE statement for PostgreSQL."""
+ if_exists_clause = "IF EXISTS " if if_exists else ""
+ return f"DROP TABLE {if_exists_clause}{table_name} CASCADE"
+
+ def alter_table_sql(
+ self,
+ table_name: str,
+ add_columns: list[dict[str, Any]] | None = None,
+ drop_columns: list[str] | None = None,
+ modify_columns: list[dict[str, Any]] | None = None,
+ ) -> str:
+ """
+ Generate ALTER TABLE statement for PostgreSQL.
+
+ Parameters
+ ----------
+ table_name : str
+ Table name.
+ add_columns : list[dict], optional
+ Columns to add.
+ drop_columns : list[str], optional
+ Column names to drop.
+ modify_columns : list[dict], optional
+ Columns to modify.
+
+ Returns
+ -------
+ str
+ ALTER TABLE SQL statement.
+ """
+ clauses = []
+
+ if add_columns:
+ for col in add_columns:
+ col_name = self.quote_identifier(col["name"])
+ col_type = col["type"]
+ nullable = "NULL" if col.get("nullable", False) else "NOT NULL"
+ clauses.append(f"ADD COLUMN {col_name} {col_type} {nullable}")
+
+ if drop_columns:
+ for col_name in drop_columns:
+ clauses.append(f"DROP COLUMN {self.quote_identifier(col_name)}")
+
+ if modify_columns:
+ # PostgreSQL requires ALTER COLUMN ... TYPE ... for type changes
+ for col in modify_columns:
+ col_name = self.quote_identifier(col["name"])
+ col_type = col["type"]
+ nullable = col.get("nullable", False)
+ clauses.append(f"ALTER COLUMN {col_name} TYPE {col_type}")
+ if nullable:
+ clauses.append(f"ALTER COLUMN {col_name} DROP NOT NULL")
+ else:
+ clauses.append(f"ALTER COLUMN {col_name} SET NOT NULL")
+
+ return f"ALTER TABLE {table_name} {', '.join(clauses)}"
+
+ def add_comment_sql(
+ self,
+ object_type: str,
+ object_name: str,
+ comment: str,
+ ) -> str | None:
+ """
+ Generate COMMENT ON statement for PostgreSQL.
+
+ Parameters
+ ----------
+ object_type : str
+ 'table' or 'column'.
+ object_name : str
+ Fully qualified object name.
+ comment : str
+ Comment text.
+
+ Returns
+ -------
+ str
+ COMMENT ON statement.
+ """
+ comment_type = object_type.upper()
+ return f"COMMENT ON {comment_type} {object_name} IS {self.quote_string(comment)}"
+
+ # =========================================================================
+ # DML Generation
+ # =========================================================================
+
+ def insert_sql(
+ self,
+ table_name: str,
+ columns: list[str],
+ on_duplicate: str | None = None,
+ ) -> str:
+ """
+ Generate INSERT statement for PostgreSQL.
+
+ Parameters
+ ----------
+ table_name : str
+ Table name.
+ columns : list[str]
+ Column names.
+ on_duplicate : str, optional
+ 'ignore' or 'update' (PostgreSQL uses ON CONFLICT).
+
+ Returns
+ -------
+ str
+ INSERT SQL with placeholders.
+ """
+ cols = ", ".join(self.quote_identifier(col) for col in columns)
+ placeholders = ", ".join([self.parameter_placeholder] * len(columns))
+
+ base_insert = f"INSERT INTO {table_name} ({cols}) VALUES ({placeholders})"
+
+ if on_duplicate == "ignore":
+ return f"{base_insert} ON CONFLICT DO NOTHING"
+ elif on_duplicate == "update":
+ # ON CONFLICT (pk_cols) DO UPDATE SET col=EXCLUDED.col
+ # Caller must provide constraint name or columns
+ updates = ", ".join(f"{self.quote_identifier(col)}=EXCLUDED.{self.quote_identifier(col)}" for col in columns)
+ return f"{base_insert} ON CONFLICT DO UPDATE SET {updates}"
+ else:
+ return base_insert
+
+ def update_sql(
+ self,
+ table_name: str,
+ set_columns: list[str],
+ where_columns: list[str],
+ ) -> str:
+ """Generate UPDATE statement for PostgreSQL."""
+ set_clause = ", ".join(f"{self.quote_identifier(col)} = {self.parameter_placeholder}" for col in set_columns)
+ where_clause = " AND ".join(f"{self.quote_identifier(col)} = {self.parameter_placeholder}" for col in where_columns)
+ return f"UPDATE {table_name} SET {set_clause} WHERE {where_clause}"
+
+ def delete_sql(self, table_name: str) -> str:
+ """Generate DELETE statement for PostgreSQL (WHERE added separately)."""
+ return f"DELETE FROM {table_name}"
+
+ def upsert_on_duplicate_sql(
+ self,
+ table_name: str,
+ columns: list[str],
+ primary_key: list[str],
+ num_rows: int,
+ ) -> str:
+ """Generate INSERT ... ON CONFLICT ... DO UPDATE statement for PostgreSQL."""
+ # Build column list
+ col_list = ", ".join(columns)
+
+ # Build placeholders for VALUES
+ placeholders = ", ".join(["(%s)" % ", ".join(["%s"] * len(columns))] * num_rows)
+
+ # Build conflict target (primary key columns)
+ conflict_cols = ", ".join(primary_key)
+
+ # Build UPDATE clause (non-PK columns only)
+ non_pk_columns = [col for col in columns if col not in primary_key]
+ update_clauses = ", ".join(f"{col} = EXCLUDED.{col}" for col in non_pk_columns)
+
+ return f"""
+ INSERT INTO {table_name} ({col_list})
+ VALUES {placeholders}
+ ON CONFLICT ({conflict_cols}) DO UPDATE SET {update_clauses}
+ """
+
+ def skip_duplicates_clause(
+ self,
+ full_table_name: str,
+ primary_key: list[str],
+ ) -> str:
+ """
+ Generate clause to skip duplicate key insertions for PostgreSQL.
+
+ Uses ON CONFLICT (pk_cols) DO NOTHING to skip duplicates without
+ raising an error.
+
+ Parameters
+ ----------
+ full_table_name : str
+ Fully qualified table name (with quotes). Unused but kept for
+ API compatibility with MySQL adapter.
+ primary_key : list[str]
+ Primary key column names (unquoted).
+
+ Returns
+ -------
+ str
+ PostgreSQL ON CONFLICT DO NOTHING clause.
+ """
+ pk_cols = ", ".join(self.quote_identifier(pk) for pk in primary_key)
+ return f" ON CONFLICT ({pk_cols}) DO NOTHING"
+
+ @property
+ def supports_inline_indexes(self) -> bool:
+ """
+ PostgreSQL does not support inline INDEX in CREATE TABLE.
+
+ Returns False to indicate indexes must be created separately
+ with CREATE INDEX statements.
+ """
+ return False
+
+ # =========================================================================
+ # Introspection
+ # =========================================================================
+
+ def list_schemas_sql(self) -> str:
+ """Query to list all schemas in PostgreSQL."""
+ return (
+ "SELECT schema_name FROM information_schema.schemata "
+ "WHERE schema_name NOT IN ('pg_catalog', 'information_schema')"
+ )
+
+ def schema_exists_sql(self, schema_name: str) -> str:
+ """Query to check if a schema exists in PostgreSQL."""
+ return f"SELECT schema_name FROM information_schema.schemata WHERE schema_name = {self.quote_string(schema_name)}"
+
+ def list_tables_sql(self, schema_name: str, pattern: str | None = None) -> str:
+ """Query to list tables in a schema."""
+ sql = (
+ f"SELECT table_name FROM information_schema.tables "
+ f"WHERE table_schema = {self.quote_string(schema_name)} "
+ f"AND table_type = 'BASE TABLE'"
+ )
+ if pattern:
+ sql += f" AND table_name LIKE '{pattern}'"
+ return sql
+
+ def get_table_info_sql(self, schema_name: str, table_name: str) -> str:
+ """Query to get table metadata including table comment."""
+ schema_str = self.quote_string(schema_name)
+ table_str = self.quote_string(table_name)
+ regclass_expr = f"({schema_str} || '.' || {table_str})::regclass"
+ return (
+ f"SELECT t.*, obj_description({regclass_expr}, 'pg_class') as table_comment "
+ f"FROM information_schema.tables t "
+ f"WHERE t.table_schema = {schema_str} "
+ f"AND t.table_name = {table_str}"
+ )
+
+ def get_columns_sql(self, schema_name: str, table_name: str) -> str:
+ """Query to get column definitions including comments."""
+ # Use col_description() to retrieve column comments stored via COMMENT ON COLUMN
+ # The regclass cast allows using schema.table notation to get the OID
+ schema_str = self.quote_string(schema_name)
+ table_str = self.quote_string(table_name)
+ regclass_expr = f"({schema_str} || '.' || {table_str})::regclass"
+ return (
+ f"SELECT c.column_name, c.data_type, c.udt_name, c.is_nullable, c.column_default, "
+ f"c.character_maximum_length, c.numeric_precision, c.numeric_scale, "
+ f"col_description({regclass_expr}, c.ordinal_position) as column_comment "
+ f"FROM information_schema.columns c "
+ f"WHERE c.table_schema = {schema_str} "
+ f"AND c.table_name = {table_str} "
+ f"ORDER BY c.ordinal_position"
+ )
+
+ def get_primary_key_sql(self, schema_name: str, table_name: str) -> str:
+ """Query to get primary key columns."""
+ return (
+ f"SELECT column_name FROM information_schema.key_column_usage "
+ f"WHERE table_schema = {self.quote_string(schema_name)} "
+ f"AND table_name = {self.quote_string(table_name)} "
+ f"AND constraint_name IN ("
+ f" SELECT constraint_name FROM information_schema.table_constraints "
+ f" WHERE table_schema = {self.quote_string(schema_name)} "
+ f" AND table_name = {self.quote_string(table_name)} "
+ f" AND constraint_type = 'PRIMARY KEY'"
+ f") "
+ f"ORDER BY ordinal_position"
+ )
+
+ def get_foreign_keys_sql(self, schema_name: str, table_name: str) -> str:
+ """Query to get foreign key constraints."""
+ return (
+ f"SELECT kcu.constraint_name, kcu.column_name, "
+ f"ccu.table_name AS foreign_table_name, ccu.column_name AS foreign_column_name "
+ f"FROM information_schema.key_column_usage AS kcu "
+ f"JOIN information_schema.constraint_column_usage AS ccu "
+ f" ON kcu.constraint_name = ccu.constraint_name "
+ f"WHERE kcu.table_schema = {self.quote_string(schema_name)} "
+ f"AND kcu.table_name = {self.quote_string(table_name)} "
+ f"AND kcu.constraint_name IN ("
+ f" SELECT constraint_name FROM information_schema.table_constraints "
+ f" WHERE table_schema = {self.quote_string(schema_name)} "
+ f" AND table_name = {self.quote_string(table_name)} "
+ f" AND constraint_type = 'FOREIGN KEY'"
+ f") "
+ f"ORDER BY kcu.constraint_name, kcu.ordinal_position"
+ )
+
+ def load_primary_keys_sql(self, schemas_list: str, like_pattern: str) -> str:
+ """Query to load all primary key columns across schemas."""
+ tab_expr = "'\"' || kcu.table_schema || '\".\"' || kcu.table_name || '\"'"
+ return (
+ f"SELECT {tab_expr} as tab, kcu.column_name "
+ f"FROM information_schema.key_column_usage kcu "
+ f"JOIN information_schema.table_constraints tc "
+ f"ON kcu.constraint_name = tc.constraint_name "
+ f"AND kcu.table_schema = tc.table_schema "
+ f"WHERE kcu.table_name NOT LIKE {like_pattern} "
+ f"AND kcu.table_schema in ({schemas_list}) "
+ f"AND tc.constraint_type = 'PRIMARY KEY'"
+ )
+
+ def load_foreign_keys_sql(self, schemas_list: str, like_pattern: str) -> str:
+ """Query to load all foreign key relationships across schemas."""
+ return (
+ f"SELECT "
+ f"c.conname as constraint_name, "
+ f"'\"' || ns1.nspname || '\".\"' || cl1.relname || '\"' as referencing_table, "
+ f"'\"' || ns2.nspname || '\".\"' || cl2.relname || '\"' as referenced_table, "
+ f"a1.attname as column_name, "
+ f"a2.attname as referenced_column_name "
+ f"FROM pg_constraint c "
+ f"JOIN pg_class cl1 ON c.conrelid = cl1.oid "
+ f"JOIN pg_namespace ns1 ON cl1.relnamespace = ns1.oid "
+ f"JOIN pg_class cl2 ON c.confrelid = cl2.oid "
+ f"JOIN pg_namespace ns2 ON cl2.relnamespace = ns2.oid "
+ f"CROSS JOIN LATERAL unnest(c.conkey, c.confkey) WITH ORDINALITY AS cols(conkey, confkey, ord) "
+ f"JOIN pg_attribute a1 ON a1.attrelid = cl1.oid AND a1.attnum = cols.conkey "
+ f"JOIN pg_attribute a2 ON a2.attrelid = cl2.oid AND a2.attnum = cols.confkey "
+ f"WHERE c.contype = 'f' "
+ f"AND cl1.relname NOT LIKE {like_pattern} "
+ f"AND (ns2.nspname in ({schemas_list}) "
+ f"OR ns1.nspname in ({schemas_list})) "
+ f"ORDER BY c.conname, cols.ord"
+ )
+
+ def find_downstream_schemas_sql(self, schemas_list: str) -> str:
+ """Find schemas with FK references to the given schemas."""
+ return (
+ f"SELECT DISTINCT ns1.nspname as schema_name "
+ f"FROM pg_constraint c "
+ f"JOIN pg_class cl1 ON c.conrelid = cl1.oid "
+ f"JOIN pg_namespace ns1 ON cl1.relnamespace = ns1.oid "
+ f"JOIN pg_class cl2 ON c.confrelid = cl2.oid "
+ f"JOIN pg_namespace ns2 ON cl2.relnamespace = ns2.oid "
+ f"WHERE c.contype = 'f' "
+ f"AND ns2.nspname IN ({schemas_list}) "
+ f"AND ns1.nspname NOT IN ({schemas_list})"
+ )
+
+ def find_upstream_schemas_sql(self, schemas_list: str) -> str:
+ """Find schemas that the given schemas reference via FK."""
+ return (
+ f"SELECT DISTINCT ns2.nspname as schema_name "
+ f"FROM pg_constraint c "
+ f"JOIN pg_class cl1 ON c.conrelid = cl1.oid "
+ f"JOIN pg_namespace ns1 ON cl1.relnamespace = ns1.oid "
+ f"JOIN pg_class cl2 ON c.confrelid = cl2.oid "
+ f"JOIN pg_namespace ns2 ON cl2.relnamespace = ns2.oid "
+ f"WHERE c.contype = 'f' "
+ f"AND ns1.nspname IN ({schemas_list}) "
+ f"AND ns2.nspname NOT IN ({schemas_list})"
+ )
+
+ def get_constraint_info_sql(self, constraint_name: str, schema_name: str, table_name: str) -> str:
+ """
+ Query to get FK constraint details from information_schema.
+
+ Returns matched pairs of (fk_column, parent_table, pk_column) for each
+ column in the foreign key constraint, ordered by position.
+ """
+ return (
+ "SELECT "
+ " kcu.column_name as fk_attrs, "
+ " '\"' || ccu.table_schema || '\".\"' || ccu.table_name || '\"' as parent, "
+ " ccu.column_name as pk_attrs "
+ "FROM information_schema.key_column_usage AS kcu "
+ "JOIN information_schema.referential_constraints AS rc "
+ " ON kcu.constraint_name = rc.constraint_name "
+ " AND kcu.constraint_schema = rc.constraint_schema "
+ "JOIN information_schema.key_column_usage AS ccu "
+ " ON rc.unique_constraint_name = ccu.constraint_name "
+ " AND rc.unique_constraint_schema = ccu.constraint_schema "
+ " AND kcu.ordinal_position = ccu.ordinal_position "
+ "WHERE kcu.constraint_name = %s "
+ " AND kcu.table_schema = %s "
+ " AND kcu.table_name = %s "
+ "ORDER BY kcu.ordinal_position"
+ )
+
+ def parse_foreign_key_error(self, error_message: str) -> dict[str, str | list[str] | None] | None:
+ """
+ Parse PostgreSQL foreign key violation error message.
+
+ PostgreSQL FK error format:
+ 'update or delete on table "X" violates foreign key constraint "Y" on table "Z"'
+ Where:
+ - "X" is the referenced table (being deleted/updated)
+ - "Z" is the referencing table (has the FK, needs cascade delete)
+ """
+ import re
+
+ pattern = re.compile(
+ r'.*table "(?P[^"]+)" violates foreign key constraint '
+ r'"(?P[^"]+)" on table "(?P[^"]+)"'
+ )
+
+ match = pattern.match(error_message)
+ if not match:
+ return None
+
+ result = match.groupdict()
+
+ # The child is the referencing table (the one with the FK that needs cascade delete)
+ # The parent is the referenced table (the one being deleted)
+ # The error doesn't include schema, so we return unqualified names
+ child = f'"{result["referencing_table"]}"'
+ parent = f'"{result["referenced_table"]}"'
+
+ return {
+ "child": child,
+ "name": f'"{result["name"]}"',
+ "fk_attrs": None, # Not in error message, will need constraint query
+ "parent": parent,
+ "pk_attrs": None, # Not in error message, will need constraint query
+ }
+
+ def get_indexes_sql(self, schema_name: str, table_name: str) -> str:
+ """Query to get index definitions."""
+ return (
+ f"SELECT indexname, indexdef FROM pg_indexes "
+ f"WHERE schemaname = {self.quote_string(schema_name)} "
+ f"AND tablename = {self.quote_string(table_name)}"
+ )
+
+ def parse_column_info(self, row: dict[str, Any]) -> dict[str, Any]:
+ """
+ Parse PostgreSQL column info into standardized format.
+
+ Parameters
+ ----------
+ row : dict
+ Row from information_schema.columns query with col_description() join.
+
+ Returns
+ -------
+ dict
+ Standardized column info with keys:
+ name, type, nullable, default, comment, key, extra
+ """
+ # For user-defined types (enums), use udt_name instead of data_type
+ # PostgreSQL reports enums as "USER-DEFINED" in data_type
+ data_type = row["data_type"]
+ if data_type == "USER-DEFINED":
+ data_type = row["udt_name"]
+
+ # Reconstruct parametrized types that PostgreSQL splits into separate fields
+ char_max_len = row.get("character_maximum_length")
+ num_precision = row.get("numeric_precision")
+ num_scale = row.get("numeric_scale")
+
+ if data_type == "character" and char_max_len is not None:
+ # char(n) - PostgreSQL reports as "character" with length in separate field
+ data_type = f"char({char_max_len})"
+ elif data_type == "character varying" and char_max_len is not None:
+ # varchar(n)
+ data_type = f"varchar({char_max_len})"
+ elif data_type == "numeric" and num_precision is not None:
+ # numeric(p,s) - reconstruct decimal type
+ if num_scale is not None and num_scale > 0:
+ data_type = f"decimal({num_precision},{num_scale})"
+ else:
+ data_type = f"decimal({num_precision})"
+
+ return {
+ "name": row["column_name"],
+ "type": data_type,
+ "nullable": row["is_nullable"] == "YES",
+ "default": row["column_default"],
+ "comment": row.get("column_comment"), # Retrieved via col_description()
+ "key": "", # PostgreSQL key info retrieved separately
+ "extra": "", # PostgreSQL doesn't have auto_increment in same way
+ }
+
+ # =========================================================================
+ # Transactions
+ # =========================================================================
+
+ def start_transaction_sql(self, isolation_level: str | None = None) -> str:
+ """Generate BEGIN statement for PostgreSQL."""
+ if isolation_level:
+ return f"BEGIN ISOLATION LEVEL {isolation_level}"
+ return "BEGIN"
+
+ def commit_sql(self) -> str:
+ """Generate COMMIT statement."""
+ return "COMMIT"
+
+ def rollback_sql(self) -> str:
+ """Generate ROLLBACK statement."""
+ return "ROLLBACK"
+
+ # =========================================================================
+ # Functions and Expressions
+ # =========================================================================
+
+ def current_timestamp_expr(self, precision: int | None = None) -> str:
+ """
+ CURRENT_TIMESTAMP expression for PostgreSQL.
+
+ Parameters
+ ----------
+ precision : int, optional
+ Fractional seconds precision (0-6).
+
+ Returns
+ -------
+ str
+ CURRENT_TIMESTAMP or CURRENT_TIMESTAMP(n).
+ """
+ if precision is not None:
+ return f"CURRENT_TIMESTAMP({precision})"
+ return "CURRENT_TIMESTAMP"
+
+ def interval_expr(self, value: int, unit: str) -> str:
+ """
+ INTERVAL expression for PostgreSQL.
+
+ Parameters
+ ----------
+ value : int
+ Interval value.
+ unit : str
+ Time unit (singular: 'second', 'minute', 'hour', 'day').
+
+ Returns
+ -------
+ str
+ INTERVAL 'n units' (e.g., "INTERVAL '5 seconds'").
+ """
+ # PostgreSQL uses plural unit names and quotes
+ unit_plural = unit.lower() + "s" if not unit.endswith("s") else unit.lower()
+ return f"INTERVAL '{value} {unit_plural}'"
+
+ def current_user_expr(self) -> str:
+ """PostgreSQL current user expression."""
+ return "current_user"
+
+ def json_path_expr(self, column: str, path: str, return_type: str | None = None) -> str:
+ """
+ Generate PostgreSQL jsonb_extract_path_text() expression.
+
+ Parameters
+ ----------
+ column : str
+ Column name containing JSON data.
+ path : str
+ JSON path (e.g., 'field' or 'nested.field').
+ return_type : str, optional
+ Return type specification for casting (e.g., 'float', 'decimal(10,2)').
+
+ Returns
+ -------
+ str
+ PostgreSQL jsonb_extract_path_text() expression, with optional cast.
+
+ Examples
+ --------
+ >>> adapter.json_path_expr('data', 'field')
+ 'jsonb_extract_path_text("data", \\'field\\')'
+ >>> adapter.json_path_expr('data', 'nested.field')
+ 'jsonb_extract_path_text("data", \\'nested\\', \\'field\\')'
+ >>> adapter.json_path_expr('data', 'value', 'float')
+ 'jsonb_extract_path_text("data", \\'value\\')::float'
+ """
+ quoted_col = self.quote_identifier(column)
+ # Split path by '.' for nested access, handling array notation
+ path_parts = []
+ for part in path.split("."):
+ # Handle array access like field[0]
+ if "[" in part:
+ base, rest = part.split("[", 1)
+ path_parts.append(base)
+ # Extract array indices
+ indices = rest.rstrip("]").split("][")
+ path_parts.extend(indices)
+ else:
+ path_parts.append(part)
+ path_args = ", ".join(f"'{part}'" for part in path_parts)
+ expr = f"jsonb_extract_path_text({quoted_col}, {path_args})"
+ # Add cast if return type specified
+ if return_type:
+ # Map DataJoint types to PostgreSQL types
+ pg_type = return_type.lower()
+ if pg_type in ("unsigned", "signed"):
+ pg_type = "integer"
+ elif pg_type == "double":
+ pg_type = "double precision"
+ expr = f"({expr})::{pg_type}"
+ return expr
+
+ def translate_expression(self, expr: str) -> str:
+ """
+ Translate SQL expression for PostgreSQL compatibility.
+
+ Converts MySQL-specific functions to PostgreSQL equivalents:
+ - GROUP_CONCAT(col) → STRING_AGG(col::text, ',')
+ - GROUP_CONCAT(col SEPARATOR 'sep') → STRING_AGG(col::text, 'sep')
+
+ Parameters
+ ----------
+ expr : str
+ SQL expression that may contain function calls.
+
+ Returns
+ -------
+ str
+ Translated expression for PostgreSQL.
