diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7ebfe9b56d0255c36e8552b86691dbf9da3cba4f..f989ba0266a4fda67ffb71bc9e900c21a20484ed 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,13 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [0.13.2] - 2023-12-15
+
+### Fixed ###
+
+* [#113](https://gitlab.com/linkahead/linkahead-pylib/-/issues/113) Container could fail to delete when there were reference properties.
+* HTTP status 431 (Headers too long) now also raises an URI too long exception.
+
## [0.13.1] - 2023-10-11 ##
### Fixed ###
diff --git a/CITATION.cff b/CITATION.cff
index d5cafac5caee39399f21aee100cf4acf909cca55..b9f249ed501bd1c6dd217e56d7ea47748c1032dc 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -20,6 +20,6 @@ authors:
given-names: Stefan
orcid: https://orcid.org/0000-0001-7214-8125
title: CaosDB - Pylib
-version: 0.13.1
+version: 0.13.2
doi: 10.3390/data4020083
date-released: 2023-10-11
diff --git a/setup.py b/setup.py
index 2b040aa0cdea75e68a005ac59f55124b0ebb144b..55e6ee154e2906494bece48c2f741e53e78aa2fe 100755
--- a/setup.py
+++ b/setup.py
@@ -49,7 +49,7 @@ from setuptools import find_packages, setup
ISRELEASED = True
MAJOR = 0
MINOR = 13
-MICRO = 1
+MICRO = 2
# Do not tag as pre-release until this commit
# https://github.com/pypa/packaging/pull/515
# has made it into a release. Probably we should wait for pypa/packaging>=21.4
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 68f970fd54e105eb6bcb18e1db1b162e74a972c4..84bdc6eac88b345e2b0dd04c5d1f9c413362746b 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -29,10 +29,10 @@ copyright = '2023, IndiScale GmbH'
author = 'Daniel Hornung'
# The short X.Y version
-version = '0.13.1'
+version = '0.13.2'
# The full version, including alpha/beta/rc tags
# release = '0.5.2-rc2'
-release = '0.13.1'
+release = '0.13.2'
# -- General configuration ---------------------------------------------------
diff --git a/src/doc/index.rst b/src/doc/index.rst
index 5e5a5e8801b0bd4c91ce225766d7973ee8fa2b92..24373d4d7c7d68be51915b25cc6201a84a6a4dc0 100644
--- a/src/doc/index.rst
+++ b/src/doc/index.rst
@@ -14,13 +14,19 @@ Welcome to PyLinkAhead's documentation!
Administration <administration>
High Level API <high_level_api>
Code gallery <gallery/index>
- API documentation<_apidoc/linkahead>
+ API documentation <_apidoc/linkahead>
+ Back to Overview <https://docs.indiscale.com/>
+
This is the documentation for the Python client library for LinkAhead, ``PyLinkAhead``.
This documentation helps you to :doc:`get started<README_SETUP>`, explains the most important
:doc:`concepts<concepts>` and offers a range of :doc:`tutorials<tutorials/index>`.
+Or go back to the general `overview`_ of the documentation.
+
+.. _overview: https://docs.indiscale.com/
+
Indices and tables
==================
diff --git a/src/linkahead/common/datatype.py b/src/linkahead/common/datatype.py
index 832844567bca31f4c46e205094daa709a8af9e71..c0c15feca240112f1f8e33a0cd37932151fcd9f0 100644
--- a/src/linkahead/common/datatype.py
+++ b/src/linkahead/common/datatype.py
@@ -37,22 +37,35 @@ BOOLEAN = "BOOLEAN"
def LIST(datatype):
+ # FIXME May be ambiguous (if name duplicate) or insufficient (if only ID exists).
if hasattr(datatype, "name"):
datatype = datatype.name
return "LIST<" + str(datatype) + ">"
-def get_list_datatype(datatype):
- """ returns the datatype of the elements in the list """
- if not isinstance(datatype, str):
- return None
- match = re.match("LIST(<|<)(?P<datatype>.*)(>|>)", datatype)
+def get_list_datatype(datatype: str, strict: bool = False):
+ """Returns the datatype of the elements in the list. If it not a list, return None."""
