datajoint 0.14.4__py3-none-any.whl → 0.14.5__py3-none-any.whl

datajoint/autopopulate.py

@@ -95,13 +95,76 @@ class AutoPopulate:
 
     def make(self, key):
         """
-        Derived classes must implement method `make` that fetches data from tables
-        above them in the dependency hierarchy, restricting by the given key,
-        computes secondary attributes, and inserts the new tuples into self.
+        This method must be implemented by derived classes to perform automated computation.
+        The method must implement the following three steps:
+
+        1. Fetch data from tables above in the dependency hierarchy, restricted by the given key.
+        2. Compute secondary attributes based on the fetched data.
+        3. Insert the new tuple(s) into the current table.
+
+        The method can be implemented either as:
+        (a) Regular method: All three steps are performed in a single database transaction.
+            The method must return None.
+        (b) Generator method:
+            The make method is split into three functions:
+            - `make_fetch`: Fetches data from the parent tables.
+            - `make_compute`: Computes secondary attributes based on the fetched data.
+            - `make_insert`: Inserts the computed data into the current table.
+
+            Then populate logic is executes as follows:
+
+            <pseudocode>
+            fetched_data1 = self.make_fetch(key)
+            computed_result = self.make_compute(key, *fetched_data1)
+            begin transaction:
+                fetched_data2 = self.make_fetch(key)
+                if fetched_data1 != fetched_data2:
+                    cancel transaction
+                else:
+                    self.make_insert(key, *computed_result)
+                    commit_transaction
+            <pseudocode>
+
+        Importantly, the output of make_fetch is a tuple that serves as the input into `make_compute`.
+        The output of `make_compute` is a tuple that serves as the input into `make_insert`.
+
+        The functionality must be strictly divided between these three methods:
+        - All database queries must be completed in `make_fetch`.
+        - All computation must be completed in `make_compute`.
+        - All database inserts must be completed in `make_insert`.
+
+        DataJoint may programmatically enforce this separation in the future.
+
+        :param key: The primary key value used to restrict the data fetching.
+        :raises NotImplementedError: If the derived class does not implement the required methods.
         """
-        raise NotImplementedError(
-            "Subclasses of AutoPopulate must implement the method `make`"
-        )
+
+        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)  # 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
 
     @property
     def target(self):
@@ -203,9 +266,8 @@ class AutoPopulate:
             self.connection.schemas[self.target.database].jobs if reserve_jobs else None
         )
 
-        # define and set up signal handler for SIGTERM:
         if reserve_jobs:
-
+            # Define a signal handler for SIGTERM
             def handler(signum, frame):
                 logger.info("Populate terminated by SIGTERM")
                 raise SystemExit("SIGTERM received")
@@ -350,9 +412,10 @@ class AutoPopulate:
                     != deepdiff.DeepHash(fetched_data, ignore_iterable_order=False)[
                         fetched_data
                     ]
-                ):  # rollback due to referential integrity fail
-                    self.connection.cancel_transaction()
-                    return False
+                ):  # 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:

datajoint/blob.py

@@ -140,7 +140,7 @@ class Blob:
                 "S": self.read_struct,  # matlab struct array
                 "C": self.read_cell_array,  # matlab cell array
                 # basic data types
-                "\xFF": self.read_none,  # None
+                "\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
@@ -401,7 +401,7 @@ class Blob:
 
     @staticmethod
     def pack_none():
-        return b"\xFF"
+        return b"\xff"
 
     def read_tuple(self):
         return tuple(

datajoint/condition.py

@@ -1,4 +1,4 @@
-""" methods for generating SQL WHERE clauses from datajoint restriction conditions """
+"""methods for generating SQL WHERE clauses from datajoint restriction conditions"""
 
 import collections
 import datetime

datajoint/diagram.py

@@ -35,7 +35,7 @@ if not diagram_active:
         Entity relationship diagram, currently disabled due to the lack of required packages: matplotlib and pygraphviz.
 