+ """
+ import re
+
+ # GROUP_CONCAT(col) → STRING_AGG(col::text, ',')
+ # GROUP_CONCAT(col SEPARATOR 'sep') → STRING_AGG(col::text, 'sep')
+ def replace_group_concat(match):
+ inner = match.group(1).strip()
+ # Check for SEPARATOR clause
+ sep_match = re.match(r"(.+?)\s+SEPARATOR\s+(['\"])(.+?)\2", inner, re.IGNORECASE)
+ if sep_match:
+ col = sep_match.group(1).strip()
+ sep = sep_match.group(3)
+ return f"STRING_AGG({col}::text, '{sep}')"
+ else:
+ return f"STRING_AGG({inner}::text, ',')"
+
+ expr = re.sub(r"GROUP_CONCAT\s*\((.+?)\)", replace_group_concat, expr, flags=re.IGNORECASE)
+
+ # Replace simple functions FIRST before complex patterns
+ # CURDATE() → CURRENT_DATE
+ expr = re.sub(r"CURDATE\s*\(\s*\)", "CURRENT_DATE", expr, flags=re.IGNORECASE)
+
+ # NOW() → CURRENT_TIMESTAMP
+ expr = re.sub(r"\bNOW\s*\(\s*\)", "CURRENT_TIMESTAMP", expr, flags=re.IGNORECASE)
+
+ # YEAR(date) → EXTRACT(YEAR FROM date)::int
+ expr = re.sub(r"\bYEAR\s*\(\s*([^)]+)\s*\)", r"EXTRACT(YEAR FROM \1)::int", expr, flags=re.IGNORECASE)
+
+ # MONTH(date) → EXTRACT(MONTH FROM date)::int
+ expr = re.sub(r"\bMONTH\s*\(\s*([^)]+)\s*\)", r"EXTRACT(MONTH FROM \1)::int", expr, flags=re.IGNORECASE)
+
+ # DAY(date) → EXTRACT(DAY FROM date)::int
+ expr = re.sub(r"\bDAY\s*\(\s*([^)]+)\s*\)", r"EXTRACT(DAY FROM \1)::int", expr, flags=re.IGNORECASE)
+
+ # TIMESTAMPDIFF(YEAR, d1, d2) → EXTRACT(YEAR FROM AGE(d2, d1))::int
+ # Use a more robust regex that handles the comma-separated arguments
+ def replace_timestampdiff(match):
+ unit = match.group(1).upper()
+ date1 = match.group(2).strip()
+ date2 = match.group(3).strip()
+ if unit == "YEAR":
+ return f"EXTRACT(YEAR FROM AGE({date2}, {date1}))::int"
+ elif unit == "MONTH":
+ return f"(EXTRACT(YEAR FROM AGE({date2}, {date1})) * 12 + EXTRACT(MONTH FROM AGE({date2}, {date1})))::int"
+ elif unit == "DAY":
+ return f"({date2}::date - {date1}::date)"
+ else:
+ return f"EXTRACT({unit} FROM AGE({date2}, {date1}))::int"
+
+ # Match TIMESTAMPDIFF with proper argument parsing
+ # The arguments are: unit, date1, date2 - we need to handle identifiers and CURRENT_DATE
+ expr = re.sub(
+ r"TIMESTAMPDIFF\s*\(\s*(\w+)\s*,\s*([^,]+)\s*,\s*([^)]+)\s*\)",
+ replace_timestampdiff,
+ expr,
+ flags=re.IGNORECASE,
+ )
+
+ # SUM(expr='value') → SUM((expr='value')::int) for PostgreSQL boolean handling
+ # This handles patterns like SUM(sex='F') which produce boolean in PostgreSQL
+ def replace_sum_comparison(match):
+ inner = match.group(1).strip()
+ # Check if inner contains a comparison operator
+ if re.search(r"[=<>!]", inner) and not inner.startswith("("):
+ return f"SUM(({inner})::int)"
+ return match.group(0) # Return unchanged if no comparison
+
+ expr = re.sub(r"\bSUM\s*\(\s*([^)]+)\s*\)", replace_sum_comparison, expr, flags=re.IGNORECASE)
+
+ return expr
+
+ # =========================================================================
+ # DDL Generation
+ # =========================================================================
+
+ def format_column_definition(
+ self,
+ name: str,
+ sql_type: str,
+ nullable: bool = False,
+ default: str | None = None,
+ comment: str | None = None,
+ ) -> str:
+ """
+ Format a column definition for PostgreSQL DDL.
+
+ Examples
+ --------
+ >>> adapter.format_column_definition('user_id', 'bigint', nullable=False, comment='user ID')
+ '"user_id" bigint NOT NULL'
+ """
+ parts = [self.quote_identifier(name), sql_type]
+ if default:
+ parts.append(default)
+ elif not nullable:
+ parts.append("NOT NULL")
+ # Note: PostgreSQL comments handled separately via COMMENT ON
+ return " ".join(parts)
+
+ def table_options_clause(self, comment: str | None = None) -> str:
+ """
+ Generate PostgreSQL table options clause (empty - no ENGINE in PostgreSQL).
+
+ Examples
+ --------
+ >>> adapter.table_options_clause('test table')
+ ''
+ >>> adapter.table_options_clause()
+ ''
+ """
+ return "" # PostgreSQL uses COMMENT ON TABLE separately
+
+ def table_comment_ddl(self, full_table_name: str, comment: str) -> str | None:
+ """
+ Generate COMMENT ON TABLE statement for PostgreSQL.
+
+ Examples
+ --------
+ >>> adapter.table_comment_ddl('"schema"."table"', 'test comment')
+ 'COMMENT ON TABLE "schema"."table" IS \\'test comment\\''
+ """
+ # Escape single quotes by doubling them
+ escaped_comment = comment.replace("'", "''")
+ return f"COMMENT ON TABLE {full_table_name} IS '{escaped_comment}'"
+
+ def column_comment_ddl(self, full_table_name: str, column_name: str, comment: str) -> str | None:
+ """
+ Generate COMMENT ON COLUMN statement for PostgreSQL.
+
+ Examples
+ --------
+ >>> adapter.column_comment_ddl('"schema"."table"', 'column', 'test comment')
+ 'COMMENT ON COLUMN "schema"."table"."column" IS \\'test comment\\''
+ """
+ quoted_col = self.quote_identifier(column_name)
+ # Escape single quotes by doubling them (PostgreSQL string literal syntax)
+ escaped_comment = comment.replace("'", "''")
+ return f"COMMENT ON COLUMN {full_table_name}.{quoted_col} IS '{escaped_comment}'"
+
+ def enum_type_ddl(self, type_name: str, values: list[str]) -> str | None:
+ """
+ Generate CREATE TYPE statement for PostgreSQL enum.
+
+ Examples
+ --------
+ >>> adapter.enum_type_ddl('status_type', ['active', 'inactive'])
+ 'CREATE TYPE "status_type" AS ENUM (\\'active\\', \\'inactive\\')'
+ """
+ quoted_values = ", ".join(f"'{v}'" for v in values)
+ return f"CREATE TYPE {self.quote_identifier(type_name)} AS ENUM ({quoted_values})"
+
+ def replica_identity_ddl(self, full_table_name: str, mode: str) -> str:
+ """
+ Generate ALTER TABLE ... REPLICA IDENTITY statement.
+
+ Controls how much of the old row PostgreSQL writes to WAL on UPDATE/DELETE.
+ ``"default"`` logs only primary-key columns; ``"full"`` logs the entire row.
+ Required by some CDC tools (e.g. Databricks Lakehouse Sync) that need the
+ full pre-image to drive Slowly-Changing-Dimension history.
+
+ The ALTER is metadata-only, instant, and idempotent — re-applying the same
+ mode is a no-op at the storage layer.
+
+ Examples
+ --------
+ >>> adapter.replica_identity_ddl('"schema"."table"', 'full')
+ 'ALTER TABLE "schema"."table" REPLICA IDENTITY FULL'
+ >>> adapter.replica_identity_ddl('"schema"."table"', 'default')
+ 'ALTER TABLE "schema"."table" REPLICA IDENTITY DEFAULT'
+ """
+ if mode not in ("default", "full"):
+ from ..errors import DataJointError
+
+ raise DataJointError(f"Unsupported replica_identity mode: {mode!r}. Expected 'default' or 'full'.")
+ return f"ALTER TABLE {full_table_name} REPLICA IDENTITY {mode.upper()}"
+
+ def get_pending_enum_ddl(self, schema_name: str) -> list[str]:
+ """
+ Get DDL statements for pending enum types and clear the pending list.
+
+ PostgreSQL requires CREATE TYPE statements before using enum types in
+ column definitions. This method returns DDL for enum types accumulated
+ during type conversion and clears the pending list.
+
+ Parameters
+ ----------
+ schema_name : str
+ Schema name to qualify enum type names.
+
+ Returns
+ -------
+ list[str]
+ List of CREATE TYPE statements (if any pending).
+ """
+ ddl_statements = []
+ if hasattr(self, "_pending_enum_types") and self._pending_enum_types:
+ for type_name, values in self._pending_enum_types.items():
+ # Generate CREATE TYPE with schema qualification
+ quoted_type = f"{self.quote_identifier(schema_name)}.{self.quote_identifier(type_name)}"
+ quoted_values = ", ".join(f"'{v}'" for v in values)
+ ddl_statements.append(f"CREATE TYPE {quoted_type} AS ENUM ({quoted_values})")
+ self._pending_enum_types = {}
+ return ddl_statements
+
+ def job_metadata_columns(self) -> list[str]:
+ """
+ Return PostgreSQL-specific job metadata column definitions.
+
+ Examples
+ --------
+ >>> adapter.job_metadata_columns()
+ ['"_job_start_time" timestamp DEFAULT NULL',
+ '"_job_duration" real DEFAULT NULL',
+ '"_job_version" varchar(64) DEFAULT \\'\\'']
+ """
+ return [
+ '"_job_start_time" timestamp DEFAULT NULL',
+ '"_job_duration" real DEFAULT NULL',
+ "\"_job_version\" varchar(64) DEFAULT ''",
+ ]
+
+ # =========================================================================
+ # Error Translation
+ # =========================================================================
+
+ def translate_error(self, error: Exception, query: str = "") -> Exception:
+ """
+ Translate PostgreSQL error to DataJoint exception.
+
+ Parameters
+ ----------
+ error : Exception
+ PostgreSQL exception (typically psycopg2 error).
+ query : str, optional
+ SQL query that caused the error (for context).
+
+ Returns
+ -------
+ Exception
+ DataJoint exception or original error.
+ """
+ if not hasattr(error, "pgcode"):
+ return error
+
+ pgcode = error.pgcode
+
+ # PostgreSQL error code mapping
+ # Reference: https://www.postgresql.org/docs/current/errcodes-appendix.html
+ match pgcode:
+ # Integrity constraint violations
+ case "23505": # unique_violation
+ return errors.DuplicateError(str(error))
+ case "23503": # foreign_key_violation
+ return errors.IntegrityError(str(error))
+ case "23502": # not_null_violation
+ return errors.MissingAttributeError(str(error))
+
+ # Syntax errors
+ case "42601": # syntax_error
+ return errors.QuerySyntaxError(str(error), "")
+
+ # Undefined errors
+ case "42P01": # undefined_table
+ return errors.MissingTableError(str(error), "")
+ case "42703": # undefined_column
+ return errors.UnknownAttributeError(str(error))
+
+ # Connection errors
+ case "08006" | "08003" | "08000": # connection_failure
+ return errors.LostConnectionError(str(error))
+ case "57P01": # admin_shutdown
+ return errors.LostConnectionError(str(error))
+
+ # Access errors
+ case "42501": # insufficient_privilege
+ return errors.AccessError("Insufficient privileges.", str(error), "")
+
+ # All other errors pass through unchanged
+ case _:
+ return error
+
+ # =========================================================================
+ # Native Type Validation
+ # =========================================================================
+
+ def validate_native_type(self, type_str: str) -> bool:
+ """
+ Check if a native PostgreSQL type string is valid.
+
+ Parameters
+ ----------
+ type_str : str
+ Type string to validate.
+
+ Returns
+ -------
+ bool
+ True if valid PostgreSQL type.
+ """
+ type_lower = type_str.lower().strip()
+
+ # PostgreSQL native types (simplified validation)
+ valid_types = {
+ # Integer types
+ "smallint",
+ "integer",
+ "int",
+ "bigint",
+ "smallserial",
+ "serial",
+ "bigserial",
+ # Floating point
+ "real",
+ "double precision",
+ "numeric",
+ "decimal",
+ # String types
+ "char",
+ "varchar",
+ "text",
+ # Binary
+ "bytea",
+ # Boolean
+ "boolean",
+ "bool",
+ # Temporal types
+ "date",
+ "time",
+ "timetz",
+ "timestamp",
+ "timestamptz",
+ "interval",
+ # UUID
+ "uuid",
+ # JSON
+ "json",
+ "jsonb",
+ # Network types
+ "inet",
+ "cidr",
+ "macaddr",
+ # Geometric types
+ "point",
+ "line",
+ "lseg",
+ "box",
+ "path",
+ "polygon",
+ "circle",
+ # Other
+ "money",
+ "xml",
+ }
+
+ # Extract base type (before parentheses or brackets)
+ base_type = type_lower.split("(")[0].split("[")[0].strip()
+
+ return base_type in valid_types
+
+ # =========================================================================
+ # PostgreSQL-Specific Enum Handling
+ # =========================================================================
+
+ def create_enum_type_sql(
+ self,
+ schema: str,
+ table: str,
+ column: str,
+ values: list[str],
+ ) -> str:
+ """
+ Generate CREATE TYPE statement for PostgreSQL enum.
+
+ Parameters
+ ----------
+ schema : str
+ Schema name.
+ table : str
+ Table name.
+ column : str
+ Column name.
+ values : list[str]
+ Enum values.
+
+ Returns
+ -------
+ str
+ CREATE TYPE ... AS ENUM statement.
+ """
+ type_name = f"{schema}_{table}_{column}_enum"
+ quoted_values = ", ".join(self.quote_string(v) for v in values)
+ return f"CREATE TYPE {self.quote_identifier(type_name)} AS ENUM ({quoted_values})"
+
+ def drop_enum_type_sql(self, schema: str, table: str, column: str) -> str:
+ """
+ Generate DROP TYPE statement for PostgreSQL enum.
+
+ Parameters
+ ----------
+ schema : str
+ Schema name.
+ table : str
+ Table name.
+ column : str
+ Column name.
+
+ Returns
+ -------
+ str
+ DROP TYPE statement.
+ """
+ type_name = f"{schema}_{table}_{column}_enum"
+ return f"DROP TYPE IF EXISTS {self.quote_identifier(type_name)} CASCADE"
+
+ def get_table_enum_types_sql(self, schema_name: str, table_name: str) -> str:
+ """
+ Query to get enum types used by a table's columns.
+
+ Parameters
+ ----------
+ schema_name : str
+ Schema name.
+ table_name : str
+ Table name.
+
+ Returns
+ -------
+ str
+ SQL query that returns enum type names (schema-qualified).
+ """
+ return f"""
+ SELECT DISTINCT
+ n.nspname || '.' || t.typname as enum_type
+ FROM pg_catalog.pg_type t
+ JOIN pg_catalog.pg_namespace n ON n.oid = t.typnamespace
+ JOIN pg_catalog.pg_attribute a ON a.atttypid = t.oid
+ JOIN pg_catalog.pg_class c ON c.oid = a.attrelid
+ JOIN pg_catalog.pg_namespace cn ON cn.oid = c.relnamespace
+ WHERE t.typtype = 'e'
+ AND cn.nspname = {self.quote_string(schema_name)}
+ AND c.relname = {self.quote_string(table_name)}
+ """
+
+ def drop_enum_types_for_table(self, schema_name: str, table_name: str) -> list[str]:
+ """
+ Generate DROP TYPE statements for all enum types used by a table.
+
+ Parameters
+ ----------
+ schema_name : str
+ Schema name.
+ table_name : str
+ Table name.
+
+ Returns
+ -------
+ list[str]
+ List of DROP TYPE IF EXISTS statements.
+ """
+ # Returns list of DDL statements - caller should execute query first
+ # to get actual enum types, then call this with results
+ return [] # Placeholder - actual implementation requires query execution
+
+ def drop_enum_type_ddl(self, enum_type_name: str) -> str:
+ """
+ Generate DROP TYPE IF EXISTS statement for a PostgreSQL enum.
+
+ Parameters
+ ----------
+ enum_type_name : str
+ Fully qualified enum type name (schema.typename).
+
+ Returns
+ -------
+ str
+ DROP TYPE IF EXISTS statement with CASCADE.
+ """
+ # Split schema.typename and quote each part
+ parts = enum_type_name.split(".")
+ if len(parts) == 2:
+ qualified_name = f"{self.quote_identifier(parts[0])}.{self.quote_identifier(parts[1])}"
+ else:
+ qualified_name = self.quote_identifier(enum_type_name)
+ return f"DROP TYPE IF EXISTS {qualified_name} CASCADE"
diff --git a/src/datajoint/autopopulate.py b/src/datajoint/autopopulate.py
new file mode 100644
index 000000000..d33e6ccf0
--- /dev/null
+++ b/src/datajoint/autopopulate.py
@@ -0,0 +1,873 @@
+"""This module defines class dj.AutoPopulate"""
+
+from __future__ import annotations
+
+import contextlib
+import datetime
+import inspect
+import logging
+import multiprocessing as mp
+import signal
+import traceback
+from typing import TYPE_CHECKING, Any, Generator
+
+from .errors import DataJointError, LostConnectionError
+from .expression import AndList, QueryExpression
+
+if TYPE_CHECKING:
+ from .jobs import Job
+ from .table import Table
+
+# noinspection PyExceptionInherit,PyCallingNonCallable
+
+logger = logging.getLogger(__name__.split(".")[0])
+
+
+# --- helper functions for multiprocessing --
+
+
+def _initialize_populate(table: Table, jobs: Job | None, populate_kwargs: dict[str, Any]) -> None:
+ """
+ Initialize a worker process for multiprocessing.
+
+ Saves the unpickled table to the current process and reconnects to database.
+
+ Parameters
+ ----------
+ table : Table
+ Table instance to populate.
+ jobs : Job or None
+ Job management object or None for direct mode.
+ populate_kwargs : dict
+ Arguments for _populate1().
+ """
+ process = mp.current_process()
+ process.table = table
+ process.jobs = jobs
+ process.populate_kwargs = populate_kwargs
+ table.connection.connect() # reconnect
+
+
+def _call_populate1(key: dict[str, Any]) -> bool | tuple[dict[str, Any], Any]:
+ """
+ Call _populate1() for a single key in the worker process.
+
+ Parameters
+ ----------
+ key : dict
+ Primary key specifying job to compute.
+
+ Returns
+ -------
+ bool or tuple
+ Result from _populate1().
+ """
+ process = mp.current_process()
+ return process.table._populate1(key, process.jobs, **process.populate_kwargs)
+
+
+class AutoPopulate:
+ """
+ Mixin class that adds automated population to Table classes.
+
+ Auto-populated tables (Computed, Imported) inherit from both Table and
+ AutoPopulate. They must implement the ``make()`` method that computes
+ and inserts data for one primary key.
+
+ Attributes
+ ----------
+ key_source : QueryExpression
+ Query yielding keys to be populated. Default is join of FK parents.
+ jobs : Job
+ Job table (``~~table_name``) for distributed processing.
+
+ Notes
+ -----
+ Subclasses may override ``key_source`` to customize population scope.
+ """
+
+ _key_source = None
+ _allow_insert = False
+ _jobs = None
+ _upstream = None # set per-make() by _populate_one; see `upstream` property below
+
+ @property
+ def upstream(self):
+ """
+ Pre-restricted ancestor view for the current ``make(self, key)`` call.
+
+ Inside ``make()``, ``self.upstream`` is a ``Diagram`` constructed via
+ :meth:`Diagram.trace(self & key) `. Use
+ ``self.upstream[T]`` to obtain a pre-restricted ``QueryExpression``
+ (or ``FreeTable``, when indexed by a string) for any ancestor of
+ ``self``.
+
+ Reading via ``self.upstream`` is the provenance-safe pattern: the
+ framework guarantees the restriction matches the current ``key``,
+ and indexing a non-ancestor table raises ``DataJointError``. See
+ :doc:`reference/specs/provenance` for the contract.
+
+ Raises
+ ------
+ DataJointError
+ If accessed outside ``make()`` execution. To construct a trace
+ explicitly, use ``dj.Diagram.trace(self & key)``.
+
+ Examples
+ --------
+ ::
+
+ def make(self, key):
+ date = self.upstream[Session].fetch1("session_date")
+ traces = self.upstream[ExtractTraces].to_arrays("trace")
+ self.insert1({**key, "summary": compute(traces, date)})
+ """
+ if self._upstream is None:
+ raise DataJointError(
+ "self.upstream is only available inside make(). "
+ "Outside make(), construct a trace explicitly: "
+ "dj.Diagram.trace(self & key)."
+ )
+ return self._upstream
+
+ class _JobsDescriptor:
+ """Descriptor allowing jobs access on both class and instance."""
+
+ def __get__(self, obj, objtype=None):
+ """
+ Access the job table for this auto-populated table.
+
+ The job table (``~~table_name``) is created lazily on first access.
+ It tracks job status, priority, scheduling, and error information
+ for distributed populate operations.
+
+ Can be accessed on either the class or an instance::
+
+ # Both work equivalently
+ Analysis.jobs.refresh()
+ Analysis().jobs.refresh()
+
+ Returns
+ -------
+ Job
+ Job management object for this table.
+ """
+ if obj is None:
+ # Accessed on class - instantiate first
+ obj = objtype()
+ if obj._jobs is None:
+ from .jobs import Job
+
+ obj._jobs = Job(obj)
+ if not obj._jobs.is_declared:
+ obj._jobs.declare()
+ return obj._jobs
+
+ jobs: Job = _JobsDescriptor()
+
+ def _declare_check(self, primary_key: list[str], fk_attribute_map: dict[str, tuple[str, str]]) -> None:
+ """
+ Validate FK-only primary key constraint for auto-populated tables.
+
+ Auto-populated tables (Computed/Imported) must derive all primary key
+ attributes from foreign key references. This ensures proper job granularity
+ for distributed populate operations.
+
+ Parameters
+ ----------
+ primary_key : list
+ List of primary key attribute names.
+ fk_attribute_map : dict
+ Mapping of child_attr -> (parent_table, parent_attr).
+
+ Raises
+ ------
+ DataJointError
+ If native (non-FK) PK attributes are found, unless bypassed via
+ ``dj.config.jobs.allow_new_pk_fields_in_computed_tables = True``.
+ """
+ # Check if validation is bypassed
+ if self.connection._config.jobs.allow_new_pk_fields_in_computed_tables:
+ return
+
+ # Check for native (non-FK) primary key attributes
+ native_pk_attrs = [attr for attr in primary_key if attr not in fk_attribute_map]
+
+ if native_pk_attrs:
+ raise DataJointError(
+ f"Auto-populated table `{self.full_table_name}` has non-FK primary key "
+ f"attribute(s): {', '.join(native_pk_attrs)}. "
+ f"Computed and Imported tables must derive all primary key attributes "
+ f"from foreign key references. The make() method is called once per entity "
+ f"(row) in the table. If you need to compute multiple entities per job, "
+ f"define a Part table to store them. "
+ f"To bypass this restriction, set: dj.config.jobs.allow_new_pk_fields_in_computed_tables = True"
+ )
+
+ @property
+ def key_source(self) -> QueryExpression:
+ """
+ Query expression yielding keys to be populated.
+
+ Returns the primary key values to be passed sequentially to ``make()``
+ when ``populate()`` is called. The default is the join of parent tables
+ referenced from the primary key.
+
+ Returns
+ -------
+ QueryExpression
+ Expression yielding keys for population.
+
+ Notes
+ -----
+ Subclasses may override to change the scope or granularity of make calls.
+ """
+
+ def _rename_attributes(table, props):
+ return (
+ table.proj(**{attr: ref for attr, ref in props["attr_map"].items() if attr != ref})
+ if props["aliased"]
+ else table.proj()
+ )
+
+ if self._key_source is None:
+ parents = self.parents(primary=True, as_objects=True, foreign_key_info=True)
+ if not parents:
+ raise DataJointError("A table must have dependencies from its primary key for auto-populate to work")
+ self._key_source = _rename_attributes(*parents[0])
+ for q in parents[1:]:
+ self._key_source *= _rename_attributes(*q)
+ return self._key_source
+
+ def make(self, key: dict[str, Any], **kwargs) -> None | Generator[Any, Any, None]:
+ """
+ Compute and insert data for one key.
+
+ Must be implemented by subclasses to perform automated computation.
+ The method implements three steps:
+
+ 1. Fetch data from parent tables, restricted by the given key
+ 2. Compute secondary attributes based on the fetched data
+ 3. Insert the new row(s) into the current table
+
+ Parameters
+ ----------
+ key : dict
+ Primary key value identifying the entity to compute.
+ **kwargs
+ Keyword arguments passed from ``populate(make_kwargs=...)``.
+ These are forwarded to ``make_fetch`` for the tripartite pattern.
+
+ Raises
+ ------
+ NotImplementedError
+ If neither ``make()`` nor the tripartite methods are implemented.
+
+ Notes
+ -----
+ **Simple make**: Implement as a regular method that performs all three
+ steps in a single database transaction. Must return None.
+
+ **Tripartite make**: For long-running computations, implement:
+
+ - ``make_fetch(key, **kwargs)``: Fetch data from parent tables
+ - ``make_compute(key, *fetched_data)``: Compute results
+ - ``make_insert(key, *computed_result)``: Insert results
+
+ The tripartite pattern allows computation outside the transaction,
+ with referential integrity checking before commit.