+ # TODO Union[str, Entity]
+ if not isinstance(datatype, str) or not datatype.lower().startswith("list"):
+ if strict:
+ raise ValueError(f"Not a list dtype: {datatype}")
+ else:
+ return None
+ pattern = r"^[Ll][Ii][Ss][Tt]((<|<)(?P<dtype1>.*)(>|>)|\((?P<dtype2>.*)\))$"
+ match = re.match(pattern, datatype)
+
+ if match and "dtype1" in match.groupdict() and match.groupdict()["dtype1"] is not None:
+ return match.groupdict()["dtype1"]
+
+ elif match and "dtype2" in match.groupdict() and match.groupdict()["dtype2"] is not None:
+ return match.groupdict()["dtype2"]
- if match is not None:
- return match.group("datatype")
else:
- return None
+ if strict:
+ raise ValueError(f"Not a list dtype: {datatype}")
+ else:
+ return None
def is_list_datatype(datatype):
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index 75ee469bfb78f43054cffd2d29d723804ababc5f..38c1349067fce68dc3dc0311dc621bd0e383d4b0 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -63,6 +63,7 @@ from ..exceptions import (AmbiguousEntityError, AuthorizationError,
UniqueNamesError, UnqualifiedParentsError,
UnqualifiedPropertiesError)
from .datatype import (BOOLEAN, DATETIME, DOUBLE, INTEGER, TEXT,
+ get_list_datatype,
is_list_datatype, is_reference)
from .state import State
from .timezone import TimeZone
@@ -3250,14 +3251,19 @@ class Container(list):
return sync_dict
- def _test_dependencies_in_container(self, container):
- """This function returns those elements of a given container that are a dependency of another element of the same container.
+ @staticmethod
+ def _find_dependencies_in_container(container):
+ """Find elements in a container that are a dependency of another element of the same.
- Args:
- container (Container): a linkahead container
+ Parameters
+ ----------
+ container : Container
+ A LinkAhead container.
- Returns:
- [set]: a set of unique elements that are a dependency of another element of `container`
+ Returns
+ -------
+ out : set
+ A set of IDs of unique elements that are a dependency of another element of ``container``.
"""
item_id = set()
is_parent = set()
@@ -3274,28 +3280,54 @@ class Container(list):
for parents in container_item.get_parents():
is_parent.add(parents.id)
- for references in container_item.get_properties():
- if is_reference(references.datatype):
- # add only if it is a reference, not a property
-
- if references.value is None:
- continue
- elif isinstance(references.value, int):
- is_being_referenced.add(references.value)
- elif is_list_datatype(references.datatype):
- for list_item in references.value:
- if isinstance(list_item, int):
- is_being_referenced.add(list_item)
- else:
- is_being_referenced.add(list_item.id)
- else:
- try:
- is_being_referenced.add(references.value.id)
- except AttributeError:
+ for prop in container_item.get_properties():
+ prop_dt = prop.datatype
+ if is_reference(prop_dt):
+ # add only if it is a reference, not a simple property
+ # Step 1: look for prop.value
+ if prop.value is not None:
+ if isinstance(prop.value, int):
+ is_being_referenced.add(prop.value)
+ elif is_list_datatype(prop_dt):
+ for list_item in prop.value:
+ if isinstance(list_item, int):
+ is_being_referenced.add(list_item)
+ else:
+ is_being_referenced.add(list_item.id)
+ else:
+ try:
+ is_being_referenced.add(prop.value.id)
+ except AttributeError:
+ pass
+ # Step 2: Reference properties
+ if prop.is_reference():
+ if is_list_datatype(prop_dt):
+ ref_name = get_list_datatype(prop_dt)
+ try:
+ is_being_referenced.add(container.get_entity_by_name(ref_name).id)
+ except KeyError:
+ pass
+ elif isinstance(prop_dt, str):
pass
-
- if hasattr(references, 'id'):
- is_property.add(references.id)
+ else:
+ is_being_referenced.add(prop_dt.id)
+
+ if hasattr(prop, 'id'):
+ is_property.add(prop.id)
+ if isinstance(container_item, Property):
+ dtype = container_item.datatype
+ if isinstance(dtype, Entity):
+ is_being_referenced.add(dtype.id)
+ elif isinstance(dtype, str):
+ if is_list_datatype(dtype):
+ dtype = get_list_datatype(dtype)
+ try:
+ is_being_referenced.add(container.get_entity_by_name(dtype).id)
+ except KeyError:
+ pass
+ else:
+ # plain old scalar datatype
+ pass
dependent_parents = item_id.intersection(is_parent)
dependent_properties = item_id.intersection(is_property)
@@ -3312,19 +3344,18 @@ class Container(list):
name otherwise. If any entity has no id and no name a
TransactionError will be raised.