         To enable Diagram feature, please install both matplotlib and pygraphviz. For instructions on how to install
-        these two packages, refer to https://datajoint.com/docs/core/datajoint-python/0.14/client/install/
+        these two packages, refer to https://docs.datajoint.com/core/datajoint-python/0.14/client/install/
         """
 
         def __init__(self, *args, **kwargs):

datajoint/preview.py

@@ -1,4 +1,4 @@
-""" methods for generating previews of query expression results in python command line and Jupyter """
+"""methods for generating previews of query expression results in python command line and Jupyter"""
 
 from .settings import config
 

datajoint/table.py

@@ -137,7 +137,7 @@ class Table(QueryExpression):
         sql, external_stores = alter(self.definition, old_definition, context)
         if not sql:
             if prompt:
-                logger.warn("Nothing to alter.")
+                logger.warning("Nothing to alter.")
         else:
             sql = "ALTER TABLE {tab}\n\t".format(
                 tab=self.full_table_name
@@ -520,7 +520,13 @@ class Table(QueryExpression):
                 try:
                     delete_count = table.delete_quick(get_count=True)
                 except IntegrityError as error:
-                    match = foreign_key_error_regexp.match(error.args[0]).groupdict()
+                    match = foreign_key_error_regexp.match(error.args[0])
+                    if match is None:
+                        raise DataJointError(
+                            "Cascading deletes failed because the error message is missing foreign key information."
+                            "Make sure you have REFERENCES privilege to all dependent tables."
+                        ) from None
+                    match = match.groupdict()
                     # if schema name missing, use table
                     if "`.`" not in match["child"]:
                         match["child"] = "{}.{}".format(
@@ -643,7 +649,7 @@ class Table(QueryExpression):
         # Confirm and commit
         if delete_count == 0:
             if safemode:
-                logger.warn("Nothing to delete.")
+                logger.warning("Nothing to delete.")
             if transaction:
                 self.connection.cancel_transaction()
         elif not transaction:
@@ -653,12 +659,12 @@ class Table(QueryExpression):
                 if transaction:
                     self.connection.commit_transaction()
                 if safemode:
-                    logger.info("Deletes committed.")
+                    logger.info("Delete committed.")
             else:
                 if transaction:
                     self.connection.cancel_transaction()
                 if safemode:
-                    logger.warn("Deletes cancelled")
+                    logger.warning("Delete cancelled")
         return delete_count
 
     def drop_quick(self):
@@ -726,11 +732,6 @@ class Table(QueryExpression):
         ).fetchone()
         return ret["Data_length"] + ret["Index_length"]
 
-    def show_definition(self):
-        raise AttributeError(
-            "show_definition is deprecated. Use the describe method instead."
-        )
-
     def describe(self, context=None, printout=False):
         """
         :return:  the definition string for the query using DataJoint DDL.

datajoint/utils.py

@@ -147,3 +147,5 @@ def parse_sql(filepath):
                     if line.endswith(delimiter):
                         yield " ".join(statement)
                         statement = []
+        if statement:
+            yield " ".join(statement)

datajoint/version.py

@@ -1,6 +1,6 @@
 # version bump auto managed by Github Actions:
 # label_prs.yaml(prep), release.yaml(bump), post_release.yaml(edit)
 # manually set this version will be eventually overwritten by the above actions
-__version__ = "0.14.4"
+__version__ = "0.14.5"
 
 assert len(__version__) <= 10  # The log table limits version to the 10 characters

{datajoint-0.14.4.dist-info → datajoint-0.14.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: datajoint
-Version: 0.14.4
+Version: 0.14.5
 Summary: 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.
 Author: Raphael Guzman, Edgar Walker
 Author-email: Dimitri Yatsenko <dimitri@datajoint.com>, DataJoint Contributors <support@datajoint.com>
@@ -510,8 +510,8 @@ License:  GNU LESSER GENERAL PUBLIC LICENSE
         
         That's all there is to it!
         