+ """
+
+ if not (hasattr(self, "make_fetch") and hasattr(self, "make_insert") and hasattr(self, "make_compute")):
+ # user must implement `make`
+ raise NotImplementedError(
+ "Subclasses of AutoPopulate must implement the method `make` "
+ "or (`make_fetch` + `make_compute` + `make_insert`)"
+ )
+
+ # User has implemented `_fetch`, `_compute`, and `_insert` methods instead
+
+ # Step 1: Fetch data from parent tables
+ fetched_data = self.make_fetch(key, **kwargs) # fetched_data is a tuple
+ computed_result = yield fetched_data # passed as input into make_compute
+
+ # Step 2: If computed result is not passed in, compute the result
+ if computed_result is None:
+ # this is only executed in the first invocation
+ computed_result = self.make_compute(key, *fetched_data)
+ yield computed_result # this is passed to the second invocation of make
+
+ # Step 3: Insert the computed result into the current table.
+ self.make_insert(key, *computed_result)
+ yield
+
+ def _jobs_to_do(self, restrictions: tuple) -> QueryExpression:
+ """
+ Return the query yielding keys to be computed.
+
+ Parameters
+ ----------
+ restrictions : tuple
+ Conditions to filter key_source.
+
+ Returns
+ -------
+ QueryExpression
+ Keys derived from key_source that need computation.
+ """
+ if self.restriction:
+ raise DataJointError(
+ "Cannot call populate on a restricted table. Instead, pass conditions to populate() as arguments."
+ )
+ todo = self.key_source
+
+ # key_source is a QueryExpression subclass -- trigger instantiation
+ if inspect.isclass(todo) and issubclass(todo, QueryExpression):
+ todo = todo()
+
+ if not isinstance(todo, QueryExpression):
+ raise DataJointError("Invalid key_source value")
+
+ try:
+ # check if target lacks any attributes from the primary key of key_source
+ raise DataJointError(
+ "The populate target lacks attribute %s "
+ "from the primary key of key_source"
+ % next(name for name in todo.heading.primary_key if name not in self.heading)
+ )
+ except StopIteration:
+ pass
+ return (todo & AndList(restrictions)).proj()
+
+ def populate(
+ self,
+ *restrictions: Any,
+ suppress_errors: bool = False,
+ return_exception_objects: bool = False,
+ reserve_jobs: bool = False,
+ max_calls: int | None = None,
+ display_progress: bool = False,
+ processes: int = 1,
+ make_kwargs: dict[str, Any] | None = None,
+ priority: int | None = None,
+ refresh: bool | None = None,
+ ) -> dict[str, Any]:
+ """
+ Populate the table by calling ``make()`` for unpopulated keys.
+
+ Calls ``make(key)`` for every primary key in ``key_source`` for which
+ there is not already a row in this table.
+
+ Parameters
+ ----------
+ *restrictions
+ Conditions to filter key_source.
+ suppress_errors : bool, optional
+ If True, collect errors instead of raising. Default False.
+ return_exception_objects : bool, optional
+ If True, return exception objects instead of messages. Default False.
+ reserve_jobs : bool, optional
+ If True, use job table for distributed processing. Default False.
+ max_calls : int, optional
+ Maximum number of ``make()`` calls.
+ display_progress : bool, optional
+ If True, show progress bar. Default False.
+ processes : int, optional
+ Number of worker processes. Default 1.
+ make_kwargs : dict, optional
+ Keyword arguments passed to each ``make()`` call.
+ priority : int, optional
+ (Distributed mode) Only process jobs at this priority or higher.
+ refresh : bool, optional
+ (Distributed mode) Refresh job queue before processing.
+ Default from ``config.jobs.auto_refresh``.
+
+ Returns
+ -------
+ dict
+ ``{"success_count": int, "error_list": list}``.
+
+ Notes
+ -----
+ **Direct mode** (``reserve_jobs=False``): Keys computed from
+ ``(key_source & restrictions) - target``. No job table. Suitable for
+ single-worker, development, and debugging.
+
+ **Distributed mode** (``reserve_jobs=True``): Uses job table
+ (``~~table_name``) for multi-worker coordination with priority and
+ status tracking.
+ """
+ if self.connection.in_transaction:
+ raise DataJointError("Populate cannot be called during a transaction.")
+
+ if reserve_jobs:
+ return self._populate_distributed(
+ *restrictions,
+ suppress_errors=suppress_errors,
+ return_exception_objects=return_exception_objects,
+ max_calls=max_calls,
+ display_progress=display_progress,
+ processes=processes,
+ make_kwargs=make_kwargs,
+ priority=priority,
+ refresh=refresh,
+ )
+ else:
+ return self._populate_direct(
+ *restrictions,
+ suppress_errors=suppress_errors,
+ return_exception_objects=return_exception_objects,
+ max_calls=max_calls,
+ display_progress=display_progress,
+ processes=processes,
+ make_kwargs=make_kwargs,
+ )
+
+ def _populate_direct(
+ self,
+ *restrictions,
+ suppress_errors,
+ return_exception_objects,
+ max_calls,
+ display_progress,
+ processes,
+ make_kwargs,
+ ):
+ """
+ Populate without job table coordination.
+
+ Computes keys directly from key_source, suitable for single-worker
+ execution, development, and debugging.
+ """
+ from tqdm import tqdm
+
+ keys = (self._jobs_to_do(restrictions) - self.proj()).keys()
+
+ logger.debug("Found %d keys to populate" % len(keys))
+
+ keys = keys[:max_calls]
+ nkeys = len(keys)
+
+ error_list = []
+ success_list = []
+
+ if nkeys:
+ processes = min(_ for _ in (processes, nkeys, mp.cpu_count()) if _)
+
+ populate_kwargs = dict(
+ suppress_errors=suppress_errors,
+ return_exception_objects=return_exception_objects,
+ make_kwargs=make_kwargs,
+ )
+
+ if processes == 1:
+ for key in tqdm(keys, desc=self.__class__.__name__) if display_progress else keys:
+ status = self._populate1(key, jobs=None, **populate_kwargs)
+ if status is True:
+ success_list.append(1)
+ elif isinstance(status, tuple):
+ error_list.append(status)
+ else:
+ assert status is False
+ else:
+ # spawn multiple processes
+ self.connection.close()
+ # Remove SSLContext if present (MySQL-specific, not pickleable)
+ if hasattr(self.connection._conn, "ctx"):
+ del self.connection._conn.ctx
+ with (
+ mp.Pool(processes, _initialize_populate, (self, None, populate_kwargs)) as pool,
+ tqdm(desc="Processes: ", total=nkeys) if display_progress else contextlib.nullcontext() as progress_bar,
+ ):
+ for status in pool.imap(_call_populate1, keys, chunksize=1):
+ if status is True:
+ success_list.append(1)
+ elif isinstance(status, tuple):
+ error_list.append(status)
+ else:
+ assert status is False
+ if display_progress:
+ progress_bar.update()
+ self.connection.connect()
+
+ return {
+ "success_count": sum(success_list),
+ "error_list": error_list,
+ }
+
+ def _populate_distributed(
+ self,
+ *restrictions,
+ suppress_errors,
+ return_exception_objects,
+ max_calls,
+ display_progress,
+ processes,
+ make_kwargs,
+ priority,
+ refresh,
+ ):
+ """
+ Populate with job table coordination.
+
+ Uses job table for multi-worker coordination, priority scheduling,
+ and status tracking.
+ """
+ from tqdm import tqdm
+
+ # Define a signal handler for SIGTERM
+ def handler(signum, frame):
+ logger.info("Populate terminated by SIGTERM")
+ raise SystemExit("SIGTERM received")
+
+ old_handler = signal.signal(signal.SIGTERM, handler)
+
+ try:
+ # Refresh job queue if configured
+ if refresh is None:
+ refresh = self.connection._config.jobs.auto_refresh
+ if refresh:
+ # Use delay=-1 to ensure jobs are immediately schedulable
+ # (avoids race condition with scheduled_time <= CURRENT_TIMESTAMP(3) check)
+ self.jobs.refresh(*restrictions, priority=priority, delay=-1)
+
+ # Fetch pending jobs ordered by priority (use CURRENT_TIMESTAMP(3) for datetime(3) precision)
+ pending_query = self.jobs.pending & "scheduled_time <= CURRENT_TIMESTAMP(3)"
+ if restrictions:
+ # Restrict to jobs whose keys match the caller's restrictions.
+ # semantic_check=False is required because the jobs table PK has
+ # different lineage than key_source (see jobs.py refresh()).
+ pending_query = pending_query.restrict(self._jobs_to_do(restrictions), semantic_check=False)
+ if priority is not None:
+ pending_query = pending_query & f"priority <= {priority}"
+
+ keys = pending_query.keys(order_by="priority ASC, scheduled_time ASC", limit=max_calls)
+
+ logger.debug("Found %d pending jobs to populate" % len(keys))
+
+ nkeys = len(keys)
+ error_list = []
+ success_list = []
+
+ if nkeys:
+ processes = min(_ for _ in (processes, nkeys, mp.cpu_count()) if _)
+
+ populate_kwargs = dict(
+ suppress_errors=suppress_errors,
+ return_exception_objects=return_exception_objects,
+ make_kwargs=make_kwargs,
+ )
+
+ if processes == 1:
+ for key in tqdm(keys, desc=self.__class__.__name__) if display_progress else keys:
+ status = self._populate1(key, jobs=self.jobs, **populate_kwargs)
+ if status is True:
+ success_list.append(1)
+ elif isinstance(status, tuple):
+ error_list.append(status)
+ # status is False means job was already reserved
+ else:
+ # spawn multiple processes
+ self.connection.close()
+ if hasattr(self.connection._conn, "ctx"):
+ del self.connection._conn.ctx # SSLContext is not pickleable
+ with (
+ mp.Pool(processes, _initialize_populate, (self, self.jobs, populate_kwargs)) as pool,
+ tqdm(desc="Processes: ", total=nkeys)
+ if display_progress
+ else contextlib.nullcontext() as progress_bar,
+ ):
+ for status in pool.imap(_call_populate1, keys, chunksize=1):
+ if status is True:
+ success_list.append(1)
+ elif isinstance(status, tuple):
+ error_list.append(status)
+ if display_progress:
+ progress_bar.update()
+ self.connection.connect()
+
+ return {
+ "success_count": sum(success_list),
+ "error_list": error_list,
+ }
+ finally:
+ signal.signal(signal.SIGTERM, old_handler)
+
+ def _populate1(
+ self,
+ key: dict[str, Any],
+ jobs: Job | None,
+ suppress_errors: bool,
+ return_exception_objects: bool,
+ make_kwargs: dict[str, Any] | None = None,
+ ) -> bool | tuple[dict[str, Any], Any]:
+ """
+ Populate table for one key, calling make() inside a transaction.
+
+ Parameters
+ ----------
+ key : dict
+ Primary key specifying the job to populate.
+ jobs : Job or None
+ Job object for distributed mode, None for direct mode.
+ suppress_errors : bool
+ If True, errors are suppressed and returned.
+ return_exception_objects : bool
+ If True, return exception objects instead of messages.
+ make_kwargs : dict, optional
+ Keyword arguments passed to ``make()``.
+
+ Returns
+ -------
+ bool or tuple
+ True if make() succeeded, False if skipped (already done or reserved),
+ (key, error) tuple if suppress_errors=True and error occurred.
+ """
+ import time
+
+ import deepdiff
+
+ # use the legacy `_make_tuples` callback.
+ make = self._make_tuples if hasattr(self, "_make_tuples") else self.make
+
+ # Try to reserve the job (distributed mode only)
+ if jobs is not None and not jobs.reserve(key):
+ return False
+
+ start_time = time.time()
+
+ # if make is a generator, transaction can be delayed until the final stage
+ is_generator = inspect.isgeneratorfunction(make)
+ if not is_generator:
+ self.connection.start_transaction()
+
+ if key in self: # already populated
+ if not is_generator:
+ self.connection.cancel_transaction()
+ if jobs is not None:
+ jobs.complete(key)
+ return False
+
+ logger.jobs(f"Making {key} -> {self.full_table_name}")
+ self.__class__._allow_insert = True
+
+ # Pre-construct the upstream view for this make() call. Lazy — only
+ # `dj.Diagram.trace(self & key)` runs here (graph copy); the
+ # expensive SQL fetch fires when the user accesses self.upstream[T].
+ from .diagram import Diagram
+
+ self._upstream = Diagram.trace(self & dict(key))
+
+ # If strict_provenance is on, push the active-make context so the
+ # runtime gates in expression.cursor / table.insert can check this
+ # make()'s reads and writes. The context is popped in the finally
+ # block below.
+ strict_token = None
+ if self.connection._config.get("strict_provenance", False):
+ from .provenance import push_strict_make_context
+ from .user_tables import Part
+
+ allowed_tables = set(self._upstream._cascade_restrictions.keys()) | {self.full_table_name}
+ # Add Part tables of self to the allowed set. Use class __dict__
+ # (not dir/getattr) to avoid triggering descriptors like the
+ # _JobsDescriptor that lazy-declares the ~~ job table.
+ for cls in type(self).__mro__:
+ for attr_name, attr in cls.__dict__.items():
+ if attr_name.startswith("_"):
+ continue
+ if isinstance(attr, type) and issubclass(attr, Part):
+ # Instantiate to get full_table_name resolved against
+ # this schema. The Part class is already attached via
+ # @schema decoration of the master.
+ try:
+ part_ftn = attr().full_table_name
+ allowed_tables.add(part_ftn)
+ except Exception:
+ pass
+ strict_token = push_strict_make_context(self, frozenset(allowed_tables), dict(key))
+
+ try:
+ if not is_generator:
+ make(dict(key), **(make_kwargs or {}))
+ else:
+ # tripartite make - transaction is delayed until the final stage
+ gen = make(dict(key), **(make_kwargs or {}))
+ fetched_data = next(gen)
+ fetch_hash = deepdiff.DeepHash(fetched_data, ignore_iterable_order=False)[fetched_data]
+ computed_result = next(gen) # perform the computation
+ # fetch and insert inside a transaction
+ self.connection.start_transaction()
+ gen = make(dict(key), **(make_kwargs or {})) # restart make
+ fetched_data = next(gen)
+ if (
+ fetch_hash != deepdiff.DeepHash(fetched_data, ignore_iterable_order=False)[fetched_data]
+ ): # raise error if fetched data has changed
+ raise DataJointError("Referential integrity failed! The `make_fetch` data has changed")
+ gen.send(computed_result) # insert
+
+ except (KeyboardInterrupt, SystemExit, Exception) as error:
+ try:
+ self.connection.cancel_transaction()
+ except LostConnectionError:
+ pass
+ error_message = "{exception}{msg}".format(
+ exception=error.__class__.__name__,
+ msg=": " + str(error) if str(error) else "",
+ )
+ logger.jobs(f"Error making {key} -> {self.full_table_name} - {error_message}")
+ if jobs is not None:
+ jobs.error(key, error_message=error_message, error_stack=traceback.format_exc())
+ if not suppress_errors or isinstance(error, SystemExit):
+ raise
+ else:
+ logger.error(error)
+ return key, error if return_exception_objects else error_message
+ else:
+ self.connection.commit_transaction()
+ duration = time.time() - start_time
+ logger.jobs(f"Success making {key} -> {self.full_table_name}")
+
+ # Update hidden job metadata if table has the columns
+ if self._has_job_metadata_attrs():
+ from .jobs import _get_job_version
+
+ self._update_job_metadata(
+ key,
+ start_time=datetime.datetime.fromtimestamp(start_time),
+ duration=duration,
+ version=_get_job_version(self.connection._config),
+ )
+
+ if jobs is not None:
+ jobs.complete(key, duration=duration)
+ return True
+ finally:
+ self.__class__._allow_insert = False
+ # Clear the per-make() upstream view so subsequent attribute
+ # access raises a clear error rather than silently using a
+ # stale trace from the previous make() call.
+ self._upstream = None
+ # Pop the strict-make context, if any.
+ if strict_token is not None:
+ from .provenance import pop_strict_make_context
+
+ pop_strict_make_context(strict_token)
+
+ def progress(self, *restrictions: Any, display: bool = False) -> tuple[int, int]:
+ """
+ Report the progress of populating the table.
+
+ Uses a single aggregation query to efficiently compute both total and
+ remaining counts.
+
+ Parameters
+ ----------
+ *restrictions
+ Conditions to restrict key_source.
+ display : bool, optional
+ If True, log the progress. Default False.
+
+ Returns
+ -------
+ tuple
+ (remaining, total) - number of keys yet to populate and total keys.
+ """
+ todo = self._jobs_to_do(restrictions)
+
+ # Get primary key attributes from key_source for join condition
+ # These are the "job keys" - the granularity at which populate() works
+ pk_attrs = todo.primary_key
+ assert pk_attrs, "key_source must have a primary key"
+
+ # Find common attributes between key_source and self for the join
+ # This handles cases where self has additional PK attributes
+ common_attrs = [attr for attr in pk_attrs if attr in self.heading.names]
+
+ if not common_attrs:
+ # No common attributes - fall back to two-query method
+ total = len(todo)
+ remaining = len(todo - self.proj())
+ else:
+ # Build a single query that computes both total and remaining
+ # Using LEFT JOIN with COUNT(DISTINCT) to handle 1:many relationships
+ todo_sql = todo.make_sql()
+ target_sql = self.make_sql()
+
+ # Get adapter for backend-specific quoting
+ adapter = self.connection.adapter
+ q = adapter.quote_identifier
+
+ # Alias names for subqueries
+ ks_alias = q("$ks")
+ tgt_alias = q("$tgt")
+
+ # Build join condition on common attributes
+ join_cond = " AND ".join(f"{ks_alias}.{q(attr)} = {tgt_alias}.{q(attr)}" for attr in common_attrs)
+
+ # Build DISTINCT key expression for counting unique jobs
+ # Use CONCAT_WS for composite keys (supported by both MySQL and PostgreSQL)
+ if len(pk_attrs) == 1:
+ distinct_key = f"{ks_alias}.{q(pk_attrs[0])}"
+ null_check = f"{tgt_alias}.{q(common_attrs[0])}"
+ else:
+ key_cols = ", ".join(f"{ks_alias}.{q(attr)}" for attr in pk_attrs)
+ distinct_key = f"CONCAT_WS('|', {key_cols})"
+ null_check = f"{tgt_alias}.{q(common_attrs[0])}"
+
+ # Single aggregation query:
+ # - COUNT(DISTINCT key) gives total unique jobs in key_source
+ # - Remaining = jobs where no matching target row exists
+ sql = f"""
+ SELECT
+ COUNT(DISTINCT {distinct_key}) AS total,
+ COUNT(DISTINCT CASE WHEN {null_check} IS NULL THEN {distinct_key} END) AS remaining
+ FROM ({todo_sql}) AS {ks_alias}
+ LEFT JOIN ({target_sql}) AS {tgt_alias} ON {join_cond}
+ """
+
+ result = self.connection.query(sql).fetchone()
+ total, remaining = result
+
+ if display:
+ logger.info(
+ "%-20s" % self.__class__.__name__
+ + " Completed %d of %d (%2.1f%%) %s"
+ % (
+ total - remaining,
+ total,
+ 100 - 100 * remaining / (total + 1e-12),
+ datetime.datetime.strftime(datetime.datetime.now(), "%Y-%m-%d %H:%M:%S"),
+ ),
+ )
+ return remaining, total
+
+ def _has_job_metadata_attrs(self):
+ """Check if table has hidden job metadata columns."""
+ # Access _attributes directly to include hidden attributes
+ all_attrs = self.heading._attributes
+ return all_attrs is not None and "_job_start_time" in all_attrs
+
+ def _update_job_metadata(self, key, start_time, duration, version):
+ """
+ Update hidden job metadata for the given key.
+
+ Parameters
+ ----------
+ key : dict
+ Primary key identifying the row(s) to update.
+ start_time : datetime
+ When computation started.
+ duration : float
+ Computation duration in seconds.
+ version : str
+ Code version (truncated to 64 chars).
+ """
+ from .condition import make_condition
+
+ pk_condition = make_condition(self, key, set())
+ self.connection.query(
+ f"UPDATE {self.full_table_name} SET "
+ "_job_start_time=%s, _job_duration=%s, _job_version=%s "
+ f"WHERE {pk_condition}",
+ args=(start_time, duration, version[:64] if version else ""),
+ )
diff --git a/src/datajoint/blob.py b/src/datajoint/blob.py
new file mode 100644
index 000000000..633f55b79
--- /dev/null
+++ b/src/datajoint/blob.py
@@ -0,0 +1,637 @@
+"""
+Binary serialization for DataJoint blob storage.
+
+Provides (de)serialization for Python/NumPy objects with backward compatibility
+for MATLAB mYm-format blobs. Supports arrays, scalars, structs, cells, and
+Python built-in types (dict, list, tuple, set, datetime, UUID, Decimal).
+"""
+
+from __future__ import annotations
+
+import collections
+import datetime
+import uuid
+import zlib
+from decimal import Decimal
+from itertools import repeat
+
+import numpy as np
+
+from .errors import DataJointError
+
+deserialize_lookup = {
+ 0: {"dtype": None, "scalar_type": "UNKNOWN"},
+ 1: {"dtype": None, "scalar_type": "CELL"},
+ 2: {"dtype": None, "scalar_type": "STRUCT"},
+ 3: {"dtype": np.dtype("bool"), "scalar_type": "LOGICAL"},
+ 4: {"dtype": np.dtype("c"), "scalar_type": "CHAR"},
+ 5: {"dtype": np.dtype("O"), "scalar_type": "VOID"},
+ 6: {"dtype": np.dtype("float64"), "scalar_type": "DOUBLE"},
+ 7: {"dtype": np.dtype("float32"), "scalar_type": "SINGLE"},
+ 8: {"dtype": np.dtype("int8"), "scalar_type": "INT8"},
+ 9: {"dtype": np.dtype("uint8"), "scalar_type": "UINT8"},
+ 10: {"dtype": np.dtype("int16"), "scalar_type": "INT16"},
+ 11: {"dtype": np.dtype("uint16"), "scalar_type": "UINT16"},
+ 12: {"dtype": np.dtype("int32"), "scalar_type": "INT32"},
+ 13: {"dtype": np.dtype("uint32"), "scalar_type": "UINT32"},
+ 14: {"dtype": np.dtype("int64"), "scalar_type": "INT64"},
+ 15: {"dtype": np.dtype("uint64"), "scalar_type": "UINT64"},
+ 16: {"dtype": None, "scalar_type": "FUNCTION"},
+ 65_536: {"dtype": np.dtype("datetime64[Y]"), "scalar_type": "DATETIME64[Y]"},
+ 65_537: {"dtype": np.dtype("datetime64[M]"), "scalar_type": "DATETIME64[M]"},
+ 65_538: {"dtype": np.dtype("datetime64[W]"), "scalar_type": "DATETIME64[W]"},
+ 65_539: {"dtype": np.dtype("datetime64[D]"), "scalar_type": "DATETIME64[D]"},
+ 65_540: {"dtype": np.dtype("datetime64[h]"), "scalar_type": "DATETIME64[h]"},
+ 65_541: {"dtype": np.dtype("datetime64[m]"), "scalar_type": "DATETIME64[m]"},
+ 65_542: {"dtype": np.dtype("datetime64[s]"), "scalar_type": "DATETIME64[s]"},
+ 65_543: {"dtype": np.dtype("datetime64[ms]"), "scalar_type": "DATETIME64[ms]"},
+ 65_544: {"dtype": np.dtype("datetime64[us]"), "scalar_type": "DATETIME64[us]"},
+ 65_545: {"dtype": np.dtype("datetime64[ns]"), "scalar_type": "DATETIME64[ns]"},
+ 65_546: {"dtype": np.dtype("datetime64[ps]"), "scalar_type": "DATETIME64[ps]"},
+ 65_547: {"dtype": np.dtype("datetime64[fs]"), "scalar_type": "DATETIME64[fs]"},
+ 65_548: {"dtype": np.dtype("datetime64[as]"), "scalar_type": "DATETIME64[as]"},
+}
+serialize_lookup = {
+ v["dtype"]: {"type_id": k, "scalar_type": v["scalar_type"]}
+ for k, v in deserialize_lookup.items()
+ if v["dtype"] is not None
+}
+
+
+compression = {b"ZL123\0": zlib.decompress}
+
+# runtime setting to read integers as 32-bit to read blobs created by the 32-bit
+# version of the mYm library for MATLAB
+use_32bit_dims = False
+
+
+def len_u64(obj):
+ return np.uint64(len(obj)).tobytes()
+
+
+def len_u32(obj):
+ return np.uint32(len(obj)).tobytes()
+
+
+class MatCell(np.ndarray):
+ """
+ NumPy ndarray subclass representing a MATLAB cell array.
+
+ Used to distinguish cell arrays from regular arrays during serialization
+ for MATLAB compatibility.
+ """
+
+ pass
+
+
+class MatStruct(np.recarray):
+ """
+ NumPy recarray subclass representing a MATLAB struct array.
+
+ Used to distinguish struct arrays from regular recarrays during
+ serialization for MATLAB compatibility.
+ """
+
+ pass
+
+
+class Blob:
+ """
+ Binary serializer/deserializer for DataJoint blob storage.