-Project-URL: Homepage, https://datajoint.com/docs
-Project-URL: Documentation, https://datajoint.com/docs
+Project-URL: Homepage, https://docs.datajoint.com/
+Project-URL: Documentation, https://docs.datajoint.com/
 Project-URL: Repository, https://github.com/datajoint/datajoint-python
 Project-URL: Bug Tracker, https://github.com/datajoint/datajoint-python/issues
 Project-URL: Release Notes, https://github.com/datajoint/datajoint-python/releases
@@ -589,8 +589,8 @@ Dynamic: license-file
 <tr>
   <td>Since Release</td>
   <td>
-    <a id="commit-since-release-link" href="https://github.com/datajoint/datajoint-python/compare/v0.14.4...master">
-      <img id="commit-since-release-img" src="https://img.shields.io/github/commits-since/datajoint/datajoint-python/v0.14.4?color=red" alt="commit since last release" />
+    <a id="commit-since-release-link" href="https://github.com/datajoint/datajoint-python/compare/v0.14.5...master">
+      <img id="commit-since-release-img" src="https://img.shields.io/github/commits-since/datajoint/datajoint-python/v0.14.5?color=red" alt="commit since last release" />
     </a>
   </td>
 </tr>
@@ -613,7 +613,7 @@ Dynamic: license-file
 <tr>
   <td>Doc Status</td>
   <td>
-    <a href="https://datajoint.com/docs">
+    <a href="https://docs.datajoint.com">
       <img src="https://github.com/datajoint/datajoint-python/actions/workflows/pages/pages-build-deployment/badge.svg" alt="doc status" />
     </a>
   </td>
@@ -627,12 +627,12 @@ Dynamic: license-file
   </td>
 </tr>
 <tr>
-	<td>Developer Chat</td>
-	<td>
-		<a href="https://datajoint.slack.com/">
+ <td>Developer Chat</td>
+ <td>
+  <a href="https://datajoint.slack.com/">
       <img src="https://img.shields.io/badge/slack-datajoint-purple.svg" alt="datajoint slack"/>
-		</a>
-	</td>
+  </a>
+ </td>
 </tr>
 <tr>
   <td>License</td>
@@ -643,21 +643,20 @@ Dynamic: license-file
   </td>
 </tr>
 <tr>
-	<td>Citation</td>
-	<td>
-		<a href="https://doi.org/10.1101/031658">
-			<img src="https://img.shields.io/badge/DOI-10.1101/bioRxiv.031658-B31B1B.svg" alt="bioRxiv">
-		</a>
+ <td>Citation</td>
+ <td>
+  <a href="https://doi.org/10.1101/031658">
+   <img src="https://img.shields.io/badge/DOI-10.1101/bioRxiv.031658-B31B1B.svg" alt="bioRxiv">
+  </a>
     <br>
     <a href="https://doi.org/10.5281/zenodo.6829062">
       <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.6829062.svg" alt="zenodo">
-		</a>
-	</td>
+  </a>
+ </td>
 </tr>
 
 </table>
 
-
 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
@@ -669,7 +668,7 @@ volumes of data streaming from regular experiments. Starting in 2011, DataJoint
 been available as an open-source project adopted by other labs and improved through
 contributions from several developers.
 Presently, the primary developer of DataJoint open-source software is the company
-DataJoint (https://datajoint.com).
+DataJoint (<https://datajoint.com>).
 
 ## Data Pipeline Example
 
@@ -691,13 +690,13 @@ DataJoint (https://datajoint.com).
      pip install datajoint
      ```
 
-- [Documentation & Tutorials](https://datajoint.com/docs/core/datajoint-python/)
+- [Documentation & Tutorials](https://docs.datajoint.com/core/datajoint-python/)
 
 - [Interactive Tutorials](https://github.com/datajoint/datajoint-tutorials) on GitHub Codespaces
 
-- [DataJoint Elements](https://datajoint.com/docs/elements/) - Catalog of example pipelines for neuroscience experiments
+- [DataJoint Elements](https://docs.datajoint.com/elements/) - Catalog of example pipelines for neuroscience experiments
 
 - Contribute
-  - [Contribution Guidelines](https://datajoint.com/docs/about/contribute/)
+  - [Contribution Guidelines](https://docs.datajoint.com/about/contribute/)
 
-  - [Developer Guide](https://datajoint.com/docs/core/datajoint-python/latest/develop/)
+  - [Developer Guide](https://docs.datajoint.com/core/datajoint-python/latest/develop/)

{datajoint-0.14.4.dist-info → datajoint-0.14.5.dist-info}/RECORD

@@ -1,14 +1,14 @@
 datajoint/__init__.py,sha256=uKCJiD2Vx-smjvfEPVBvxE3VXfm27WfHwKmF2s0r31w,2048
 datajoint/admin.py,sha256=4FEQxrFtWz3Q9h9OCvytDsnx-W6HxXgsjF-TypHfRd8,4500
 datajoint/attribute_adapter.py,sha256=bMcTyb0hIPb6CMVaevZ3FUMkWPbzMCoIj8gJvkQ8tI8,2333
-datajoint/autopopulate.py,sha256=F3JCslaHMpQMn1tZ2m5YU6LeG9m3kX5XqRKSZNj9s8c,15706
-datajoint/blob.py,sha256=1QJ394gPsYc87x8mdJ3nal5tYc2YxZIKxkwqBTAswb4,21968
+datajoint/autopopulate.py,sha256=ZhWmIcuxpW9Dd_vYUMalFeAccd9M_y7PQ0w7RKeye0I,18681
+datajoint/blob.py,sha256=0XK_UBesZja-UjDOPY0gNLVURaXcTCN-rDWTc2VbEXU,21968
 datajoint/cli.py,sha256=4ZZAtAn3_7bqi2hMbn_I541RIWDEcwHOwqZyEvHbr0E,2065
-datajoint/condition.py,sha256=kZdc7u4F77IPuAoc6YUq71ljgPU_-zcNfZt3jplke3Y,11850
+datajoint/condition.py,sha256=zZhq2F0FslZkp2oiMvaCee0FGxxd9mlvZPVeDvM69SU,11848
 datajoint/connection.py,sha256=zOh3Akvxlb7WeciTFQNuUBhWxhziwWReGCRVGDxZ1z8,15984
 datajoint/declare.py,sha256=rXtH8riupNGXWIouxLvwta9Zwm4I2quTktBrP0fPZTA,21106
 datajoint/dependencies.py,sha256=LDMVZ7tKZWrh7mbjECk73Jk1gXSxVOsLefwJSRXe3vg,8413
-datajoint/diagram.py,sha256=9k_UHXH-thBbFSNbehUqCJ6MOnX7rBLitBt0yF9R5TA,18027
+datajoint/diagram.py,sha256=3a5Wrz9cjbOp4YD7C-fRsvZY1zqGLw8g6qso16ml-4E,18027
 datajoint/errors.py,sha256=FuD5QO-cIt4fNf8BSmjwypuM-k0P3qNYcjjuhPiE7jM,3337
 datajoint/expression.py,sha256=HKS-Gt1HbOs1hgwFHci2d2MbQgecZWaKtJtE1HaPVSA,39098