+
+ Handles packing Python objects into binary format and unpacking binary
+ data back to Python objects. Supports two protocols:
+
+ - ``mYm``: Original MATLAB-compatible format (default)
+ - ``dj0``: Extended format for Python-specific types
+
+ Parameters
+ ----------
+ squeeze : bool, optional
+ If True, remove singleton dimensions from arrays and convert
+ 0-dimensional arrays to scalars. Default False.
+
+ Attributes
+ ----------
+ protocol : bytes or None
+ Current serialization protocol (``b"mYm\\0"`` or ``b"dj0\\0"``).
+ """
+
+ def __init__(self, squeeze: bool = False) -> None:
+ self._squeeze = squeeze
+ self._blob = None
+ self._pos = 0
+ self.protocol = None
+
+ def set_dj0(self) -> None:
+ """Switch to dj0 protocol for extended type support."""
+ self.protocol = b"dj0\0" # when using new blob features
+
+ def squeeze(self, array: np.ndarray, convert_to_scalar: bool = True) -> np.ndarray:
+ """
+ Remove singleton dimensions from an array.
+
+ Parameters
+ ----------
+ array : np.ndarray
+ Input array.
+ convert_to_scalar : bool, optional
+ If True, convert 0-dimensional arrays to Python scalars. Default True.
+
+ Returns
+ -------
+ np.ndarray or scalar
+ Squeezed array or scalar value.
+ """
+ if not self._squeeze:
+ return array
+ array = array.squeeze()
+ return array.item() if array.ndim == 0 and convert_to_scalar else array
+
+ def unpack(self, blob):
+ # PostgreSQL returns bytea as memoryview; convert to bytes for string operations
+ if isinstance(blob, memoryview):
+ blob = bytes(blob)
+ self._blob = blob
+ try:
+ # decompress
+ prefix = next(p for p in compression if self._blob[self._pos :].startswith(p))
+ except StopIteration:
+ pass # assume uncompressed but could be unrecognized compression
+ else:
+ self._pos += len(prefix)
+ blob_size = self.read_value()
+ blob = compression[prefix](self._blob[self._pos :])
+ if len(blob) != blob_size:
+ raise DataJointError(f"Blob size mismatch: expected {blob_size}, got {len(blob)}")
+ self._blob = blob
+ self._pos = 0
+ blob_format = self.read_zero_terminated_string()
+ if blob_format in ("mYm", "dj0"):
+ return self.read_blob(n_bytes=len(self._blob) - self._pos)
+
+ def read_blob(self, n_bytes=None):
+ start = self._pos
+ data_structure_code = chr(self.read_value("uint8"))
+ try:
+ call = {
+ # MATLAB-compatible, inherited from original mYm
+ "A": self.read_array, # matlab-compatible numeric arrays and scalars with ndim==0
+ "P": self.read_sparse_array, # matlab sparse array -- not supported yet
+ "S": self.read_struct, # matlab struct array
+ "C": self.read_cell_array, # matlab cell array
+ # basic data types
+ "\xff": self.read_none, # None
+ "\x01": self.read_tuple, # a Sequence (e.g. tuple)
+ "\x02": self.read_list, # a MutableSequence (e.g. list)
+ "\x03": self.read_set, # a Set
+ "\x04": self.read_dict, # a Mapping (e.g. dict)
+ "\x05": self.read_string, # a UTF8-encoded string
+ "\x06": self.read_bytes, # a ByteString
+ "\x0a": self.read_int, # unbounded scalar int
+ "\x0b": self.read_bool, # scalar boolean
+ "\x0c": self.read_complex, # scalar 128-bit complex number
+ "\x0d": self.read_float, # scalar 64-bit float
+ "F": self.read_recarray, # numpy array with fields, including recarrays
+ "d": self.read_decimal, # a decimal
+ "t": self.read_datetime, # date, time, or datetime
+ "u": self.read_uuid, # UUID
+ }[data_structure_code]
+ except KeyError:
+ raise DataJointError('Unknown data structure code "%s". Upgrade datajoint.' % data_structure_code)
+ v = call()
+ if n_bytes is not None and self._pos - start != n_bytes:
+ raise DataJointError("Blob length check failed! Invalid blob")
+ return v
+
+ def pack_blob(self, obj):
+ # original mYm-based serialization from datajoint-matlab
+ if isinstance(obj, MatCell):
+ return self.pack_cell_array(obj)
+ if isinstance(obj, MatStruct):
+ return self.pack_struct(obj)
+ if isinstance(obj, np.ndarray) and obj.dtype.fields is None:
+ return self.pack_array(obj)
+
+ # blob types in the expanded dj0 blob format
+ self.set_dj0()
+ if not isinstance(obj, (np.ndarray, np.number)):
+ # python built-in data types
+ if isinstance(obj, bool):
+ return self.pack_bool(obj)
+ if isinstance(obj, int):
+ return self.pack_int(obj)
+ if isinstance(obj, complex):
+ return self.pack_complex(obj)
+ if isinstance(obj, float):
+ return self.pack_float(obj)
+ if isinstance(obj, np.ndarray) and obj.dtype.fields:
+ return self.pack_recarray(np.array(obj))
+ if isinstance(obj, (np.number, np.datetime64)):
+ return self.pack_array(np.array(obj))
+ if isinstance(obj, (bool, np.bool_)):
+ return self.pack_array(np.array(obj))
+ if isinstance(obj, (float, int, complex)):
+ return self.pack_array(np.array(obj))
+ if isinstance(obj, (datetime.datetime, datetime.date, datetime.time)):
+ return self.pack_datetime(obj)
+ if isinstance(obj, Decimal):
+ return self.pack_decimal(obj)
+ if isinstance(obj, uuid.UUID):
+ return self.pack_uuid(obj)
+ if isinstance(obj, collections.abc.Mapping):
+ return self.pack_dict(obj)
+ if isinstance(obj, str):
+ return self.pack_string(obj)
+ if isinstance(obj, (bytes, bytearray)):
+ return self.pack_bytes(obj)
+ if isinstance(obj, collections.abc.MutableSequence):
+ return self.pack_list(obj)
+ if isinstance(obj, collections.abc.Sequence):
+ return self.pack_tuple(obj)
+ if isinstance(obj, collections.abc.Set):
+ return self.pack_set(obj)
+ if obj is None:
+ return self.pack_none()
+ raise DataJointError("Packing object of type %s currently not supported!" % type(obj))
+
+ def read_array(self):
+ n_dims = int(self.read_value())
+ shape = self.read_value(count=n_dims)
+ n_elem = np.prod(shape, dtype=int)
+ dtype_id, is_complex = self.read_value("uint32", 2)
+
+ # Get dtype from type id
+ dtype = deserialize_lookup[dtype_id]["dtype"]
+
+ # Check if name is void
+ if deserialize_lookup[dtype_id]["scalar_type"] == "VOID":
+ data = np.array(
+ list(self.read_blob(self.read_value()) for _ in range(n_elem)),
+ dtype=np.dtype("O"),
+ )
+ # Check if name is char
+ elif deserialize_lookup[dtype_id]["scalar_type"] == "CHAR":
+ # compensate for MATLAB packing of char arrays
+ data = self.read_value(dtype, count=2 * n_elem)
+ data = data[::2].astype("U1")
+ if n_dims == 2 and shape[0] == 1 or n_dims == 1:
+ compact = data.squeeze()
+ data = compact if compact.shape == () else np.array("".join(data.squeeze()))
+ shape = (1,)
+ else:
+ data = self.read_value(dtype, count=n_elem)
+ if is_complex:
+ data = data + 1j * self.read_value(dtype, count=n_elem)
+ return self.squeeze(data.reshape(shape, order="F"))
+
+ def pack_array(self, array: np.ndarray) -> bytes:
+ """
+ Serialize a NumPy array into bytes.
+
+ Parameters
+ ----------
+ array : np.ndarray
+ Array to serialize. Scalars are encoded with ndim=0.
+
+ Returns
+ -------
+ bytes
+ Serialized array data.
+ """
+ if "datetime64" in array.dtype.name:
+ self.set_dj0()
+ blob = b"A" + np.uint64(array.ndim).tobytes() + np.array(array.shape, dtype=np.uint64).tobytes()
+ is_complex = np.iscomplexobj(array)
+ if is_complex:
+ array, imaginary = np.real(array), np.imag(array)
+ try:
+ type_id = serialize_lookup[array.dtype]["type_id"]
+ except KeyError:
+ # U is for unicode string
+ if array.dtype.char == "U":
+ type_id = serialize_lookup[np.dtype("O")]["type_id"]
+ else:
+ raise DataJointError(f"Type {array.dtype} is ambiguous or unknown")
+
+ blob += np.array([type_id, is_complex], dtype=np.uint32).tobytes()
+ if array.dtype.char == "U" or serialize_lookup[array.dtype]["scalar_type"] == "VOID":
+ blob += b"".join(len_u64(it) + it for it in (self.pack_blob(e) for e in array.flatten(order="F")))
+ self.set_dj0() # not supported by original mym
+ elif serialize_lookup[array.dtype]["scalar_type"] == "CHAR":
+ blob += array.view(np.uint8).astype(np.uint16).tobytes() # convert to 16-bit chars for MATLAB
+ else: # numeric arrays
+ if array.ndim == 0: # not supported by original mym
+ self.set_dj0()
+ blob += array.tobytes(order="F")
+ if is_complex:
+ blob += imaginary.tobytes(order="F")
+ return blob
+
+ def read_recarray(self):
+ """
+ Serialize an np.ndarray with fields, including recarrays
+ """
+ n_fields = self.read_value("uint32")
+ if not n_fields:
+ return np.array(None) # empty array
+ field_names = [self.read_zero_terminated_string() for _ in range(n_fields)]
+ arrays = [self.read_blob() for _ in range(n_fields)]
+ rec = np.empty(
+ arrays[0].shape,
+ np.dtype([(f, t.dtype) for f, t in zip(field_names, arrays)]),
+ )
+ for f, t in zip(field_names, arrays):
+ rec[f] = t
+ return rec.view(np.recarray)
+
+ def pack_recarray(self, array):
+ """Serialize a Matlab struct array"""
+ return (
+ b"F"
+ + len_u32(array.dtype)
+ + "\0".join(array.dtype.names).encode() # number of fields
+ + b"\0"
+ + b"".join( # field names
+ (self.pack_recarray(array[f]) if array[f].dtype.fields else self.pack_array(array[f]))
+ for f in array.dtype.names
+ )
+ )
+
+ def read_sparse_array(self):
+ raise DataJointError("datajoint-python does not yet support sparse arrays. Issue (#590)")
+
+ def read_int(self):
+ return int.from_bytes(self.read_binary(self.read_value("uint16")), byteorder="little", signed=True)
+
+ @staticmethod
+ def pack_int(v):
+ n_bytes = v.bit_length() // 8 + 1
+ if not (0 < n_bytes <= 0xFFFF):
+ raise DataJointError("Integers are limited to 65535 bytes")
+ return b"\x0a" + np.uint16(n_bytes).tobytes() + v.to_bytes(n_bytes, byteorder="little", signed=True)
+
+ def read_bool(self):
+ return bool(self.read_value("bool"))
+
+ @staticmethod
+ def pack_bool(v):
+ return b"\x0b" + np.array(v, dtype="bool").tobytes()
+
+ def read_complex(self):
+ return complex(self.read_value("complex128"))
+
+ @staticmethod
+ def pack_complex(v):
+ return b"\x0c" + np.array(v, dtype="complex128").tobytes()
+
+ def read_float(self):
+ return float(self.read_value("float64"))
+
+ @staticmethod
+ def pack_float(v):
+ return b"\x0d" + np.array(v, dtype="float64").tobytes()
+
+ def read_decimal(self):
+ return Decimal(self.read_string())
+
+ @staticmethod
+ def pack_decimal(d):
+ s = str(d)
+ return b"d" + len_u64(s) + s.encode()
+
+ def read_string(self):
+ return self.read_binary(self.read_value()).decode()
+
+ @staticmethod
+ def pack_string(s):
+ blob = s.encode()
+ return b"\5" + len_u64(blob) + blob
+
+ def read_bytes(self):
+ return self.read_binary(self.read_value())
+
+ @staticmethod
+ def pack_bytes(s):
+ return b"\6" + len_u64(s) + s
+
+ def read_none(self):
+ pass
+
+ @staticmethod
+ def pack_none():
+ return b"\xff"
+
+ def read_tuple(self):
+ return tuple(self.read_blob(self.read_value()) for _ in range(self.read_value()))
+
+ def pack_tuple(self, t):
+ return b"\1" + len_u64(t) + b"".join(len_u64(it) + it for it in (self.pack_blob(i) for i in t))
+
+ def read_list(self):
+ return list(self.read_blob(self.read_value()) for _ in range(self.read_value()))
+
+ def pack_list(self, t):
+ return b"\2" + len_u64(t) + b"".join(len_u64(it) + it for it in (self.pack_blob(i) for i in t))
+
+ def read_set(self):
+ return set(self.read_blob(self.read_value()) for _ in range(self.read_value()))
+
+ def pack_set(self, t):
+ return b"\3" + len_u64(t) + b"".join(len_u64(it) + it for it in (self.pack_blob(i) for i in t))
+
+ def read_dict(self):
+ return dict((self.read_blob(self.read_value()), self.read_blob(self.read_value())) for _ in range(self.read_value()))
+
+ def pack_dict(self, d):
+ return (
+ b"\4"
+ + len_u64(d)
+ + b"".join(
+ b"".join((len_u64(it) + it) for it in packed) for packed in (map(self.pack_blob, pair) for pair in d.items())
+ )
+ )
+
+ def read_struct(self):
+ """deserialize matlab struct"""
+ n_dims = self.read_value()
+ shape = self.read_value(count=n_dims)
+ n_elem = np.prod(shape, dtype=int)
+ n_fields = self.read_value("uint32")
+ if not n_fields:
+ return np.array(None) # empty array
+ field_names = [self.read_zero_terminated_string() for _ in range(n_fields)]
+ raw_data = [tuple(self.read_blob(n_bytes=int(self.read_value())) for _ in range(n_fields)) for __ in range(n_elem)]
+ data = np.array(raw_data, dtype=list(zip(field_names, repeat(object))))
+ return self.squeeze(data.reshape(shape, order="F"), convert_to_scalar=False).view(MatStruct)
+
+ def pack_struct(self, array):
+ """Serialize a Matlab struct array"""
+ return (
+ b"S"
+ + np.array((array.ndim,) + array.shape, dtype=np.uint64).tobytes()
+ + len_u32(array.dtype.names) # dimensionality
+ + "\0".join(array.dtype.names).encode() # number of fields
+ + b"\0"
+ + b"".join( # field names
+ len_u64(it) + it for it in (self.pack_blob(e) for rec in array.flatten(order="F") for e in rec)
+ )
+ ) # values
+
+ def read_cell_array(self):
+ """
+ Deserialize MATLAB cell array.
+
+ Handles edge cases from MATLAB:
+ - Empty cell arrays ({})
+ - Cell arrays with empty elements ({[], [], []})
+ - Nested arrays ({[1,2], [3,4,5]}) - ragged arrays
+ - Cell matrices with mixed content
+ """
+ n_dims = self.read_value()
+ shape = self.read_value(count=n_dims)
+ n_elem = int(np.prod(shape))
+ result = [self.read_blob(n_bytes=self.read_value()) for _ in range(n_elem)]
+
+ # Handle empty cell array
+ if n_elem == 0:
+ return np.empty(0, dtype=object).view(MatCell)
+
+ # Use object dtype to handle ragged/nested arrays without reshape errors.
+ # This avoids NumPy's array homogeneity requirements that cause failures
+ # with MATLAB cell arrays containing arrays of different sizes.
+ arr = np.empty(n_elem, dtype=object)
+ arr[:] = result
+ return self.squeeze(arr.reshape(shape, order="F"), convert_to_scalar=False).view(MatCell)
+
+ def pack_cell_array(self, array):
+ return (
+ b"C"
+ + np.array((array.ndim,) + array.shape, dtype=np.uint64).tobytes()
+ + b"".join(len_u64(it) + it for it in (self.pack_blob(e) for e in array.flatten(order="F")))
+ )
+
+ def read_datetime(self):
+ """deserialize datetime.date, .time, or .datetime"""
+ date, time = self.read_value("int32"), self.read_value("int64")
+ date = datetime.date(year=date // 10000, month=(date // 100) % 100, day=date % 100) if date >= 0 else None
+ time = (
+ datetime.time(
+ hour=(time // 10000000000) % 100,
+ minute=(time // 100000000) % 100,
+ second=(time // 1000000) % 100,
+ microsecond=time % 1000000,
+ )
+ if time >= 0
+ else None
+ )
+ return time and date and datetime.datetime.combine(date, time) or time or date
+
+ @staticmethod
+ def pack_datetime(d):
+ if isinstance(d, datetime.datetime):
+ date, time = d.date(), d.time()
+ elif isinstance(d, datetime.date):
+ date, time = d, None
+ else:
+ date, time = None, d
+ return b"t" + (
+ np.int32(-1 if date is None else (date.year * 100 + date.month) * 100 + date.day).tobytes()
+ + np.int64(
+ -1 if time is None else ((time.hour * 100 + time.minute) * 100 + time.second) * 1000000 + time.microsecond
+ ).tobytes()
+ )
+
+ def read_uuid(self):
+ q = self.read_binary(16)
+ return uuid.UUID(bytes=q)
+
+ @staticmethod
+ def pack_uuid(obj):
+ return b"u" + obj.bytes
+
+ def read_zero_terminated_string(self):
+ target = self._blob.find(b"\0", self._pos)
+ data = self._blob[self._pos : target].decode()
+ self._pos = target + 1
+ return data
+
+ def read_value(self, dtype=None, count=1):
+ if dtype is None:
+ dtype = "uint32" if use_32bit_dims else "uint64"
+ data = np.frombuffer(self._blob, dtype=dtype, count=count, offset=self._pos)
+ self._pos += data.dtype.itemsize * data.size
+ return data[0] if count == 1 else data
+
+ def read_binary(self, size):
+ self._pos += int(size)
+ return self._blob[self._pos - int(size) : self._pos]
+
+ def pack(self, obj, compress):
+ self.protocol = b"mYm\0" # will be replaced with dj0 if new features are used
+ blob = self.pack_blob(obj) # this may reset the protocol and must precede protocol evaluation
+ blob = self.protocol + blob
+ if compress and len(blob) > 1000:
+ compressed = b"ZL123\0" + len_u64(blob) + zlib.compress(blob)
+ if len(compressed) < len(blob):
+ blob = compressed
+ return blob
+
+
+def pack(obj, compress: bool = True) -> bytes:
+ """
+ Serialize a Python object to binary blob format.
+
+ Parameters
+ ----------
+ obj : any
+ Object to serialize. Supports NumPy arrays, Python scalars,
+ collections (dict, list, tuple, set), datetime objects, UUID,
+ Decimal, and MATLAB-compatible MatCell/MatStruct.
+ compress : bool, optional
+ If True (default), compress blobs larger than 1000 bytes using zlib.
+
+ Returns
+ -------
+ bytes
+ Serialized binary data.
+
+ Raises
+ ------
+ DataJointError
+ If the object type is not supported.
+
+ Examples
+ --------
+ >>> data = np.array([1, 2, 3])
+ >>> blob = pack(data)
+ >>> unpacked = unpack(blob)
+ """
+ return Blob().pack(obj, compress=compress)
+
+
+def unpack(blob: bytes, squeeze: bool = False):
+ """
+ Deserialize a binary blob to a Python object.
+
+ Parameters
+ ----------
+ blob : bytes
+ Binary data from ``pack()`` or MATLAB mYm serialization.
+ squeeze : bool, optional
+ If True, remove singleton dimensions from arrays. Default False.
+
+ Returns
+ -------
+ any
+ Deserialized Python object.
+
+ Examples
+ --------
+ >>> blob = pack({'a': 1, 'b': [1, 2, 3]})
+ >>> data = unpack(blob)
+ >>> data['b']
+ [1, 2, 3]
+ """
+ if blob is not None:
+ return Blob(squeeze=squeeze).unpack(blob)
diff --git a/src/datajoint/builtin_codecs/__init__.py b/src/datajoint/builtin_codecs/__init__.py
new file mode 100644
index 000000000..1f2dd2ec7
--- /dev/null
+++ b/src/datajoint/builtin_codecs/__init__.py
@@ -0,0 +1,77 @@
+"""
+Built-in DataJoint codecs.
+
+This package defines the standard codecs that ship with DataJoint.
+These serve as both useful built-in codecs and as examples for users who
+want to create their own custom codecs.
+
+Built-in Codecs:
+ - ````: Serialize Python objects (in-table storage)
+ - ````: Serialize Python objects (in-store with hash-addressed dedup)
+ - ````: File attachment (in-table storage)
+ - ````: File attachment (in-store with hash-addressed dedup)
+ - ````: Hash-addressed storage with MD5 deduplication (store only)
+ - ````: Schema-addressed storage for files/folders (store only)
+ - ````: Store numpy arrays as portable .npy files (store only)
+ - ````: Reference to existing file in store (store only)
+
+Example - Creating a Custom Codec:
+ Here's how to define your own codec, modeled after the built-in codecs::
+
+ import datajoint as dj
+ import networkx as nx
+
+ class GraphCodec(dj.Codec):
+ '''Store NetworkX graphs as edge lists.'''
+
+ name = "graph" # Use as in definitions
+
+ def get_dtype(self, is_store: bool) -> str:
+ return "" # Compose with blob for serialization
+
+ def encode(self, graph, *, key=None, store_name=None):
+ # Convert graph to a serializable format
+ return {
+ 'nodes': list(graph.nodes(data=True)),
+ 'edges': list(graph.edges(data=True)),
+ }
+
+ def decode(self, stored, *, key=None):
+ # Reconstruct graph from stored format
+ G = nx.Graph()
+ G.add_nodes_from(stored['nodes'])
+ G.add_edges_from(stored['edges'])
+ return G
+
+ def validate(self, value):
+ if not isinstance(value, nx.Graph):
+ raise TypeError(f"Expected nx.Graph, got {type(value).__name__}")
+
+ # Now use in table definitions:
+ @schema
+ class Networks(dj.Manual):
+ definition = '''
+ network_id : int
+ ---
+ topology :
+ '''
+"""
+
+from .attach import AttachCodec
+from .blob import BlobCodec
+from .filepath import FilepathCodec
+from .hash import HashCodec
+from .npy import NpyCodec, NpyRef
+from .object import ObjectCodec
+from .schema import SchemaCodec
+
+__all__ = [
+ "BlobCodec",
+ "HashCodec",
+ "SchemaCodec",
+ "ObjectCodec",
+ "AttachCodec",
+ "FilepathCodec",
+ "NpyCodec",
+ "NpyRef",
+]
diff --git a/src/datajoint/builtin_codecs/attach.py b/src/datajoint/builtin_codecs/attach.py
new file mode 100644
index 000000000..9aff7bbde
--- /dev/null
+++ b/src/datajoint/builtin_codecs/attach.py
@@ -0,0 +1,138 @@
+"""
+File attachment codec with filename preservation.
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+from ..codecs import Codec
+
+
+class AttachCodec(Codec):
+ """
+ File attachment with filename preserved.
+
+ Supports both in-table and in-store storage:
+ - ````: Stored in database (bytes → LONGBLOB)
+ - ````: Stored in object store via ```` with deduplication
+ - ````: Stored in specific named store
+
+ The filename is preserved and the file is extracted to the configured
+ download path on fetch.
+
+ Example::
+
+ @schema
+ class Documents(dj.Manual):
+ definition = '''
+ doc_id : int
+ ---
+ config : # in-table (small file in DB)
+ dataset : # in-store (default store)
+ archive : # in-store (specific store)
+ '''
+
+ # Insert a file
+ table.insert1({'doc_id': 1, 'config': '/path/to/config.json'})
+
+ # Fetch extracts to download_path and returns local path
+ local_path = (table & 'doc_id=1').fetch1('config')
+
+ Storage Format (internal):
+ The blob contains: ``filename\\0contents``
+ - Filename (UTF-8 encoded) + null byte + raw file contents
+ """
+
+ name = "attach"
+
+ def get_dtype(self, is_store: bool) -> str:
+ """Return bytes for in-table, for in-store storage."""
+ return "" if is_store else "bytes"
+
+ def encode(self, value: Any, *, key: dict | None = None, store_name: str | None = None) -> bytes:
+ """
+ Read file and encode as filename + contents.
+
+ Parameters
+ ----------
+ value : str or Path
+ Path to file.
+ key : dict, optional
+ Primary key values (unused).
+ store_name : str, optional
+ Unused for internal storage.
+
+ Returns
+ -------
+ bytes
+ Filename (UTF-8) + null byte + file contents.
+ """
+ from pathlib import Path
+
+ path = Path(value)
+ if not path.exists():
+ raise FileNotFoundError(f"Attachment file not found: {path}")
+ if path.is_dir():
+ raise IsADirectoryError(f" does not support directories: {path}")
+
+ filename = path.name
+ contents = path.read_bytes()
+ return filename.encode("utf-8") + b"\x00" + contents
+
+ def decode(self, stored: bytes, *, key: dict | None = None) -> str:
+ """
+ Extract file to download path and return local path.
+
+ Parameters
+ ----------
+ stored : bytes
+ Blob containing filename + null + contents.
+ key : dict, optional
+ Primary key values (unused).
+
+ Returns
+ -------
+ str
+ Path to extracted file.
+ """
+ from pathlib import Path
+
+ # Split on first null byte
+ null_pos = stored.index(b"\x00")
+ filename = stored[:null_pos].decode("utf-8")
+ contents = stored[null_pos + 1 :]
+
+ # Write to download path
+ config = (key or {}).get("_config")
+ if config is None:
+ from ..settings import config # type: ignore[assignment]
+ assert config is not None
+ download_path = Path(config.get("download_path", "."))
+ download_path.mkdir(parents=True, exist_ok=True)
+ local_path = download_path / filename
+
+ # Handle filename collision - if file exists with different content, add suffix
+ if local_path.exists():
+ existing_contents = local_path.read_bytes()
+ if existing_contents != contents:
+ # Find unique filename
+ stem = local_path.stem
+ suffix = local_path.suffix
+ counter = 1
+ while local_path.exists() and local_path.read_bytes() != contents:
+ local_path = download_path / f"{stem}_{counter}{suffix}"
+ counter += 1
+
+ # Only write if file doesn't exist or has different content
+ if not local_path.exists():
+ local_path.write_bytes(contents)
+
+ return str(local_path)
+
+ def validate(self, value: Any) -> None:
+ """Validate that value is a valid file path."""
+ from pathlib import Path
+
+ if not isinstance(value, (str, Path)):
+ raise TypeError(f" expects a file path, got {type(value).__name__}")
diff --git a/src/datajoint/builtin_codecs/blob.py b/src/datajoint/builtin_codecs/blob.py
new file mode 100644
index 000000000..ff65161f4
--- /dev/null
+++ b/src/datajoint/builtin_codecs/blob.py
@@ -0,0 +1,61 @@
+"""
+Blob codec for Python object serialization.
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+from ..codecs import Codec
+
+
+class BlobCodec(Codec):
+ """
+ Serialize Python objects using DataJoint's blob format.
+
+ The ```` codec handles serialization of arbitrary Python objects
+ including NumPy arrays, dictionaries, lists, datetime objects, and UUIDs.
+
+ Supports both in-table and in-store storage:
+ - ````: Stored in database (bytes → LONGBLOB)
+ - ````: Stored in object store via ```` with deduplication
+ - ````: Stored in specific named store
+
+ Format Features:
+ - Protocol headers (``mYm`` for MATLAB-compatible, ``dj0`` for Python-native)
+ - Optional zlib compression for data > 1KB
+ - Support for nested structures
+
+ Example::
+
+ @schema
+ class ProcessedData(dj.Manual):
+ definition = '''
+ data_id : int
+ ---
+ small_result : # in-table (in database)
+ large_result : # in-store (default store)
+ archive : # in-store (specific store)
+ '''
+
+ # Insert any serializable object
+ table.insert1({'data_id': 1, 'small_result': {'scores': [0.9, 0.8]}})
+ """
+
+ name = "blob"
+
+ def get_dtype(self, is_store: bool) -> str:
+ """Return bytes for in-table, for in-store storage."""
+ return "" if is_store else "bytes"
+
+ def encode(self, value: Any, *, key: dict | None = None, store_name: str | None = None) -> bytes:
+ """Serialize a Python object to DataJoint's blob format."""
+ from .. import blob
+
+ return blob.pack(value, compress=True)
+
+ def decode(self, stored: bytes, *, key: dict | None = None) -> Any:
+ """Deserialize blob bytes back to a Python object."""
+ from .. import blob
+
+ return blob.unpack(stored, squeeze=False)
diff --git a/src/datajoint/builtin_codecs/filepath.py b/src/datajoint/builtin_codecs/filepath.py
new file mode 100644
index 000000000..034d5b53a
--- /dev/null
+++ b/src/datajoint/builtin_codecs/filepath.py
@@ -0,0 +1,196 @@
+"""
+Filepath reference codec for existing files in storage.
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+from ..codecs import Codec
+from ..errors import DataJointError
+
+
+class FilepathCodec(Codec):
+ """
+ Reference to existing file in configured store.
+
+ The ```` codec stores a reference to a file that already
+ exists in the storage backend. Unlike ```` or ````, no
+ file copying occurs - only the path is recorded.
+
+ Store only - requires @store.
+
+ This codec gives users maximum freedom in organizing their files while
+ reusing DataJoint's store configuration. Files can be placed anywhere
+ in the store EXCEPT the reserved ``_hash/`` and ``_schema/`` sections
+ which are managed by DataJoint.
+
+ This is useful when:
+ - Files are managed externally (e.g., by acquisition software)
+ - Files are too large to copy
+ - You want to reference shared datasets
+ - You need custom directory structures
+
+ Example::
+
+ @schema
+ class Recordings(dj.Manual):
+ definition = '''
+ recording_id : int
+ ---
+ raw_data :
+ '''
+
+ # Reference an existing file (no copy)
+ # Path is relative to store location
+ table.insert1({'recording_id': 1, 'raw_data': 'subject01/session001/data.bin'})
+
+ # Fetch returns ObjectRef for lazy access
+ ref = (table & 'recording_id=1').fetch1('raw_data')
+ ref.read() # Read file content
+ ref.download() # Download to local path
+
+ Storage Format:
+ JSON metadata: ``{path, store, size, timestamp}``
+
+ Reserved Sections:
+ Paths cannot start with ``_hash/`` or ``_schema/`` - these are managed by DataJoint.
+
+ Warning:
+ The file must exist in the store at the specified path.
+ DataJoint does not manage the lifecycle of referenced files.
+ """
+
+ name = "filepath"
+
+ def get_dtype(self, is_store: bool) -> str:
+ """Filepath requires a store (use @store syntax)."""
+ if not is_store:
+ raise DataJointError(
+ " requires @ symbol. Use for default store or to specify store."
+ )
+ return "json"
+
+ def encode(self, value: Any, *, key: dict | None = None, store_name: str | None = None) -> dict:
+ """
+ Store path reference as JSON metadata.
+
+ Parameters
+ ----------
+ value : str
+ Relative path within the store. Cannot use reserved sections (_hash/, _schema/).
+ key : dict, optional
+ Primary key values (unused).
+ store_name : str, optional
+ Store where the file exists.
+
+ Returns
+ -------
+ dict
+ Metadata dict: ``{path, store}``.
+
+ Raises
+ ------
+ ValueError
+ If path uses reserved sections (_hash/ or _schema/).
+ FileNotFoundError
+ If file does not exist in the store.
+ """
+ from datetime import datetime, timezone
+
+ from ..hash_registry import get_store_backend
+
+ config = (key or {}).get("_config")
+ if config is None:
+ from ..settings import config # type: ignore[assignment]
+ assert config is not None
+
+ path = str(value)
+
+ # Get store spec to check prefix configuration
+ # Use filepath_default if no store specified (filepath is not part of OAS)
+ spec = config.get_store_spec(store_name, use_filepath_default=True)
+
+ # Validate path doesn't use reserved sections (hash and schema)
+ path_normalized = path.lstrip("/")
+ reserved_prefixes = []
+
+ hash_prefix = spec.get("hash_prefix")
+ if hash_prefix:
+ reserved_prefixes.append(("hash_prefix", hash_prefix))
+
+ schema_prefix = spec.get("schema_prefix")
+ if schema_prefix:
+ reserved_prefixes.append(("schema_prefix", schema_prefix))
+
+ # Check if path starts with any reserved prefix
+ for prefix_name, prefix_value in reserved_prefixes:
+ prefix_normalized = prefix_value.strip("/") + "/"
+ if path_normalized.startswith(prefix_normalized):
+ raise ValueError(
+ f" cannot use reserved section '{prefix_value}' ({prefix_name}). "
+ f"This section is managed by DataJoint. "
+ f"Got path: {path}"
+ )
+
+ # If filepath_prefix is configured, enforce it
+ filepath_prefix = spec.get("filepath_prefix")
+ if filepath_prefix:
+ filepath_prefix_normalized = filepath_prefix.strip("/") + "/"
+ if not path_normalized.startswith(filepath_prefix_normalized):
+ raise ValueError(f" must use prefix '{filepath_prefix}' (filepath_prefix). Got path: {path}")
+
+ # Verify file exists
+ backend = get_store_backend(store_name, config=config)
+ if not backend.exists(path):
+ raise FileNotFoundError(f"File not found in store '{store_name or 'default'}': {path}")
+
+ # Detect whether the path is a directory or a file
+ is_dir = backend.isdir(path)
+
+ # Get file size (not applicable for directories)
+ size = None
+ if not is_dir:
+ try:
+ size = backend.size(path)
+ except (FileNotFoundError, OSError):
+ pass
+
+ return {
+ "path": path,
+ "store": store_name,
+ "size": size,
+ "is_dir": is_dir,
+ "timestamp": datetime.now(timezone.utc).isoformat(),
+ }
+
+ def decode(self, stored: dict, *, key: dict | None = None) -> Any:
+ """
+ Create ObjectRef handle for lazy access.
+
+ Parameters
+ ----------
+ stored : dict
+ Metadata dict with path and store.
+ key : dict, optional
+ Primary key values (unused).
+
+ Returns
+ -------
+ ObjectRef
+ Handle for accessing the file.
+ """
+ from ..objectref import ObjectRef
+ from ..hash_registry import get_store_backend
+
+ config = (key or {}).get("_config")
+ store_name = stored.get("store")
+ backend = get_store_backend(store_name, config=config)
+ return ObjectRef.from_json(stored, backend=backend)
+
+ def validate(self, value: Any) -> None:
+ """Validate that value is a path string or Path object."""
+ from pathlib import Path
+
+ if not isinstance(value, (str, Path)):
+ raise TypeError(f" expects a path string or Path, got {type(value).__name__}")
diff --git a/src/datajoint/builtin_codecs/hash.py b/src/datajoint/builtin_codecs/hash.py
new file mode 100644
index 000000000..bb3a3852f
--- /dev/null
+++ b/src/datajoint/builtin_codecs/hash.py
@@ -0,0 +1,106 @@
+"""
+Hash-addressed storage codec with SHA256 deduplication.
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+from ..codecs import Codec
+from ..errors import DataJointError
+
+
+class HashCodec(Codec):
+ """
+ Hash-addressed storage with SHA256 deduplication.
+
+ The ```` codec stores raw bytes using hash-addressed storage.
+ Data is identified by its SHA256 hash and stored in a hierarchical directory:
+ ``_hash/{hash[:2]}/{hash[2:4]}/{hash}``
+
+ The database column stores JSON metadata: ``{hash, store, size}``.
+ Duplicate content is automatically deduplicated across all tables.
+
+ Deletion: Requires garbage collection via ``dj.gc.collect()``.
+
+ External only - requires @ modifier.
+
+ Example::
+
+ @schema
+ class RawContent(dj.Manual):
+ definition = '''
+ content_id : int
+ ---
+ data :
+ '''
+
+ # Insert raw bytes
+ table.insert1({'content_id': 1, 'data': b'raw binary content'})
+
+ Note:
+ This codec accepts only ``bytes``. For Python objects, use ````.
+ Typically used indirectly via ```` or ```` rather than directly.
+
+ See Also
+ --------
+ datajoint.gc : Garbage collection for orphaned storage.
+ """
+
+ name = "hash"
+
+ def get_dtype(self, is_store: bool) -> str:
+ """Hash storage is in-store only."""
+ if not is_store:
+ raise DataJointError(" requires @ (in-store storage only)")
+ return "json"
+
+ def encode(self, value: bytes, *, key: dict | None = None, store_name: str | None = None) -> dict:
+ """
+ Store content and return metadata.
+
+ Parameters
+ ----------
+ value : bytes
+ Raw bytes to store.
+ key : dict, optional
+ Context dict with ``_schema`` for path isolation.
+ store_name : str, optional
+ Store to use. If None, uses default store.
+
+ Returns
+ -------
+ dict
+ Metadata dict: ``{hash, path, schema, store, size}``.
+ """
+ from ..hash_registry import put_hash
+
+ schema_name = (key or {}).get("_schema", "unknown")
+ config = (key or {}).get("_config")
+ return put_hash(value, schema_name=schema_name, store_name=store_name, config=config)
+
+ def decode(self, stored: dict, *, key: dict | None = None) -> bytes:
+ """
+ Retrieve content using stored metadata.
+
+ Parameters
+ ----------
+ stored : dict
+ Metadata dict with ``'path'``, ``'hash'``, and optionally ``'store'``.
+ key : dict, optional
+ Context dict (unused - path is in metadata).
+
+ Returns
+ -------
+ bytes
+ Original bytes.
+ """
+ from ..hash_registry import get_hash
+
+ config = (key or {}).get("_config")
+ return get_hash(stored, config=config)
+
+ def validate(self, value: Any) -> None:
+ """Validate that value is bytes."""
+ if not isinstance(value, bytes):
+ raise TypeError(f" expects bytes, got {type(value).__name__}")
diff --git a/src/datajoint/builtin_codecs/npy.py b/src/datajoint/builtin_codecs/npy.py
new file mode 100644
index 000000000..54853437b
--- /dev/null
+++ b/src/datajoint/builtin_codecs/npy.py
@@ -0,0 +1,379 @@
+"""
+NumPy array codec using .npy format.
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+from ..errors import DataJointError
+from .schema import SchemaCodec
+
+
+class NpyRef:
+ """
+ Lazy reference to a numpy array stored as a .npy file.
+
+ This class provides metadata access without I/O and transparent
+ integration with numpy operations via the ``__array__`` protocol.
+
+ Attributes
+ ----------
+ shape : tuple[int, ...]
+ Array shape (from metadata, no I/O).
+ dtype : numpy.dtype
+ Array dtype (from metadata, no I/O).
+ path : str
+ Storage path within the store.
+ store : str or None
+ Store name (None for default).
+
+ Examples
+ --------
+ Metadata access without download::
+
+ ref = (Recording & key).fetch1('waveform')
+ print(ref.shape) # (1000, 32) - no download
+ print(ref.dtype) # float64 - no download
+
+ Explicit loading::
+
+ arr = ref.load() # Downloads and returns np.ndarray
+
+ Transparent numpy integration::
+
+ # These all trigger automatic download via __array__
+ result = ref + 1
+ result = np.mean(ref)
+ result = ref[0:100] # Slicing works too
+ """
+
+ __slots__ = ("_meta", "_backend", "_cached")
+
+ def __init__(self, metadata: dict, backend: Any):
+ """
+ Initialize NpyRef from metadata and storage backend.
+
+ Parameters
+ ----------
+ metadata : dict
+ JSON metadata containing path, store, dtype, shape.
+ backend : StorageBackend
+ Storage backend for file operations.
+ """
+ self._meta = metadata
+ self._backend = backend
+ self._cached = None
+
+ @property
+ def shape(self) -> tuple:
+ """Array shape (no I/O required)."""
+ return tuple(self._meta["shape"])
+
+ @property
+ def dtype(self):
+ """Array dtype (no I/O required)."""
+ import numpy as np
+
+ return np.dtype(self._meta["dtype"])
+
+ @property
+ def ndim(self) -> int:
+ """Number of dimensions (no I/O required)."""
+ return len(self._meta["shape"])
+
+ @property
+ def size(self) -> int:
+ """Total number of elements (no I/O required)."""
+ import math
+
+ return math.prod(self._meta["shape"])
+
+ @property
+ def nbytes(self) -> int:
+ """Total bytes (estimated from shape and dtype, no I/O required)."""
+ return self.size * self.dtype.itemsize
+
+ @property
+ def path(self) -> str:
+ """Storage path within the store."""
+ return self._meta["path"]
+
+ @property
+ def store(self) -> str | None:
+ """Store name (None for default store)."""
+ return self._meta.get("store")
+
+ @property
+ def is_loaded(self) -> bool:
+ """True if array data has been downloaded and cached."""
+ return self._cached is not None
+
+ def load(self, mmap_mode=None):
+ """
+ Download and return the array.
+
+ Parameters
+ ----------
+ mmap_mode : str, optional
+ Memory-map mode for lazy, random-access loading of large arrays:
+
+ - ``'r'``: Read-only
+ - ``'r+'``: Read-write
+ - ``'c'``: Copy-on-write (changes not saved to disk)
+
+ If None (default), loads entire array into memory.
+
+ Returns
+ -------
+ numpy.ndarray or numpy.memmap
+ The array data. Returns ``numpy.memmap`` if mmap_mode is specified.
+
+ Notes
+ -----
+ When ``mmap_mode`` is None, the array is cached after first load.
+
+ For local filesystem stores, memory mapping accesses the file directly
+ with no download. For remote stores (S3, etc.), the file is downloaded
+ to a local cache (``{tempdir}/datajoint_mmap/``) before memory mapping.
+
+ Examples
+ --------
+ Standard loading::
+
+ arr = ref.load() # Loads entire array into memory
+
+ Memory-mapped for random access to large arrays::
+
+ arr = ref.load(mmap_mode='r')
+ slice = arr[1000:2000] # Only reads the needed portion from disk
+ """
+ import io
+
+ import numpy as np
+
+ if mmap_mode is None:
+ # Standard loading with caching
+ if self._cached is None:
+ buffer = self._backend.get_buffer(self.path)
+ self._cached = np.load(io.BytesIO(buffer), allow_pickle=False)
+ return self._cached
+ else:
+ # Memory-mapped loading
+ if self._backend.protocol == "file":
+ # Local filesystem - mmap directly, no download needed
+ local_path = self._backend._full_path(self.path)
+ return np.load(local_path, mmap_mode=mmap_mode, allow_pickle=False)
+ else:
+ # Remote storage - download to local cache first
+ import hashlib
+ import tempfile
+ from pathlib import Path
+
+ path_hash = hashlib.md5(self.path.encode()).hexdigest()[:12]
+ cache_dir = Path(tempfile.gettempdir()) / "datajoint_mmap"
+ cache_dir.mkdir(exist_ok=True)
+ cache_path = cache_dir / f"{path_hash}.npy"
+
+ if not cache_path.exists():
+ buffer = self._backend.get_buffer(self.path)
+ cache_path.write_bytes(buffer)
+
+ return np.load(str(cache_path), mmap_mode=mmap_mode, allow_pickle=False)
+
+ def __array__(self, dtype=None):
+ """
+ NumPy array protocol for transparent integration.
+
+ This method is called automatically when the NpyRef is used
+ in numpy operations (arithmetic, ufuncs, etc.).
+
+ Parameters
+ ----------
+ dtype : numpy.dtype, optional
+ Desired output dtype.
+
+ Returns
+ -------
+ numpy.ndarray
+ The array data, optionally cast to dtype.
+ """
+ arr = self.load()
+ if dtype is not None:
+ return arr.astype(dtype)
+ return arr
+
+ def __getitem__(self, key):
+ """Support indexing/slicing by loading then indexing."""
+ return self.load()[key]
+
+ def __len__(self) -> int:
+ """Length of first dimension."""
+ if not self._meta["shape"]:
+ raise TypeError("len() of 0-dimensional array")
+ return self._meta["shape"][0]
+
+ def __repr__(self) -> str:
+ status = "loaded" if self.is_loaded else "not loaded"
+ return f"NpyRef(shape={self.shape}, dtype={self.dtype}, {status})"
+
+ def __str__(self) -> str:
+ return repr(self)
+
+
+class NpyCodec(SchemaCodec):
+ """
+ Schema-addressed storage for numpy arrays as .npy files.
+
+ The ```` codec stores numpy arrays as standard ``.npy`` files
+ using schema-addressed paths: ``{schema}/{table}/{pk}/{attribute}.npy``.
+ Arrays are fetched lazily via ``NpyRef``, which provides metadata access
+ without I/O and transparent numpy integration via ``__array__``.
+
+ Store only - requires ``@`` modifier.
+
+ Key Features:
+ - **Portable**: Standard .npy format readable by numpy, MATLAB, etc.
+ - **Lazy loading**: Metadata (shape, dtype) available without download
+ - **Transparent**: Use in numpy operations triggers automatic download
+ - **Safe bulk fetch**: Fetching many rows doesn't download until needed
+ - **Schema-addressed**: Browsable paths that mirror database structure
+
+ Example::
+
+ @schema
+ class Recording(dj.Manual):
+ definition = '''
+ recording_id : int
+ ---
+ waveform : # default store
+ spectrogram : # specific store
+ '''
+
+ # Insert - just pass the array
+ Recording.insert1({
+ 'recording_id': 1,
+ 'waveform': np.random.randn(1000, 32),
+ })
+
+ # Fetch - returns NpyRef (lazy)
+ ref = (Recording & 'recording_id=1').fetch1('waveform')
+ ref.shape # (1000, 32) - no download
+ ref.dtype # float64 - no download
+
+ # Use in numpy ops - downloads automatically
+ result = np.mean(ref, axis=0)
+
+ # Or load explicitly
+ arr = ref.load()
+
+ Storage Details:
+ - File format: NumPy .npy (version 1.0 or 2.0)
+ - Path: ``{schema}/{table}/{pk}/{attribute}.npy``
+ - Database column: JSON with ``{path, store, dtype, shape}``
+
+ Deletion: Requires garbage collection via ``dj.gc.collect()``.
+
+ See Also
+ --------
+ datajoint.gc : Garbage collection for orphaned storage.
+ NpyRef : The lazy array reference returned on fetch.
+ SchemaCodec : Base class for schema-addressed codecs.
+ ObjectCodec : Schema-addressed storage for files/folders.
+ """
+
+ name = "npy"
+
+ def validate(self, value: Any) -> None:
+ """
+ Validate that value is a numpy array suitable for .npy storage.
+
+ Parameters
+ ----------
+ value : Any
+ Value to validate.
+
+ Raises
+ ------
+ DataJointError
+ If value is not a numpy array or has object dtype.
+ """
+ import numpy as np
+
+ if not isinstance(value, np.ndarray):
+ raise DataJointError(f" requires numpy.ndarray, got {type(value).__name__}")
+ if value.dtype == object:
+ raise DataJointError(" does not support object dtype arrays")
+
+ def encode(
+ self,
+ value: Any,
+ *,
+ key: dict | None = None,
+ store_name: str | None = None,
+ ) -> dict:
+ """
+ Serialize array to .npy and upload to storage.
+
+ Parameters
+ ----------
+ value : numpy.ndarray
+ Array to store.
+ key : dict, optional
+ Context dict with ``_schema``, ``_table``, ``_field``,
+ and primary key values for path construction.
+ store_name : str, optional
+ Target store. If None, uses default store.
+
+ Returns
+ -------
+ dict
+ JSON metadata: ``{path, store, dtype, shape}``.
+ """
+ import io
+
+ import numpy as np
+
+ # Extract context using inherited helper
+ schema, table, field, primary_key = self._extract_context(key)
+ config = (key or {}).get("_config")
+
+ # Build schema-addressed storage path
+ path, _ = self._build_path(schema, table, field, primary_key, ext=".npy", store_name=store_name, config=config)
+
+ # Serialize to .npy format
+ buffer = io.BytesIO()
+ np.save(buffer, value, allow_pickle=False)
+ npy_bytes = buffer.getvalue()
+
+ # Upload to storage using inherited helper
+ backend = self._get_backend(store_name, config=config)
+ backend.put_buffer(npy_bytes, path)
+
+ # Return metadata (includes numpy-specific shape/dtype)
+ return {
+ "path": path,
+ "store": store_name,
+ "dtype": str(value.dtype),
+ "shape": list(value.shape),
+ }
+
+ def decode(self, stored: dict, *, key: dict | None = None) -> NpyRef:
+ """
+ Create lazy NpyRef from stored metadata.
+
+ Parameters
+ ----------
+ stored : dict
+ JSON metadata from database.
+ key : dict, optional
+ Primary key values (unused).
+
+ Returns
+ -------
+ NpyRef
+ Lazy array reference with metadata access and numpy integration.
+ """
+ config = (key or {}).get("_config")
+ backend = self._get_backend(stored.get("store"), config=config)
+ return NpyRef(stored, backend)
diff --git a/src/datajoint/builtin_codecs/object.py b/src/datajoint/builtin_codecs/object.py
new file mode 100644
index 000000000..1c0d8c673
--- /dev/null
+++ b/src/datajoint/builtin_codecs/object.py
@@ -0,0 +1,215 @@
+"""
+Schema-addressed storage for files and folders.
+"""
+
+from __future__ import annotations
+
+from typing import Any
+
+from ..errors import DataJointError
+from .schema import SchemaCodec
+
+
+class ObjectCodec(SchemaCodec):
+ """
+ Schema-addressed storage for files and folders.
+
+ The ```` codec provides managed file/folder storage using
+ schema-addressed paths: ``{schema}/{table}/{pk}/{field}/``. This creates
+ a browsable organization in object storage that mirrors the database schema.