 datajoint/external.py,sha256=9p0M81zR8ifks2_Q4KMP9Rq14bqAAZJGHLXR5OiMjFU,19127
@@ -18,17 +18,17 @@ datajoint/heading.py,sha256=LJLIYMT2hwT2XgNbxOKBUcU3fcyuHpD2J5l9nWDI05k,19417
 datajoint/jobs.py,sha256=T1m921P_QOo7keY9bm1RUE0hvZi2G4VWhb4zgTpMWmw,5630
 datajoint/logging.py,sha256=n_dRV3CuTef7wYrVIbhSm9pAKDMWm_XD4oOJ1kMIen4,687
 datajoint/plugin.py,sha256=VA0Wc8gxDMB1cy4MoBN40TbrkfWD-Cqi_j1JQN-HXYA,1555
-datajoint/preview.py,sha256=MXOEJaivLRZe48QtTKK4oNJGeZ5kQP_Srnm4_-s5HRk,4808
+datajoint/preview.py,sha256=woHXMVVkW1E9AkAoNjRQdcCkcaW4svB0oHrL4oEXCNE,4806
 datajoint/s3.py,sha256=-BU65VYY3I1l9wD1JeIotfOr-PQ5BzT85fbFE6iYtIY,4083
 datajoint/schemas.py,sha256=xRY5OMlBV9Qup22CFP5gwcvRCOnOUbzNSn7EGtGHe40,20063
 datajoint/settings.py,sha256=fJ5A7HR8aTb0HvN4GQ4eLwtmQxdyB11l6sMiguaQoz8,9406
-datajoint/table.py,sha256=6Eep0EAadkhhe8TTSLQrj8zduvSLLznkrHl6w8bMb14,44962
+datajoint/table.py,sha256=vVzeec-z1tFKYFDWCh6ArJi5sysdNTJWaTteAavwIsE,45185
 datajoint/user_tables.py,sha256=vcnO-8NET543LwlzvI6y8yTmw-UHMUe7VuMk1EKp-8I,6941
-datajoint/utils.py,sha256=E5-YCModfkqwmQCm74TpGu9fum5hFTiXoZCE0LUFSQk,4516
-datajoint/version.py,sha256=5qCfK0oUQNWIG95OVu9yn6G7SCQogZq_nd86Q1Kk-Oc,302
-datajoint-0.14.4.dist-info/licenses/LICENSE.txt,sha256=7VXUyqv9idbgJNkr3OFy0vfuSqZa3JHmC2TpSavBpss,26444
-datajoint-0.14.4.dist-info/METADATA,sha256=3SIR7YJ2BHpOLVrGCD_RlXURYGQVQyBj6vwr5aLXQdA,37819
-datajoint-0.14.4.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-datajoint-0.14.4.dist-info/entry_points.txt,sha256=RLoyQD_Hz9HdlKG-ei0SlHDxuaTpasDJ6gZcvj9iZG0,71
-datajoint-0.14.4.dist-info/top_level.txt,sha256=GLPeIbF_-lu3lpcSazCl0KUco1v2rr5uyUvieYAniLU,10
-datajoint-0.14.4.dist-info/RECORD,,
+datajoint/utils.py,sha256=m-tnRa65dkwdCV6qqUG7kYHsIaFJGPSVr22QpHzeCZc,4576
+datajoint/version.py,sha256=0J3S_RIdt9bVt0MteMQlEy0auezr5cWmUqFiP90qpzw,302
+datajoint-0.14.5.dist-info/licenses/LICENSE.txt,sha256=7VXUyqv9idbgJNkr3OFy0vfuSqZa3JHmC2TpSavBpss,26444
+datajoint-0.14.5.dist-info/METADATA,sha256=vnpbGSX4jahjFspaxbLoq972sKd5qKxi4hl_r_iU5UA,37822
+datajoint-0.14.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+datajoint-0.14.5.dist-info/entry_points.txt,sha256=RLoyQD_Hz9HdlKG-ei0SlHDxuaTpasDJ6gZcvj9iZG0,71
+datajoint-0.14.5.dist-info/top_level.txt,sha256=GLPeIbF_-lu3lpcSazCl0KUco1v2rr5uyUvieYAniLU,10
+datajoint-0.14.5.dist-info/RECORD,,

{datajoint-0.14.4.dist-info → datajoint-0.14.5.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any