+
+ Unlike hash-addressed storage (````), each row has its own unique path
+ (no deduplication). Ideal for:
+
+ - Zarr arrays (hierarchical chunked data)
+ - HDF5 files
+ - Complex multi-file outputs
+ - Any content that shouldn't be deduplicated
+
+ Store only - requires @ modifier.
+
+ Example::
+
+ @schema
+ class Analysis(dj.Computed):
+ definition = '''
+ -> Recording
+ ---
+ results :
+ '''
+
+ def make(self, key):
+ # Store a file
+ self.insert1({**key, 'results': '/path/to/results.zarr'})
+
+ # Fetch returns ObjectRef for lazy access
+ ref = (Analysis & key).fetch1('results')
+ ref.path # Storage path
+ ref.read() # Read file content
+ ref.fsmap # For zarr.open(ref.fsmap)
+
+ Storage Structure:
+ Objects are stored at::
+
+ {store_root}/{schema}/{table}/{pk}/{field}/
+
+ Deletion: Requires garbage collection via ``dj.gc.collect()``.
+
+ Comparison with hash-addressed::
+
+ | Aspect | | |
+ |----------------|---------------------|---------------------|
+ | Addressing | Schema-addressed | Hash-addressed |
+ | Deduplication | No | Yes |
+ | Deletion | GC required | GC required |
+ | Use case | Zarr, HDF5 | Blobs, attachments |
+
+ See Also
+ --------
+ datajoint.gc : Garbage collection for orphaned storage.
+ SchemaCodec : Base class for schema-addressed codecs.
+ NpyCodec : Schema-addressed storage for numpy arrays.
+ HashCodec : Hash-addressed storage with deduplication.
+ """
+
+ name = "object"
+
+ def encode(
+ self,
+ value: Any,
+ *,
+ key: dict | None = None,
+ store_name: str | None = None,
+ ) -> dict:
+ """
+ Store content and return metadata.
+
+ Parameters
+ ----------
+ value : bytes, str, or Path
+ Content to store: bytes (raw data), or str/Path (file/folder to upload).
+ key : dict, optional
+ Context for path construction with keys ``_schema``, ``_table``,
+ ``_field``, plus primary key values.
+ store_name : str, optional
+ Store to use. If None, uses default store.
+
+ Returns
+ -------
+ dict
+ Metadata dict suitable for ``ObjectRef.from_json()``.
+ """
+ from datetime import datetime, timezone
+ from pathlib import Path
+
+ # Extract context using inherited helper
+ schema, table, field, primary_key = self._extract_context(key)
+ config = (key or {}).get("_config")
+
+ # Check for pre-computed metadata (from staged insert)
+ if isinstance(value, dict) and "path" in value:
+ # Already encoded, pass through
+ return value
+
+ # Determine content type and extension
+ is_dir = False
+ ext = None
+ size = None
+ item_count = None
+
+ if isinstance(value, bytes):
+ content = value
+ size = len(content)
+ elif isinstance(value, tuple) and len(value) == 2:
+ # Tuple format: (extension, data) where data is bytes or file-like
+ ext, data = value
+ if hasattr(data, "read"):
+ content = data.read()
+ else:
+ content = data
+ size = len(content)
+ elif isinstance(value, (str, Path)):
+ source_path = Path(value)
+ if not source_path.exists():
+ raise DataJointError(f"Source path not found: {source_path}")
+ is_dir = source_path.is_dir()
+ ext = source_path.suffix if not is_dir else None
+ if is_dir:
+ # For directories, we'll upload later
+ content = None
+ # Count items in directory
+ item_count = sum(1 for _ in source_path.rglob("*") if _.is_file())
+ else:
+ content = source_path.read_bytes()
+ size = len(content)
+ else:
+ raise TypeError(f"
".join(
+ [
+ "\n".join(["
%s
" % get_html_display_value(tup, name, idx) for name in heading.names])
+ for idx, tup in enumerate(tuples)
+ ]
+ ),
+ count=(("
Total: %d
" % len(rel)) if config["display.show_tuple_count"] else ""),
+ )
diff --git a/src/datajoint/provenance.py b/src/datajoint/provenance.py
new file mode 100644
index 000000000..8f196194f
--- /dev/null
+++ b/src/datajoint/provenance.py
@@ -0,0 +1,206 @@
+"""
+Runtime gates for ``dj.config["strict_provenance"]``.
+
+When the flag is enabled, this module's context (set by ``AutoPopulate._populate_one``)
+tracks which tables and primary key the currently-executing ``make()`` is
+allowed to read and write. The read gate in :func:`assert_read_allowed`
+fires inside ``QueryExpression.cursor``. The write gate has two parts: the
+target check in :func:`assert_write_allowed` fires inside ``Table.insert``
+(before rows are materialized), and the per-row key-consistency check in
+:func:`assert_row_key_allowed` fires inside ``Table._insert_rows`` as each row
+is materialized — so the gate never consumes the caller's ``rows`` iterable.
+
+The contract is documented in
+``datajoint-docs/src/reference/specs/provenance.md`` §3.
+
+Implementation note: the active-make context is stored in a
+``contextvars.ContextVar`` so it propagates correctly across threads
+that share the parent's context (e.g. the populate-in-subprocess path
+which uses ``multiprocessing`` workers, each of which inherits its
+parent's contextvar binding at fork time).
+"""
+
+from __future__ import annotations
+
+from contextvars import ContextVar
+from typing import TYPE_CHECKING, Optional, Tuple
+
+from .errors import DataJointError
+
+if TYPE_CHECKING:
+ from .table import Table
+
+
+# Active context: (the target table, the set of allowed full table names, the current key dict)
+_active_strict_make: ContextVar[Optional[Tuple["Table", frozenset[str], dict]]] = ContextVar(
+ "_dj_active_strict_make", default=None
+)
+
+
+def push_strict_make_context(target: "Table", allowed_tables: frozenset[str], key: dict):
+ """
+ Push a strict-make context for the duration of one ``make()`` invocation.
+
+ Returns a token that the caller must pass to :func:`pop_strict_make_context`
+ in a ``finally`` block.
+ """
+ return _active_strict_make.set((target, allowed_tables, key))
+
+
+def pop_strict_make_context(token) -> None:
+ """Pop the strict-make context using a token from :func:`push_strict_make_context`."""
+ _active_strict_make.reset(token)
+
+
+def get_active_context():
+ """Return the currently-active strict-make context, or None."""
+ return _active_strict_make.get()
+
+
+def _base_tables(query_expression) -> set[str]:
+ """
+ Return the set of base-table SQL names that a QueryExpression reads from.
+
+ For a single-table expression (FreeTable / Table / restricted variants),
+ returns ``{full_table_name}``. For compound expressions (joins,
+ projections of joins), traverses ``support`` recursively.
+ """
+ # FreeTable / Table: has full_table_name directly
+ ftn = getattr(query_expression, "full_table_name", None)
+ if isinstance(ftn, str):
+ return {ftn}
+
+ bases: set[str] = set()
+ support = getattr(query_expression, "_support", None) or []
+ for s in support:
+ if isinstance(s, str):
+ # Direct table name in the support list
+ bases.add(s)
+ else:
+ # Subquery — recurse
+ bases.update(_base_tables(s))
+ return bases
+
+
+def assert_read_allowed(query_expression) -> None:
+ """
+ Verify a fetch is allowed under the active strict-make context.
+
+ Called from ``QueryExpression.cursor`` before SQL is issued. No-op when
+ no strict-make context is active (i.e. outside ``make()`` or when
+ ``strict_provenance`` is False).
+
+ Allowed reads:
+
+ - Any table in the active context's ``allowed_tables`` set. The set is
+ built from ``self.upstream`` (the ancestor graph) plus the target
+ table and its Parts.
+
+ Anything else raises ``DataJointError``.
+
+ Known limitation (will sharpen in a follow-up): the check does not
+ distinguish reads that came *through* ``self.upstream`` from reads of
+ the same ancestor via a direct expression. Both are allowed if the
+ table is in the allowed set. The intent is to catch reads from
+ *undeclared* dependencies; tightening the "must come through
+ ``self.upstream``" path requires propagating an attribution marker
+ through QueryExpression composition and is deferred.
+ """
+ ctx = _active_strict_make.get()
+ if ctx is None:
+ return # strict mode off, or outside make()
+
+ _target, allowed_tables, _key = ctx
+ bases = _base_tables(query_expression)
+ if not bases:
+ return # nothing to check (e.g. dj.U expressions)
+
+ disallowed = bases - allowed_tables
+ if disallowed:
+ raise DataJointError(
+ f"strict_provenance=True: read from undeclared table(s) "
+ f"{sorted(disallowed)} is not permitted inside make(). "
+ f"Use self.upstream[T] for declared ancestors, or declare a "
+ f"foreign-key dependency on the table you want to read."
+ )
+
+
+def assert_write_allowed(target_table) -> None:
+ """
+ Verify the *target* of an insert is allowed under the active strict-make context.
+
+ Called from ``Table.insert`` after the existing ``_allow_insert`` check and
+ before any rows are materialized. No-op when no strict-make context is active.
+
+ Allowed targets:
+
+ - The current ``make()`` target (``self``) or one of its Part tables.
+
+ Per-row key consistency is checked separately by :func:`assert_row_key_allowed`
+ as rows are materialized, so this gate never consumes the caller's ``rows``
+ iterable — a one-shot generator must survive to reach ``insert``.
+
+ Raises ``DataJointError`` if the target is not permitted.
+ """
+ ctx = _active_strict_make.get()
+ if ctx is None:
+ return
+
+ make_target, _allowed_tables, _key = ctx
+
+ # Target must be `make_target` (self) or one of its Parts.
+ target_name = getattr(target_table, "full_table_name", None)
+ target_set = {make_target.full_table_name}
+ # Collect Part tables of make_target via class __dict__ (not dir/getattr,
+ # which would trigger descriptors like the _JobsDescriptor).
+ from .user_tables import Part # local import to avoid circular dep
+
+ for cls in type(make_target).__mro__:
+ for attr_name, attr in cls.__dict__.items():
+ if attr_name.startswith("_"):
+ continue
+ if isinstance(attr, type) and issubclass(attr, Part):
+ try:
+ part_ftn = attr().full_table_name
+ target_set.add(part_ftn)
+ except Exception:
+ pass
+
+ if target_name not in target_set:
+ raise DataJointError(
+ f"strict_provenance=True: insert into {target_name!r} is not permitted "
+ f"inside make() for {make_target.full_table_name!r}. Only the target "
+ f"table and its Part tables may be written."
+ )
+
+
+def assert_row_key_allowed(row) -> None:
+ """
+ Verify a single insert row's key columns match the active ``make()`` key.
+
+ Called per row from ``Table._insert_rows`` as rows are materialized, so the
+ check sees a concrete row without the write gate having to consume the
+ caller's ``rows`` iterable. No-op when no strict-make context is active or
+ when ``row`` is not a dict (numpy records / bare sequences carry no field
+ names to check by — same as the previous behavior).
+
+ Raises ``DataJointError`` on a mismatch.
+ """
+ ctx = _active_strict_make.get()
+ if ctx is None:
+ return
+ if not isinstance(row, dict):
+ return
+ _make_target, _allowed_tables, key = ctx
+ _check_row_key(row, key)
+
+
+def _check_row_key(row: dict, current_key: dict) -> None:
+ """Raise if any row attribute overlapping with the current key has a different value."""
+ for k, v in current_key.items():
+ if k in row and row[k] != v:
+ raise DataJointError(
+ f"strict_provenance=True: inserted row's {k!r}={row[k]!r} does not "
+ f"match the current make() key's {k!r}={v!r}. Inserts must be "
+ f"consistent with the key being populated."
+ )
diff --git a/src/datajoint/schemas.py b/src/datajoint/schemas.py
new file mode 100644
index 000000000..fa934d569
--- /dev/null
+++ b/src/datajoint/schemas.py
@@ -0,0 +1,838 @@
+"""
+Schema management for DataJoint.
+
+This module provides the Schema class for binding Python table classes to
+database schemas, and utilities for schema introspection and management.
+"""
+
+from __future__ import annotations
+
+import inspect
+import logging
+import re
+import types
+import warnings
+from typing import TYPE_CHECKING, Any
+
+from .errors import AccessError, DataJointError
+from .instance import _get_singleton_connection
+
+if TYPE_CHECKING:
+ from .connection import Connection
+from .heading import Heading
+from .jobs import Job
+from .table import FreeTable, lookup_class_name
+from .user_tables import Computed, Imported, Lookup, Manual, Part, _get_tier
+from .utils import to_camel_case, user_choice
+
+logger = logging.getLogger(__name__.split(".")[0])
+
+
+def ordered_dir(class_: type) -> list[str]:
+ """
+ List class attributes respecting declaration order.
+
+ Similar to the ``dir()`` built-in, but preserves attribute declaration
+ order as much as possible.
+
+ Parameters
+ ----------
+ class_ : type
+ Class to list members for.
+
+ Returns
+ -------
+ list[str]
+ Attributes declared in class_ and its superclasses.
+ """
+ attr_list = list()
+ for c in reversed(class_.mro()):
+ attr_list.extend(e for e in c.__dict__ if e not in attr_list)
+ return attr_list
+
+
+class _Schema:
+ """
+ Decorator that binds table classes to a database schema.
+
+ Schema objects associate Python table classes with database schemas and
+ provide the namespace context for foreign key resolution.
+
+ Parameters
+ ----------
+ schema_name : str, optional
+ Database schema name. If omitted, call ``activate()`` later.
+ context : dict, optional
+ Namespace for foreign key lookup. None uses caller's context.
+ connection : Connection, optional
+ Database connection. Defaults to ``dj.conn()``.
+ create_schema : bool, optional
+ If False, raise error if schema doesn't exist. Default True.
+ create_tables : bool, optional
+ If False, raise error when accessing missing tables.
+ Default from ``dj.config.database.create_tables`` (True unless configured).
+ add_objects : dict, optional
+ Additional objects for the declaration context.
+
+ Examples
+ --------
+ >>> schema = dj.Schema('my_schema')
+ >>> @schema
+ ... class Session(dj.Manual):
+ ... definition = '''
+ ... session_id : int
+ ... '''
+ """
+
+ def __init__(
+ self,
+ schema_name: str | None = None,
+ context: dict[str, Any] | None = None,
+ *,
+ connection: Connection | None = None,
+ create_schema: bool = True,
+ create_tables: bool | None = None,
+ add_objects: dict[str, Any] | None = None,
+ ) -> None:
+ """
+ Initialize the schema object.
+
+ Parameters
+ ----------
+ schema_name : str, optional
+ Database schema name. If omitted, call ``activate()`` later.
+ context : dict, optional
+ Namespace for foreign key lookup. None uses caller's context.
+ connection : Connection, optional
+ Database connection. Defaults to ``dj.conn()``.
+ create_schema : bool, optional
+ If False, raise error if schema doesn't exist. Default True.
+ create_tables : bool, optional
+ If False, raise error when accessing missing tables.
+ Default from ``dj.config.database.create_tables`` (True unless configured).
+ add_objects : dict, optional
+ Additional objects for the declaration context.
+ """
+ self.connection = connection
+ self.database = None
+ self.context = context
+ self.create_schema = create_schema
+ self.create_tables = create_tables # None means "use connection config default"
+ self.add_objects = add_objects
+ self.declare_list = []
+ if schema_name:
+ self.activate(schema_name)
+
+ def is_activated(self) -> bool:
+ """Check if the schema has been activated."""
+ return self.database is not None
+
+ def activate(
+ self,
+ schema_name: str | None = None,
+ *,
+ connection: Connection | None = None,
+ create_schema: bool | None = None,
+ create_tables: bool | None = None,
+ add_objects: dict[str, Any] | None = None,
+ ) -> None:
+ """
+ Associate with a database schema.
+
+ If the schema does not exist, attempts to create it on the server.
+
+ Parameters
+ ----------
+ schema_name : str, optional
+ Database schema name. None asserts schema is already activated.
+ connection : Connection, optional
+ Database connection. Defaults to ``dj.conn()``.
+ create_schema : bool, optional
+ If False, raise error if schema doesn't exist.
+ create_tables : bool, optional
+ If False, raise error when accessing missing tables.
+ add_objects : dict, optional
+ Additional objects for the declaration context.
+
+ Raises
+ ------
+ DataJointError
+ If schema_name is None and schema not yet activated, or if
+ schema already activated for a different database.
+ """
+ if schema_name is None:
+ if self.exists:
+ return
+ raise DataJointError("Please provide a schema_name to activate the schema.")
+ if self.database is not None and self.exists:
+ if self.database == schema_name: # already activated
+ return
+ raise DataJointError("The schema is already activated for schema {db}.".format(db=self.database))
+ if connection is not None:
+ self.connection = connection
+ if self.connection is None:
+ self.connection = _get_singleton_connection()
+ if self.connection._config.get("database.database_prefix"):
+ warnings.warn(
+ "database_prefix is deprecated and will be removed in DataJoint 2.3. "
+ "Use database.name to select a PostgreSQL database instead.",
+ DeprecationWarning,
+ stacklevel=2,
+ )
+ self.database = schema_name
+ if create_schema is not None:
+ self.create_schema = create_schema
+ if create_tables is not None:
+ self.create_tables = create_tables
+ if add_objects:
+ self.add_objects = add_objects
+ if not self.exists:
+ if not self.create_schema or not self.database:
+ raise DataJointError(
+ "Database `{name}` has not yet been declared. Set argument create_schema=True to create it.".format(
+ name=schema_name
+ )
+ )
+ # create database
+ logger.debug("Creating schema `{name}`.".format(name=schema_name))
+ try:
+ create_sql = self.connection.adapter.create_schema_sql(schema_name)
+ self.connection.query(create_sql)
+ except AccessError:
+ raise DataJointError(
+ "Schema `{name}` does not exist and could not be created. Check permissions.".format(name=schema_name)
+ )
+ self.connection.register(self)
+
+ # decorate all tables already decorated
+ for cls, context in self.declare_list:
+ if self.add_objects:
+ context = dict(context, **self.add_objects)
+ self._decorate_master(cls, context)
+
+ def _assert_exists(self, message=None):
+ if not self.exists:
+ raise DataJointError(message or "Schema `{db}` has not been created.".format(db=self.database))
+
+ def __call__(self, cls: type, *, context: dict[str, Any] | None = None) -> type:
+ """
+ Bind a table class to this schema. Used as a decorator.
+
+ Parameters
+ ----------
+ cls : type
+ Table class to decorate.
+ context : dict, optional
+ Declaration context. Supplied by make_classes.
+
+ Returns
+ -------
+ type
+ The decorated class.
+
+ Raises
+ ------
+ DataJointError
+ If applied to a Part table (use on master only).
+ """
+ context = context or self.context or inspect.currentframe().f_back.f_locals
+ if issubclass(cls, Part):
+ raise DataJointError("The schema decorator should not be applied to Part tables.")
+ if self.is_activated():
+ self._decorate_master(cls, context)
+ else:
+ self.declare_list.append((cls, context))
+ return cls
+
+ def _decorate_master(self, cls: type, context: dict[str, Any]) -> None:
+ """
+ Process a master table class and its part tables.
+
+ Parameters
+ ----------
+ cls : type
+ Master table class to process.
+ context : dict
+ Declaration context for foreign key resolution.
+ """
+ self._decorate_table(cls, context=dict(context, self=cls, **{cls.__name__: cls}))
+ # Process part tables
+ for part in ordered_dir(cls):
+ if part[0].isupper():
+ part = getattr(cls, part)
+ if inspect.isclass(part) and issubclass(part, Part):
+ part._master = cls
+ # allow addressing master by name or keyword 'master'
+ self._decorate_table(
+ part,
+ context=dict(context, master=cls, self=part, **{cls.__name__: cls}),
+ )
+
+ def _decorate_table(self, table_class: type, context: dict[str, Any], assert_declared: bool = False) -> None:
+ """
+ Assign schema properties to the table class and declare the table.
+
+ Parameters
+ ----------
+ table_class : type
+ Table class to decorate.
+ context : dict
+ Declaration context for foreign key resolution.
+ assert_declared : bool, optional
+ If True, assert table is already declared. Default False.
+ """
+ table_class.database = self.database
+ table_class._connection = self.connection
+ table_class._heading = Heading(
+ table_info=dict(
+ conn=self.connection,
+ database=self.database,
+ table_name=table_class.table_name,
+ context=context,
+ )
+ )
+ table_class._support = [table_class.full_table_name]
+ table_class.declaration_context = context
+
+ # instantiate the class, declare the table if not already
+ instance = table_class()
+ is_declared = instance.is_declared
+ create_tables = (
+ self.create_tables if self.create_tables is not None else self.connection._config.database.create_tables
+ )
+ if not is_declared and not assert_declared and create_tables:
+ instance.declare(context)
+ self.connection.dependencies.clear()
+ elif is_declared and create_tables:
+ # Table already exists — declare() didn't run, so _populate_lineage
+ # didn't either. Scan the already-loaded heading for the symptom
+ # of stale/missing lineage rows (#1454): any PK attribute with
+ # lineage=None indicates the ~lineage table is missing rows for
+ # this table. Only then trigger a refresh — no extra DB queries
+ # on healthy schemas, automatic repair when the bug is present.
+ #
+ # Note: stale-but-non-None rows (DJ version skew that wrote a
+ # different string format) are not auto-detected here; users hit
+ # the tailored "rebuild_lineage" error message on first join.
+ try:
+ pk_lineages = [instance.heading[attr].lineage for attr in instance.primary_key]
+ except Exception:
+ pk_lineages = []
+ if pk_lineages and any(lineage is None for lineage in pk_lineages):
+ instance._refresh_lineage(context)
+ is_declared = is_declared or instance.is_declared
+
+ # add table definition to the doc string
+ if isinstance(table_class.definition, str):
+ table_class.__doc__ = (table_class.__doc__ or "") + "\nTable definition:\n\n" + table_class.definition
+
+ # fill values in Lookup tables from their contents property
+ if isinstance(instance, Lookup) and hasattr(instance, "contents") and is_declared:
+ contents = list(instance.contents)
+ if len(contents) > len(instance):
+ if instance.heading.has_autoincrement:
+ warnings.warn(
+ ("Contents has changed but cannot be inserted because {table} has autoincrement.").format(
+ table=instance.__class__.__name__
+ )
+ )
+ else:
+ instance.insert(contents, skip_duplicates=True)
+
+ def __repr__(self):
+ return "Schema `{name}`\n".format(name=self.database)
+
+ def make_classes(self, into: dict[str, Any] | None = None) -> None:
+ """
+ Create Python table classes for tables in the schema.
+
+ Introspects the database schema and creates appropriate Python classes
+ (Lookup, Manual, Imported, Computed, Part) for tables that don't have
+ corresponding classes in the target namespace.
+
+ Parameters
+ ----------
+ into : dict, optional
+ Namespace to place created classes into. Defaults to caller's
+ local namespace.
+ """
+ self._assert_exists()
+ if into is None:
+ if self.context is not None:
+ into = self.context
+ else:
+ # if into is missing, use the calling namespace
+ frame = inspect.currentframe().f_back
+ into = frame.f_locals
+ del frame
+ adapter = self.connection.adapter
+ tables = [
+ row[0]
+ for row in self.connection.query(adapter.list_tables_sql(self.database))
+ if lookup_class_name(adapter.make_full_table_name(self.database, row[0]), into, 0) is None
+ ]
+ master_classes = (Lookup, Manual, Imported, Computed)
+ part_tables = []
+ for table_name in tables:
+ class_name = to_camel_case(table_name)
+ if class_name not in into:
+ try:
+ cls = next(cls for cls in master_classes if re.fullmatch(cls.tier_regexp, table_name))
+ except StopIteration:
+ if re.fullmatch(Part.tier_regexp, table_name):
+ part_tables.append(table_name)
+ else:
+ # declare and decorate master table classes
+ into[class_name] = self(type(class_name, (cls,), dict()), context=into)
+
+ # attach parts to masters
+ for table_name in part_tables:
+ groups = re.fullmatch(Part.tier_regexp, table_name).groupdict()
+ class_name = to_camel_case(groups["part"])
+ try:
+ master_class = into[to_camel_case(groups["master"])]
+ except KeyError:
+ raise DataJointError("The table %s does not follow DataJoint naming conventions" % table_name)
+ part_class = type(class_name, (Part,), dict(definition=...))
+ part_class._master = master_class
+ self._decorate_table(part_class, context=into, assert_declared=True)
+ setattr(master_class, class_name, part_class)
+
+ def drop(self, prompt: bool | None = None) -> None:
+ """
+ Drop the associated schema and all its tables.
+
+ Parameters
+ ----------
+ prompt : bool, optional
+ If True, show confirmation prompt before dropping.
+ If False, drop without confirmation.
+ If None (default), use ``dj.config['safemode']`` setting.
+
+ Raises
+ ------
+ AccessError
+ If insufficient permissions to drop the schema.
+ """
+ prompt = self.connection._config["safemode"] if prompt is None else prompt
+
+ if not self.exists:
+ logger.info("Schema named `{database}` does not exist. Doing nothing.".format(database=self.database))
+ elif not prompt or user_choice("Proceed to delete entire schema `%s`?" % self.database, default="no") == "yes":
+ logger.debug("Dropping `{database}`.".format(database=self.database))
+ try:
+ drop_sql = self.connection.adapter.drop_schema_sql(self.database)
+ self.connection.query(drop_sql)
+ logger.debug("Schema `{database}` was dropped successfully.".format(database=self.database))
+ except AccessError:
+ raise AccessError(
+ "An attempt to drop schema `{database}` has failed. Check permissions.".format(database=self.database)
+ )
+
+ @property
+ def exists(self) -> bool:
+ """
+ Check if the associated schema exists on the server.
+
+ Returns
+ -------
+ bool
+ True if the schema exists.
+
+ Raises
+ ------
+ DataJointError
+ If schema has not been activated.
+ """
+ if self.database is None:
+ raise DataJointError("Schema must be activated first.")
+ return bool(self.connection.query(self.connection.adapter.schema_exists_sql(self.database)).rowcount)
+
+ @property
+ def lineage_table_exists(self) -> bool:
+ """
+ Check if the ~lineage table exists in this schema.
+
+ Returns
+ -------
+ bool
+ True if the lineage table exists.
+ """
+ from .lineage import lineage_table_exists
+
+ self._assert_exists()
+ return lineage_table_exists(self.connection, self.database)
+
+ @property
+ def lineage(self) -> dict[str, str]:
+ """
+ Get all lineages for tables in this schema.
+
+ Returns
+ -------
+ dict[str, str]
+ Mapping of ``'schema.table.attribute'`` to its lineage origin.
+ """
+ from .lineage import get_schema_lineages
+
+ self._assert_exists()
+ return get_schema_lineages(self.connection, self.database)
+
+ def rebuild_lineage(self) -> None:
+ """
+ Rebuild the ~lineage table for all tables in this schema.
+
+ Recomputes lineage for all attributes by querying FK relationships
+ from the information_schema. Use to restore lineage for schemas that
+ predate the lineage system or after corruption.
+
+ Notes
+ -----
+ After rebuilding, restart the Python kernel and reimport to pick up
+ the new lineage information.
+
+ Upstream schemas (referenced via cross-schema foreign keys) must
+ have their lineage rebuilt first.
+ """
+ from .lineage import rebuild_schema_lineage
+
+ self._assert_exists()
+ rebuild_schema_lineage(self.connection, self.database)
+
+ @property
+ def jobs(self) -> list[Job]:
+ """
+ Return Job objects for auto-populated tables with job tables.
+
+ Only returns Job objects when both the target table and its
+ ``~~table_name`` job table exist in the database. Job tables are
+ created lazily on first access to ``table.jobs`` or
+ ``populate(reserve_jobs=True)``.
+
+ Returns
+ -------
+ list[Job]
+ Job objects for existing job tables.
+ """
+ self._assert_exists()
+ jobs_list = []
+
+ # Get all existing job tables (~~prefix)
+ # Note: %% escapes the % in pymysql/psycopg2
+ adapter = self.connection.adapter
+ sql = adapter.list_tables_sql(self.database, pattern="~~%%")
+ result = self.connection.query(sql).fetchall()
+ existing_job_tables = {row[0] for row in result}
+
+ # Iterate over auto-populated tables and check if their job table exists
+ for table_name in self.list_tables():
+ adapter = self.connection.adapter
+ full_name = adapter.make_full_table_name(self.database, table_name)
+ table = FreeTable(self.connection, full_name)
+ tier = _get_tier(table.full_table_name)
+ if tier in (Computed, Imported):
+ # Compute expected job table name: ~~base_name
+ base_name = table_name.lstrip("_")
+ job_table_name = f"~~{base_name}"
+ if job_table_name in existing_job_tables:
+ jobs_list.append(Job(table))
+
+ return jobs_list
+
+ def list_tables(self) -> list[str]:
+ """
+ Return all user tables in the schema.
+
+ Excludes hidden tables (starting with ``~``) such as ``~lineage``
+ and job tables (``~~``).
+
+ Returns
+ -------
+ list[str]
+ Table names in topological order.
+ """
+ self.connection.dependencies.load()
+ return [
+ t
+ for d, t in (
+ self.connection.adapter.split_full_table_name(table_name)
+ for table_name in self.connection.dependencies.topo_sort()
+ )
+ if d == self.database
+ ]
+
+ def _find_table_name(self, name: str) -> str | None:
+ """
+ Find the actual SQL table name for a given base name.
+
+ Handles tier prefixes: Manual (none), Lookup (#), Imported (_), Computed (__).
+
+ Parameters
+ ----------
+ name : str
+ Base table name without tier prefix.
+
+ Returns
+ -------
+ str or None
+ The actual SQL table name, or None if not found.
+ """
+ tables = self.list_tables()
+ # Check exact match first
+ if name in tables:
+ return name
+ # Check with tier prefixes
+ for prefix in ("", "#", "_", "__"):
+ candidate = f"{prefix}{name}"
+ if candidate in tables:
+ return candidate
+ return None
+
+ def get_table(self, name: str) -> FreeTable:
+ """
+ Get a table instance by name.
+
+ Returns a FreeTable instance for the given table name. This is useful
+ for accessing tables when you don't have the Python class available.
+
+ Parameters
+ ----------
+ name : str
+ Table name (e.g., 'experiment', 'session__trial' for parts).
+ Can be snake_case (SQL name) or CamelCase (class name).
+ Tier prefixes are optional and will be auto-detected.
+
+ Returns
+ -------
+ FreeTable
+ A FreeTable instance for the table.
+
+ Raises
+ ------
+ DataJointError
+ If the table does not exist.
+
+ Examples
+ --------
+ >>> schema = dj.Schema('my_schema')
+ >>> experiment = schema.get_table('experiment')
+ >>> experiment.fetch()
+ """
+ self._assert_exists()
+ # Convert CamelCase to snake_case if needed
+ if name[0].isupper():
+ name = re.sub(r"(? FreeTable:
+ """
+ Get a table instance by name using bracket notation.
+
+ Parameters
+ ----------
+ name : str
+ Table name (snake_case or CamelCase).
+
+ Returns
+ -------
+ FreeTable
+ A FreeTable instance for the table.
+
+ Examples
+ --------
+ >>> schema = dj.Schema('my_schema')
+ >>> schema['Experiment'].fetch()
+ >>> schema['session'].fetch()
+ """
+ return self.get_table(name)
+
+ def __iter__(self):
+ """
+ Iterate over all tables in the schema.
+
+ Yields FreeTable instances for each table in topological order.
+
+ Yields
+ ------
+ FreeTable
+ Table instances in dependency order.
+
+ Examples
+ --------
+ >>> for table in schema:
+ ... print(table.full_table_name, len(table))
+ """
+ self._assert_exists()
+ for table_name in self.list_tables():
+ yield self.get_table(table_name)
+
+ def __contains__(self, name: str) -> bool:
+ """
+ Check if a table exists in the schema.
+
+ Parameters
+ ----------
+ name : str
+ Table name (snake_case or CamelCase).
+ Tier prefixes are optional and will be auto-detected.
+
+ Returns
+ -------
+ bool
+ True if the table exists.
+
+ Examples
+ --------
+ >>> 'Experiment' in schema
+ True
+ """
+ if name[0].isupper():
+ name = re.sub(r"(?>> lab = dj.VirtualModule('lab', 'my_lab_schema')
+ >>> lab.Subject.fetch()
+ """
+
+ def __init__(
+ self,
+ module_name: str,
+ schema_name: str,
+ *,
+ create_schema: bool = False,
+ create_tables: bool = False,
+ connection: Connection | None = None,
+ add_objects: dict[str, Any] | None = None,
+ ) -> None:
+ """
+ Initialize the virtual module.
+
+ Parameters
+ ----------
+ module_name : str
+ Display name for the module.
+ schema_name : str
+ Database schema name.
+ create_schema : bool, optional
+ If True, create the schema if it doesn't exist. Default False.
+ create_tables : bool, optional
+ If True, allow declaring new tables. Default False.
+ connection : Connection, optional
+ Database connection. Defaults to ``dj.conn()``.
+ add_objects : dict, optional
+ Additional objects to add to the module namespace.
+ """
+ super(VirtualModule, self).__init__(name=module_name)
+ _schema = _Schema(
+ schema_name,
+ create_schema=create_schema,
+ create_tables=create_tables,
+ connection=connection,
+ )
+ if add_objects:
+ self.__dict__.update(add_objects)
+ self.__dict__["schema"] = _schema
+ _schema.make_classes(into=self.__dict__)
+
+
+def list_schemas(connection: Connection | None = None) -> list[str]:
+ """
+ List all accessible schemas on the server.
+
+ Parameters
+ ----------
+ connection : Connection, optional
+ Database connection. Defaults to ``dj.conn()``.
+
+ Returns
+ -------
+ list[str]
+ Names of all accessible schemas.
+ """
+ conn = connection or _get_singleton_connection()
+ return [r[0] for r in conn.query(conn.adapter.list_schemas_sql())]
+
+
+def virtual_schema(
+ schema_name: str,
+ *,
+ connection: Connection | None = None,
+ create_schema: bool = False,
+ create_tables: bool = False,
+ add_objects: dict[str, Any] | None = None,
+) -> VirtualModule:
+ """
+ Create a virtual module for an existing database schema.
+
+ This is the recommended way to access database schemas when you don't have
+ the Python source code that defined them. Returns a module-like object with
+ table classes as attributes.
+
+ Parameters
+ ----------
+ schema_name : str
+ Database schema name.
+ connection : Connection, optional
+ Database connection. Defaults to ``dj.conn()``.
+ create_schema : bool, optional
+ If True, create the schema if it doesn't exist. Default False.
+ create_tables : bool, optional
+ If True, allow declaring new tables. Default False.
+ add_objects : dict, optional
+ Additional objects to add to the module namespace.
+
+ Returns
+ -------
+ VirtualModule
+ A module-like object with table classes as attributes.
+
+ Examples
+ --------
+ >>> lab = dj.virtual_schema('my_lab')
+ >>> lab.Subject.fetch()
+ >>> lab.Session & "subject_id='M001'"
+
+ See Also
+ --------
+ Schema : For defining new schemas with Python classes.
+ VirtualModule : The underlying class (prefer virtual_schema function).
+ """
+ return VirtualModule(
+ schema_name,
+ schema_name,
+ connection=connection,
+ create_schema=create_schema,
+ create_tables=create_tables,
+ add_objects=add_objects,
+ )
diff --git a/src/datajoint/settings.py b/src/datajoint/settings.py
new file mode 100644
index 000000000..6ae23478b
--- /dev/null
+++ b/src/datajoint/settings.py
@@ -0,0 +1,1050 @@
+"""
+DataJoint configuration system using pydantic-settings.
+
+This module provides strongly-typed configuration with automatic loading
+from environment variables, secrets directories, and JSON config files.
+
+Configuration sources (in priority order):
+
+1. Environment variables (``DJ_*``)
+2. Secrets directories (``.secrets/`` in project, ``/run/secrets/datajoint/``)
+3. Project config file (``datajoint.json``, searched recursively up to ``.git/.hg``)
+
+Examples
+--------
+>>> import datajoint as dj
+>>> dj.config.database.host
+'localhost'
+>>> dj.config.database.backend
+'mysql'
+>>> dj.config.database.port # Auto-detects: 3306 for MySQL, 5432 for PostgreSQL
+3306
+>>> with dj.config.override(safemode=False):
+... # dangerous operations here
+... pass
+
+Project structure::
+
+ myproject/
+ ├── .git/
+ ├── datajoint.json # Project config (commit this)
+ ├── .secrets/ # Local secrets (gitignore this)
+ │ ├── database.password
+ │ └── aws.secret_access_key
+ └── src/
+ └── analysis.py # Config found via parent search
+"""
+
+from __future__ import annotations
+
+import json
+import logging
+import os
+import warnings
+from contextlib import contextmanager
+from copy import deepcopy
+from enum import Enum
+from pathlib import Path
+from typing import Any, Iterator, Literal
+
+from pydantic import Field, SecretStr, field_validator, model_validator
+from pydantic_settings import BaseSettings, SettingsConfigDict
+
+from .errors import DataJointError
+
+CONFIG_FILENAME = "datajoint.json"
+SECRETS_DIRNAME = ".secrets"
+SYSTEM_SECRETS_DIR = Path("/run/secrets/datajoint")
+DEFAULT_SUBFOLDING = (2, 2)
+
+# Mapping of config keys to environment variables
+# Environment variables take precedence over config file values
+ENV_VAR_MAPPING = {
+ "database.host": "DJ_HOST",
+ "database.user": "DJ_USER",
+ "database.password": "DJ_PASS",
+ "database.backend": "DJ_BACKEND",
+ "database.port": "DJ_PORT",
+ "database.name": "DJ_DATABASE_NAME",
+ "database.database_prefix": "DJ_DATABASE_PREFIX",
+ "database.create_tables": "DJ_CREATE_TABLES",
+ "loglevel": "DJ_LOG_LEVEL",
+ "strict_provenance": "DJ_STRICT_PROVENANCE",
+ "display.diagram_direction": "DJ_DIAGRAM_DIRECTION",
+}
+
+Role = Enum("Role", "manual lookup imported computed job")
+role_to_prefix = {
+ Role.manual: "",
+ Role.lookup: "#",
+ Role.imported: "_",
+ Role.computed: "__",
+ Role.job: "~",
+}
+prefix_to_role = dict(zip(role_to_prefix.values(), role_to_prefix))
+
+logger = logging.getLogger(__name__.split(".")[0])
+
+
+def find_config_file(start: Path | None = None) -> Path | None:
+ """
+ Search for datajoint.json in current and parent directories.
+
+ Searches upward from ``start`` until finding the config file or hitting
+ a project boundary (``.git``, ``.hg``) or filesystem root.
+
+ Parameters
+ ----------
+ start : Path, optional
+ Directory to start search from. Defaults to current working directory.
+
+ Returns
+ -------
+ Path or None
+ Path to config file if found, None otherwise.
+ """
+ current = (start or Path.cwd()).resolve()
+
+ while True:
+ config_path = current / CONFIG_FILENAME
+ if config_path.is_file():
+ return config_path
+
+ # Stop at project/repo root
+ if (current / ".git").exists() or (current / ".hg").exists():
+ return None
+
+ # Stop at filesystem root
+ if current == current.parent:
+ return None
+
+ current = current.parent
+
+
+def find_secrets_dir(config_path: Path | None = None) -> Path | None:
+ """
+ Find the secrets directory.
+
+ Priority:
+
+ 1. ``.secrets/`` in same directory as datajoint.json (project secrets)
+ 2. ``/run/secrets/datajoint/`` (Docker/Kubernetes secrets)
+
+ Parameters
+ ----------
+ config_path : Path, optional
+ Path to datajoint.json if found.
+
+ Returns
+ -------
+ Path or None
+ Path to secrets directory if found, None otherwise.
+ """
+ # Check project secrets directory (next to config file)
+ if config_path is not None:
+ project_secrets = config_path.parent / SECRETS_DIRNAME
+ if project_secrets.is_dir():
+ return project_secrets
+
+ # Check system secrets directory (Docker/Kubernetes)
+ if SYSTEM_SECRETS_DIR.is_dir():
+ return SYSTEM_SECRETS_DIR
+
+ return None
+
+
+def read_secret_file(secrets_dir: Path | None, name: str) -> str | None:
+ """
+ Read a secret value from a file in the secrets directory.
+
+ Parameters
+ ----------
+ secrets_dir : Path or None
+ Path to secrets directory.
+ name : str
+ Name of the secret file (e.g., ``'database.password'``).
+
+ Returns
+ -------
+ str or None
+ Secret value as string, or None if not found.
+ """
+ if secrets_dir is None:
+ return None
+
+ secret_path = secrets_dir / name
+ if secret_path.is_file():
+ return secret_path.read_text().strip()
+
+ return None
+
+
+class DatabaseSettings(BaseSettings):
+ """Database connection settings."""
+
+ model_config = SettingsConfigDict(
+ env_prefix="DJ_",
+ case_sensitive=False,
+ extra="forbid",
+ validate_assignment=True,
+ )
+
+ host: str = Field(default="localhost", validation_alias="DJ_HOST")
+ user: str | None = Field(default=None, validation_alias="DJ_USER")
+ password: SecretStr | None = Field(default=None, validation_alias="DJ_PASS")
+ backend: Literal["mysql", "postgresql"] = Field(
+ default="mysql",
+ validation_alias="DJ_BACKEND",
+ description="Database backend: 'mysql' or 'postgresql'",
+ )
+ port: int | None = Field(default=None, validation_alias="DJ_PORT")
+ name: str | None = Field(
+ default=None,
+ validation_alias="DJ_DATABASE_NAME",
+ description="Database name for PostgreSQL connections. Defaults to 'postgres' if not set.",
+ )
+ reconnect: bool = True
+ use_tls: bool | None = Field(default=None, validation_alias="DJ_USE_TLS")
+ database_prefix: str = Field(
+ default="",
+ validation_alias="DJ_DATABASE_PREFIX",
+ description="Deprecated. Use database.name instead.",
+ )
+ create_tables: bool = Field(
+ default=True,
+ validation_alias="DJ_CREATE_TABLES",
+ description="Default for Schema create_tables parameter. "
+ "Set to False for production mode to prevent automatic table creation.",
+ )
+
+ @model_validator(mode="after")
+ def set_default_port_from_backend(self) -> "DatabaseSettings":
+ """Set default port based on backend if not explicitly provided."""
+ if self.port is None:
+ self.port = 5432 if self.backend == "postgresql" else 3306
+ return self
+
+
+class ConnectionSettings(BaseSettings):
+ """Connection behavior settings."""
+
+ model_config = SettingsConfigDict(extra="forbid", validate_assignment=True)
+
+ charset: str = "" # pymysql uses '' as default
+
+
+class DisplaySettings(BaseSettings):
+ """Display and preview settings."""
+
+ model_config = SettingsConfigDict(extra="forbid", validate_assignment=True)
+
+ limit: int = 12
+ width: int = 14
+ show_tuple_count: bool = True
+ diagram_direction: Literal["TB", "LR"] = Field(
+ default="LR",
+ validation_alias="DJ_DIAGRAM_DIRECTION",
+ description="Default diagram layout direction: 'TB' (top-to-bottom) or 'LR' (left-to-right)",
+ )
+
+
+class StoresSettings(BaseSettings):
+ """
+ Unified object storage configuration.
+
+ Stores configuration supports both hash-addressed and schema-addressed storage
+ using the same named stores with _hash and _schema sections.
+ """
+
+ model_config = SettingsConfigDict(
+ case_sensitive=False,
+ extra="allow", # Allow dynamic store names
+ validate_assignment=True,
+ )
+
+ default: str | None = Field(default=None, description="Name of the default store")
+
+ # Named stores are added dynamically as stores..*
+ # Structure: stores..protocol, stores..location, etc.
+
+
+class JobsSettings(BaseSettings):
+ """Job queue configuration for AutoPopulate 2.0."""
+
+ model_config = SettingsConfigDict(
+ env_prefix="DJ_JOBS_",
+ case_sensitive=False,
+ extra="forbid",
+ validate_assignment=True,
+ )
+
+ auto_refresh: bool = Field(default=True, description="Auto-refresh jobs queue on populate")
+ keep_completed: bool = Field(default=False, description="Keep success records in jobs table")
+ stale_timeout: int = Field(default=3600, ge=0, description="Seconds before pending job is checked for staleness")
+ default_priority: int = Field(default=5, ge=0, le=255, description="Default priority for new jobs (lower = more urgent)")
+ version_method: Literal["git", "none"] | None = Field(
+ default=None, description="Method to obtain version: 'git' (commit hash), 'none' (empty), or None (disabled)"
+ )
+ allow_new_pk_fields_in_computed_tables: bool = Field(
+ default=False,
+ description="Allow native (non-FK) primary key fields in Computed/Imported tables. "
+ "When True, bypasses the FK-only PK validation. Job granularity will be degraded for such tables.",
+ )
+ add_job_metadata: bool = Field(
+ default=False,
+ description="Add hidden job metadata attributes (_job_start_time, _job_duration, _job_version) "
+ "to Computed and Imported tables during declaration. Tables created without this setting "
+ "will not receive metadata updates during populate.",
+ )
+
+
+class Config(BaseSettings):
+ """
+ Main DataJoint configuration.
+
+ Settings are loaded from (in priority order):
+
+ 1. Environment variables (``DJ_*``)
+ 2. Secrets directory (``.secrets/`` or ``/run/secrets/datajoint/``)
+ 3. Config file (``datajoint.json``, searched in parent directories)
+ 4. Default values
+
+ Examples
+ --------
+ Access settings via attributes:
+
+ >>> config.database.host
+ >>> config.safemode
+
+ Override temporarily with context manager:
+
+ >>> with config.override(safemode=False):
+ ... pass
+ """
+
+ model_config = SettingsConfigDict(
+ env_prefix="DJ_",
+ case_sensitive=False,
+ extra="forbid",
+ validate_assignment=True,
+ )
+
+ # Nested settings groups
+ database: DatabaseSettings = Field(default_factory=DatabaseSettings)
+ connection: ConnectionSettings = Field(default_factory=ConnectionSettings)
+ display: DisplaySettings = Field(default_factory=DisplaySettings)
+ jobs: JobsSettings = Field(default_factory=JobsSettings)
+
+ # Unified stores configuration (replaces external and object_storage)
+ # ``validation_alias`` redirects pydantic-settings' env source away from the
+ # natural ``DJ_STORES`` so it doesn't auto-parse on Config() construction.
+ # ``DJ_STORES`` is handled by ``_apply_stores_env`` after the config file
+ # load so env-var precedence is honored. *New in 2.2.3.*
+ stores: dict[str, Any] = Field(
+ default_factory=dict,
+ validation_alias="_DJ_STORES_PYDANTIC_DISABLED",
+ description="Unified object storage configuration. "
+ "Use stores.default to designate default store. "
+ "Configure named stores as stores..protocol, stores..location, etc. "
+ "Set via DJ_STORES (JSON object) or in datajoint.json. *New in 2.2.3* for "
+ "DJ_STORES env-var support.",
+ )
+
+ # Top-level settings
+ loglevel: Literal["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] = Field(default="INFO", validation_alias="DJ_LOG_LEVEL")
+ safemode: bool = True
+
+ ignore_config_file: bool = Field(
+ default=False,
+ validation_alias="DJ_IGNORE_CONFIG_FILE",
+ description="If True, skip loading datajoint.json and the secrets directory. "
+ "Intended for env-var-only deployments (e.g. the DataJoint platform). "
+ "*New in 2.2.3.*",
+ )
+
+ strict_provenance: bool = Field(
+ default=False,
+ validation_alias="DJ_STRICT_PROVENANCE",
+ description="If True, enforces the upstream-only convention inside make(): "
+ "reads must go through self.upstream[Ancestor], writes must target self "
+ "or self's Part tables with primary keys consistent with the current key. "
+ "Off by default; opt-in for deployments that need runtime provenance "
+ "guarantees backing downstream lineage / CDC tooling. *New in 2.3.*",
+ )
+
+ # Cache path for query results
+ query_cache: Path | None = None
+
+ # Download path for attachments and filepaths
+ download_path: str = "."
+
+ # Internal: track where config was loaded from
+ _config_path: Path | None = None
+ _secrets_dir: Path | None = None
+
+ @field_validator("loglevel", mode="after")
+ @classmethod
+ def set_logger_level(cls, v: str) -> str:
+ """Update logger level when loglevel changes."""
+ logger.setLevel(v)
+ return v
+
+ @field_validator("query_cache", mode="before")
+ @classmethod
+ def convert_path(cls, v: Any) -> Path | None:
+ """Convert string paths to Path objects."""
+ if v is None:
+ return None
+ return Path(v) if not isinstance(v, Path) else v
+
+ def get_store_spec(self, store: str | None = None, *, use_filepath_default: bool = False) -> dict[str, Any]:
+ """
+ Get configuration for a storage store.
+
+ Parameters
+ ----------
+ store : str, optional
+ Name of the store to retrieve. If None, uses the appropriate default.
+ use_filepath_default : bool, optional
+ If True and store is None, uses stores.filepath_default instead of
+ stores.default. Use for filepath references which are not part of OAS.
+ Default: False (use stores.default for integrated storage).
+
+ Returns
+ -------
+ dict[str, Any]
+ Store configuration dict with validated fields.
+
+ Raises
+ ------
+ DataJointError
+ If store is not configured or has invalid config.
+ """
+ # Handle default store
+ if store is None:
+ if use_filepath_default:
+ # Filepath references use separate default (not part of OAS)
+ if "filepath_default" not in self.stores:
+ raise DataJointError(
+ "stores.filepath_default is not configured. "
+ "Set stores.filepath_default or specify store explicitly with "
+ )
+ store = self.stores["filepath_default"]
+ else:
+ # Integrated storage (hash, schema) uses stores.default
+ if "default" not in self.stores:
+ raise DataJointError("stores.default is not configured")
+ store = self.stores["default"]
+
+ if not isinstance(store, str):
+ default_key = "filepath_default" if use_filepath_default else "default"
+ raise DataJointError(f"stores.{default_key} must be a string")
+
+ # Check store exists
+ if store not in self.stores:
+ raise DataJointError(f"Storage '{store}' is requested but not configured in stores")
+
+ spec = dict(self.stores[store])
+
+ self._apply_common_store_defaults(spec)
+
+ # Validate protocol
+ protocol = spec.get("protocol", "").lower()
+ supported_protocols = ("file", "s3", "gcs", "azure")
+ if protocol not in supported_protocols:
+ from .storage_adapter import get_storage_adapter
+
+ adapter = get_storage_adapter(protocol)
+ if adapter is None:
+ raise DataJointError(
+ f'Unknown protocol "{protocol}" in config.stores["{store}"]. '
+ f"Built-in: {', '.join(supported_protocols)}. "
+ f"Install a plugin package for additional protocols."
+ )
+ adapter.validate_spec(spec)
+ self._validate_prefix_separation(
+ store_name=store,
+ hash_prefix=spec.get("hash_prefix"),
+ schema_prefix=spec.get("schema_prefix"),
+ filepath_prefix=spec.get("filepath_prefix"),
+ )
+ return spec
+
+ # Set protocol-specific defaults
+ if protocol == "s3":
+ spec.setdefault("secure", True) # HTTPS by default for S3
+
+ # Define required and allowed keys by protocol
+ required_keys: dict[str, tuple[str, ...]] = {
+ "file": ("protocol", "location"),
+ "s3": ("protocol", "endpoint", "bucket", "access_key", "secret_key", "location"),
+ "gcs": ("protocol", "bucket", "location"),
+ "azure": ("protocol", "container", "location"),
+ }
+ allowed_keys: dict[str, tuple[str, ...]] = {
+ "file": (
+ "protocol",
+ "location",
+ "subfolding",
+ "partition_pattern",
+ "token_length",
+ "hash_prefix",
+ "schema_prefix",
+ "filepath_prefix",
+ "stage",
+ ),
+ "s3": (
+ "protocol",
+ "endpoint",
+ "bucket",
+ "access_key",
+ "secret_key",
+ "location",
+ "secure",
+ "subfolding",
+ "partition_pattern",
+ "token_length",
+ "hash_prefix",
+ "schema_prefix",
+ "filepath_prefix",
+ "stage",
+ "proxy_server",
+ ),
+ "gcs": (
+ "protocol",
+ "bucket",
+ "location",
+ "token",
+ "project",
+ "subfolding",
+ "partition_pattern",
+ "token_length",
+ "hash_prefix",
+ "schema_prefix",
+ "filepath_prefix",
+ "stage",
+ ),
+ "azure": (
+ "protocol",
+ "container",
+ "location",
+ "account_name",
+ "account_key",
+ "connection_string",
+ "subfolding",
+ "partition_pattern",
+ "token_length",
+ "hash_prefix",
+ "schema_prefix",
+ "filepath_prefix",
+ "stage",
+ ),
+ }
+
+ # Check required keys
+ missing = [k for k in required_keys[protocol] if k not in spec]
+ if missing:
+ raise DataJointError(f'config.stores["{store}"] is missing: {", ".join(missing)}')
+
+ # Check for invalid keys
+ invalid = [k for k in spec if k not in allowed_keys[protocol]]
+ if invalid:
+ raise DataJointError(f'Invalid key(s) in config.stores["{store}"]: {", ".join(invalid)}')
+
+ # Validate prefix separation to prevent overlap
+ self._validate_prefix_separation(
+ store_name=store,
+ hash_prefix=spec.get("hash_prefix"),
+ schema_prefix=spec.get("schema_prefix"),
+ filepath_prefix=spec.get("filepath_prefix"),
+ )
+
+ return spec
+
+ def _validate_prefix_separation(
+ self,
+ store_name: str,
+ hash_prefix: str | None,
+ schema_prefix: str | None,
+ filepath_prefix: str | None,
+ ) -> None:
+ """
+ Validate that storage section prefixes don't overlap.
+
+ Parameters
+ ----------
+ store_name : str
+ Name of the store being validated (for error messages).
+ hash_prefix : str or None
+ Prefix for hash-addressed storage.
+ schema_prefix : str or None
+ Prefix for schema-addressed storage.
+ filepath_prefix : str or None
+ Prefix for filepath storage (None means unrestricted).
+
+ Raises
+ ------
+ DataJointError
+ If any prefixes overlap (one is a parent/child of another).
+ """
+ # Collect non-null prefixes with their names
+ prefixes = []
+ if hash_prefix:
+ prefixes.append(("hash_prefix", hash_prefix))
+ if schema_prefix:
+ prefixes.append(("schema_prefix", schema_prefix))
+ if filepath_prefix:
+ prefixes.append(("filepath_prefix", filepath_prefix))
+
+ # Normalize prefixes: remove leading/trailing slashes, ensure trailing slash for comparison
+ def normalize(p: str) -> str:
+ return p.strip("/") + "/"
+
+ normalized = [(name, normalize(prefix)) for name, prefix in prefixes]
+
+ # Check each pair for overlap
+ for i, (name1, p1) in enumerate(normalized):
+ for j, (name2, p2) in enumerate(normalized[i + 1 :], start=i + 1):
+ # Check if one prefix is a parent of another
+ if p1.startswith(p2) or p2.startswith(p1):
+ raise DataJointError(
+ f'config.stores["{store_name}"]: {name1}="{prefixes[i][1]}" and '
+ f'{name2}="{prefixes[j][1]}" overlap. '
+ f"Storage section prefixes must be mutually exclusive."
+ )
+
+ @staticmethod
+ def _apply_common_store_defaults(spec: dict[str, Any]) -> None:
+ """Apply defaults shared by every store protocol (built-in and plugin)."""
+ spec.setdefault("subfolding", None)
+ spec.setdefault("partition_pattern", None)
+ spec.setdefault("token_length", 8)
+ spec.setdefault("hash_prefix", "_hash")
+ spec.setdefault("schema_prefix", "_schema")
+ spec.setdefault("filepath_prefix", None)
+
+ def load(self, filename: str | Path) -> None:
+ """
+ Load settings from a JSON file.
+
+ Parameters
+ ----------
+ filename : str or Path
+ Path to load configuration from.
+ """
+ filepath = Path(filename)
+ if not filepath.exists():
+ raise FileNotFoundError(f"Config file not found: {filepath}")
+
+ logger.info(f"Loading configuration from {filepath.absolute()}")
+
+ with open(filepath) as f:
+ data = json.load(f)
+
+ self._update_from_flat_dict(data)
+ self._config_path = filepath
+
+ def _update_from_flat_dict(self, data: dict[str, Any]) -> None:
+ """
+ Update settings from a dict (flat dot-notation or nested).
+
+ Environment variables take precedence over config file values.
+ If an env var is set for a setting, the file value is skipped.
+ """
+ for key, value in data.items():
+ # Special handling for stores - accept nested dict directly
+ if key == "stores" and isinstance(value, dict):
+ # Merge stores dict
+ for store_key, store_value in value.items():
+ self.stores[store_key] = store_value
+ continue
+
+ # Handle nested dicts by recursively updating
+ if isinstance(value, dict) and hasattr(self, key):
+ group_obj = getattr(self, key)
+ for nested_key, nested_value in value.items():
+ if hasattr(group_obj, nested_key):
+ # Check if env var is set for this nested key
+ full_key = f"{key}.{nested_key}"
+ env_var = ENV_VAR_MAPPING.get(full_key)
+ if env_var and os.environ.get(env_var):
+ logger.debug(f"Skipping {full_key} from file (env var {env_var} takes precedence)")
+ continue
+ setattr(group_obj, nested_key, nested_value)
+ continue
+
+ # Handle flat dot-notation keys
+ parts = key.split(".")
+ if len(parts) == 1:
+ if hasattr(self, key) and not key.startswith("_"):
+ # Check if env var is set for this key
+ env_var = ENV_VAR_MAPPING.get(key)
+ if env_var and os.environ.get(env_var):
+ logger.debug(f"Skipping {key} from file (env var {env_var} takes precedence)")
+ continue
+ setattr(self, key, value)
+ elif len(parts) == 2:
+ group, attr = parts
+ if hasattr(self, group):
+ group_obj = getattr(self, group)
+ if hasattr(group_obj, attr):
+ # Check if env var is set for this key
+ env_var = ENV_VAR_MAPPING.get(key)
+ if env_var and os.environ.get(env_var):
+ logger.debug(f"Skipping {key} from file (env var {env_var} takes precedence)")
+ continue
+ setattr(group_obj, attr, value)
+ elif len(parts) == 3:
+ # Handle stores.. pattern
+ group, store_name, attr = parts
+ if group == "stores":
+ if store_name not in self.stores:
+ self.stores[store_name] = {}
+ self.stores[store_name][attr] = value
+
+ def _load_secrets(self, secrets_dir: Path) -> None:
+ """Load secrets from a secrets directory."""
+ self._secrets_dir = secrets_dir
+
+ # Load database secrets
+ db_user = read_secret_file(secrets_dir, "database.user")
+ if db_user is not None and self.database.user is None:
+ self.database.user = db_user
+ logger.debug(f"Loaded database.user from {secrets_dir}")
+
+ db_password = read_secret_file(secrets_dir, "database.password")
+ if db_password is not None and self.database.password is None:
+ self.database.password = db_password
+ logger.debug(f"Loaded database.password from {secrets_dir}")
+
+ # Load per-store secrets from any stores.. file.
+ # The attr name is recorded as-is on stores.; this lets
+ # plugin-registered adapters define their own secret fields
+ # (e.g. a Bearer ``token`` for HTTP-based protocols) without
+ # forcing AWS-style ``access_key`` / ``secret_key`` naming.
+ if secrets_dir.is_dir():
+ for secret_file in secrets_dir.iterdir():
+ if not secret_file.is_file() or secret_file.name.startswith("."):
+ continue
+
+ parts = secret_file.name.split(".")
+ if len(parts) == 3 and parts[0] == "stores":
+ store_name, attr = parts[1], parts[2]
+ value = secret_file.read_text().strip()
+ # Initialize store dict if needed
+ if store_name not in self.stores:
+ self.stores[store_name] = {}
+ # Only set if not already present (config / env vars win)
+ if attr not in self.stores[store_name]:
+ self.stores[store_name][attr] = value
+ logger.debug(f"Loaded stores.{store_name}.{attr} from {secrets_dir}")
+
+ def _apply_stores_env(self) -> None:
+ """Replace ``self.stores`` from the ``DJ_STORES`` env var if set.
+
+ ``DJ_STORES`` holds a JSON object in the same shape as the ``stores``
+ block of ``datajoint.json``. This lets env-var-only deployments
+ configure plugin-registered storage adapters with arbitrary attr
+ names (e.g. a Bearer ``token`` field) without negotiating an env-var
+ naming scheme per attr.
+
+ *New in 2.2.3.*
+ """
+ raw = os.environ.get("DJ_STORES")
+ if not raw:
+ return
+ try:
+ data = json.loads(raw)
+ except json.JSONDecodeError as e:
+ raise ValueError(f"DJ_STORES contains invalid JSON: {e}") from e
+ if not isinstance(data, dict):
+ raise ValueError(f"DJ_STORES must be a JSON object, got {type(data).__name__}")
+ self.stores = data
+ logger.debug("Loaded stores from DJ_STORES env var")
+
+ @contextmanager
+ def override(self, **kwargs: Any) -> Iterator["Config"]:
+ """
+ Temporarily override configuration values.
+
+ Parameters
+ ----------
+ **kwargs : Any
+ Settings to override. Use double underscore for nested settings
+ (e.g., ``database__host="localhost"``).
+
+ Yields
+ ------
+ Config
+ The config instance with overridden values.
+
+ Examples
+ --------
+ >>> with config.override(safemode=False, database__host="test"):
+ ... # config.safemode is False here
+ ... pass
+ >>> # config.safemode is restored
+ """
+ # Store original values
+ backup = {}
+
+ # Convert double underscore to nested access
+ converted = {}
+ for key, value in kwargs.items():
+ if "__" in key:
+ parts = key.split("__")
+ converted[tuple(parts)] = value
+ else:
+ converted[(key,)] = value
+
+ try:
+ # Save originals and apply overrides
+ for key_parts, value in converted.items():
+ if len(key_parts) == 1:
+ key = key_parts[0]
+ if hasattr(self, key):
+ backup[key_parts] = deepcopy(getattr(self, key))
+ setattr(self, key, value)
+ elif len(key_parts) == 2:
+ group, attr = key_parts
+ if hasattr(self, group):
+ group_obj = getattr(self, group)
+ if hasattr(group_obj, attr):
+ backup[key_parts] = deepcopy(getattr(group_obj, attr))
+ setattr(group_obj, attr, value)
+
+ yield self
+
+ finally:
+ # Restore original values
+ for key_parts, original in backup.items():
+ if len(key_parts) == 1:
+ setattr(self, key_parts[0], original)
+ elif len(key_parts) == 2:
+ group, attr = key_parts
+ setattr(getattr(self, group), attr, original)
+
+ @staticmethod
+ def save_template(
+ path: str | Path = "datajoint.json",
+ minimal: bool = True,
+ create_secrets_dir: bool = True,
+ ) -> Path:
+ """
+ Create a template datajoint.json configuration file.
+
+ Credentials should NOT be stored in datajoint.json. Instead, use either:
+
+ - Environment variables (``DJ_USER``, ``DJ_PASS``, ``DJ_HOST``,
+ ``DJ_STORES`` for JSON-encoded store configs, etc.)
+ - The ``.secrets/`` directory (created alongside datajoint.json)
+
+ Set ``DJ_IGNORE_CONFIG_FILE=true`` to skip both ``datajoint.json`` and
+ the secrets directory entirely (env-var-only configuration).
+
+ Parameters
+ ----------
+ path : str or Path, optional
+ Where to save the template. Default ``'datajoint.json'``.
+ minimal : bool, optional
+ If True (default), create minimal template with just database settings.
+ If False, create full template with all available settings.
+ create_secrets_dir : bool, optional
+ If True (default), also create a ``.secrets/`` directory with
+ template files for credentials.
+
+ Returns
+ -------
+ Path
+ Absolute path to the created config file.
+
+ Raises
+ ------
+ FileExistsError
+ If config file already exists (won't overwrite).
+
+ Examples
+ --------
+ >>> import datajoint as dj
+ >>> dj.config.save_template() # Creates minimal template + .secrets/
+ >>> dj.config.save_template("full-config.json", minimal=False)
+ """
+ filepath = Path(path)
+ if filepath.exists():
+ raise FileExistsError(f"File already exists: {filepath}. Remove it first or choose a different path.")
+
+ if minimal:
+ template = {
+ "database": {
+ "host": "localhost",
+ "port": 3306,
+ },
+ }
+ else:
+ template = {
+ "database": {
+ "host": "localhost",
+ "port": 3306,
+ "reconnect": True,
+ "use_tls": None,
+ },
+ "connection": {
+ "charset": "",
+ },
+ "display": {
+ "limit": 12,
+ "width": 14,
+ "show_tuple_count": True,
+ },
+ "stores": {
+ "default": "main",
+ "filepath_default": "raw_data",
+ "main": {
+ "protocol": "file",
+ "location": "/data/my-project/main",
+ "partition_pattern": None,
+ "token_length": 8,
+ "subfolding": None,
+ },
+ "raw_data": {
+ "protocol": "file",
+ "location": "/data/my-project/raw",
+ },
+ },
+ "loglevel": "INFO",
+ "safemode": True,
+ "query_cache": None,
+ "download_path": ".",
+ }
+
+ with open(filepath, "w") as f:
+ json.dump(template, f, indent=2)
+ f.write("\n")
+
+ logger.info(f"Created template configuration at {filepath.absolute()}")
+
+ # Create .secrets/ directory with template files
+ if create_secrets_dir:
+ secrets_dir = filepath.parent / SECRETS_DIRNAME
+ secrets_dir.mkdir(exist_ok=True)
+
+ # Create placeholder secret files
+ secret_templates = {
+ "database.user": "your_username",
+ "database.password": "your_password",
+ }
+ for secret_name, placeholder in secret_templates.items():
+ secret_file = secrets_dir / secret_name
+ if not secret_file.exists():
+ secret_file.write_text(placeholder)
+
+ # Create .gitignore to prevent committing secrets
+ gitignore_path = secrets_dir / ".gitignore"
+ if not gitignore_path.exists():
+ gitignore_path.write_text("# Never commit secrets\n*\n!.gitignore\n")
+
+ logger.info(
+ f"Created {SECRETS_DIRNAME}/ directory with credential templates. "
+ f"Edit the files in {secrets_dir.absolute()}/ to set your credentials."
+ )
+
+ return filepath.absolute()
+
+ # Dict-like access for convenience
+ def __getitem__(self, key: str) -> Any:
+ """Get setting by dot-notation key (e.g., 'database.host')."""
+ parts = key.split(".")
+ obj: Any = self
+ for part in parts:
+ if hasattr(obj, part):
+ obj = getattr(obj, part)
+ elif isinstance(obj, dict):
+ obj = obj[part]
+ else:
+ raise KeyError(f"Setting '{key}' not found")
+ # Unwrap SecretStr for compatibility
+ if isinstance(obj, SecretStr):
+ return obj.get_secret_value()
+ return obj
+
+ def __setitem__(self, key: str, value: Any) -> None:
+ """Set setting by dot-notation key (e.g., 'database.host')."""
+ parts = key.split(".")
+ if len(parts) == 1:
+ if hasattr(self, key):
+ setattr(self, key, value)
+ else:
+ raise KeyError(f"Setting '{key}' not found")
+ else:
+ obj: Any = self
+ for part in parts[:-1]:
+ obj = getattr(obj, part)
+ setattr(obj, parts[-1], value)
+
+ def __delitem__(self, key: str) -> None:
+ """Reset setting to default by dot-notation key."""
+ # Get the default value from the model fields (access from class, not instance)
+ parts = key.split(".")
+ if len(parts) == 1:
+ field_info = type(self).model_fields.get(key)
+ if field_info is not None:
+ default = field_info.default
+ if default is not None:
+ setattr(self, key, default)
+ elif field_info.default_factory is not None:
+ setattr(self, key, field_info.default_factory())
+ else:
+ setattr(self, key, None)
+ else:
+ raise KeyError(f"Setting '{key}' not found")
+ else:
+ # For nested settings, reset to None or empty
+ obj: Any = self
+ for part in parts[:-1]:
+ obj = getattr(obj, part)
+ setattr(obj, parts[-1], None)
+
+ def get(self, key: str, default: Any = None) -> Any:
+ """Get setting with optional default value."""
+ try:
+ return self[key]
+ except KeyError:
+ return default
+
+
+def _create_config() -> Config:
+ """Create and initialize the global config instance."""
+ cfg = Config()
+
+ config_path: Path | None = None
+ if not cfg.ignore_config_file:
+ config_path = find_config_file()
+ if config_path is not None:
+ try:
+ cfg.load(config_path)
+ except Exception as e:
+ warnings.warn(f"Failed to load config from {config_path}: {e}")
+ else:
+ warnings.warn(
+ f"No {CONFIG_FILENAME} found. Using defaults and environment variables. "
+ f"Run `dj.config.save_template()` to create a template configuration.",
+ stacklevel=2,
+ )
+
+ # DJ_STORES (if set) overrides the stores dict from the config file
+ cfg._apply_stores_env()
+
+ # Secrets fill missing attrs in whatever ended up in self.stores
+ if not cfg.ignore_config_file:
+ secrets_dir = find_secrets_dir(config_path)
+ if secrets_dir is not None:
+ cfg._load_secrets(secrets_dir)
+
+ # Set initial log level
+ logger.setLevel(cfg.loglevel)
+
+ return cfg
+
+
+# Global config instance
+config = _create_config()
diff --git a/src/datajoint/spark.py b/src/datajoint/spark.py
new file mode 100644
index 000000000..29397b64f
--- /dev/null
+++ b/src/datajoint/spark.py
@@ -0,0 +1,92 @@
+"""
+SparkAdapter Codec Protocol.
+
+Opt-in contract for codecs that adapt their decoded values to Spark-native
+types — primitives, lists, dicts, and nested combinations.
+
+Codecs implement this method when they want their column eligible for
+downstream typed-query systems (Spark SQL, Delta Sharing, BI tools).
+Generic codecs like ```` and ```` deliberately do not
+implement it: their decoded values can be arbitrary Python objects with
+no fixed Spark-native shape.
+
+The contract is intentionally a Protocol rather than an abstract method
+on :class:`datajoint.Codec`:
+
+- Generic codecs need no acknowledgement (no ``NotImplementedError`` stubs).
+- Existing plugin codecs continue to work unchanged.
+- Codec authors opt in by adding the method on their own release cadence.
+- Consumers detect support structurally via ``isinstance(codec, SparkAdapter)``.
+
+See ``datajoint-docs/src/reference/specs/spark-adapter.md`` for the
+normative specification (signature, return-value shape constraints,
+worked codec examples).
+"""
+
+from __future__ import annotations
+
+from typing import Any, Protocol, runtime_checkable
+
+
+@runtime_checkable
+class SparkAdapter(Protocol):
+ """
+ A codec that adapts its decoded values to Spark-native types.
+
+ Opt-in. Codecs implementing this method declare that their decoded
+ values can be expressed as primitives, lists, or dicts of the same —
+ i.e., shapes that map cleanly to Spark's ``StructType`` /
+ ``ArrayType`` / ``MapType``.
+
+ Consumers (e.g., a Databricks silver-layer publish pipeline) check
+ ``isinstance(codec, SparkAdapter)`` per column to determine eligibility.
+
+ Allowed return-value shapes:
+
+ - Primitives: ``bool``, ``int``, ``float``, ``str``, ``bytes``,
+ ``None``, ``datetime.date``, ``datetime.datetime``.
+ - ``list[T]`` where ``T`` is any allowed shape (→ Spark ``ArrayType``).
+ - ``dict[str, T]`` where ``T`` is any allowed shape (→ Spark
+ ``StructType`` or ``MapType``, consumer-decided).
+
+ NumPy arrays must be converted to lists; no tuples, sets, or custom
+ objects in the return value.
+
+ Examples
+ --------
+ A 1D float-array codec (shipped as a plugin, not in datajoint-python)::
+
+ class FloatArrayCodec(dj.Codec):
+ name = "float_array"
+
+ def encode(self, value, *, key=None, store_name=None): ...
+ def decode(self, stored, *, key=None) -> np.ndarray: ...
+
+ def to_spark(self, decoded: np.ndarray, *, key=None) -> list[float]:
+ return decoded.tolist() # → Spark ARRAY
+
+ Eligibility check::
+
+ from datajoint import SparkAdapter
+ isinstance(FloatArrayCodec(), SparkAdapter) # True
+ """
+
+ def to_spark(self, decoded: Any, *, key: dict | None = None) -> Any:
+ """
+ Adapt a decoded codec value to a Spark-native shape.
+
+ Parameters
+ ----------
+ decoded : Any
+ The Python value produced by the codec's ``decode()``.
+ key : dict, optional
+ Optional context dict — same shape as ``Codec.encode``'s
+ ``key`` parameter. Most codecs ignore it.
+
+ Returns
+ -------
+ Any
+ A value composed entirely of allowed Spark-native shapes
+ (see class docstring).
+ """
+ ...
diff --git a/src/datajoint/staged_insert.py b/src/datajoint/staged_insert.py
new file mode 100644
index 000000000..ffbe8a8f2
--- /dev/null
+++ b/src/datajoint/staged_insert.py
@@ -0,0 +1,274 @@
+"""
+Staged insert context manager for direct object storage writes.
+
+This module provides the StagedInsert class which allows writing directly
+to object storage before finalizing the database insert.
+"""
+
+from contextlib import contextmanager
+from datetime import datetime, timezone
+from typing import IO, TYPE_CHECKING, Any
+
+import fsspec
+
+from .codecs import resolve_dtype
+from .errors import DataJointError
+from .hash_registry import get_store_backend
+from .storage import build_object_path
+
+if TYPE_CHECKING:
+ from .storage import StorageBackend
+
+
+class StagedInsert:
+ """
+ Context manager for staged insert operations.
+
+ Allows direct writes to object storage before finalizing the database insert.
+ Used for large objects like Zarr arrays where copying from local storage
+ is inefficient.
+
+ Usage:
+ with table.staged_insert1 as staged:
+ staged.rec['subject_id'] = 123
+ staged.rec['session_id'] = 45
+
+ # Write directly to object storage
+ z = zarr.open(staged.store('raw_data', '.zarr'), mode='w', shape=(1000, 1000))
+ z[:] = data
+
+ # On clean exit: metadata is computed and the row is inserted.
+ # The caller does NOT assign anything to staged.rec[
+
+ 
+
+ 
+
+ 
+
+ 
+
+ 
+
+