- Note: If only a name is given this could lead to ambiguities. If
- this happens, none of them will be deleted. It occurs an error
- instead.
+ Note: If only a name is given this could lead to ambiguities. If this happens, none of them
+ will be deleted. An error is raised instead.
+
"""
item_count = len(self)
# Split Container in 'chunk_size'-sized containers (if necessary) to avoid error 414 Request-URI Too Long
if item_count > chunk_size:
- dependencies = self._test_dependencies_in_container(self)
- '''
- If there are as many dependencies as entities in the container and it is larger than chunk_size it cannot be split and deleted.
- This case cannot be handled at the moment.
- '''
+ dependencies = Container._find_dependencies_in_container(self)
+
+ # If there are as many dependencies as entities in the container and it is larger than
+ # chunk_size it cannot be split and deleted. This case cannot be handled at the moment.
if len(dependencies) == item_count:
if raise_exception_on_error:
diff --git a/src/linkahead/connection/connection.py b/src/linkahead/connection/connection.py
index db6b66f17dd3eb8c4415119912d5586c6543b953..91b4a01da455d0f365e39b0b0f7359e07096e707 100644
--- a/src/linkahead/connection/connection.py
+++ b/src/linkahead/connection/connection.py
@@ -509,7 +509,8 @@ def _handle_response_status(http_response):
raise LoginFailedError(standard_message)
elif status == 403:
raise HTTPForbiddenError(standard_message)
- elif status in (413, 414):
+ elif status in (413, 414, 431):
+ # Content (413), URI (414) or complete HTTP headers (URI+headers) (431) too long
raise HTTPURITooLongError(standard_message)
elif 399 < status < 500:
raise HTTPClientError(msg=standard_message, status=status, body=body)
diff --git a/unittests/docker/Dockerfile b/unittests/docker/Dockerfile
index a5f355fe23d00449ea470fa80f81a4e8e1914242..9b848cf69c829408f3f3edd599323b6b0321e041 100644
--- a/unittests/docker/Dockerfile
+++ b/unittests/docker/Dockerfile
@@ -10,6 +10,6 @@ RUN apt-get update && \
python3-sphinx
ARG COMMIT="dev"
# TODO Rename to linkahead
-RUN git clone -b dev https://gitlab.indiscale.com/caosdb/src/linkahead-pylib.git linkahead-pylib && \
+RUN git clone -b dev https://gitlab.indiscale.com/caosdb/src/caosdb-pylib.git linkahead-pylib && \
cd linkahead-pylib && git checkout $COMMIT && pip3 install .
RUN pip3 install recommonmark sphinx-rtd-theme
diff --git a/unittests/test_apiutils.py b/unittests/test_apiutils.py
index bb6f978bb83c4ee32cc485f538b8807c8f7012dd..b9a02926803c1e7b8134cde904ea2021d0281ff4 100644
--- a/unittests/test_apiutils.py
+++ b/unittests/test_apiutils.py
@@ -362,6 +362,20 @@ def test_bug_109():
r_a)
+@pytest.mark.xfail(reason="Issue https://gitlab.com/linkahead/linkahead-pylib/-/issues/111")
+def test_failing_merge_entities_111():
+ prop_a = db.Property()
+ prop_parent = db.Property(name="prop_parent")
+ prop_b = db.Property(name="b", datatype=db.DOUBLE, unit="µs", value=1.1).add_parent(prop_parent)
+ print(prop_b)
+ db.apiutils.merge_entities(prop_a, prop_b)
+ assert prop_a.name == prop_b.name # OK
+ assert prop_parent.name in [par.name for par in prop_a.get_parents()] # OK
+ assert prop_a.value == prop_b.value # fails
+ assert prop_a.datatype == db.DOUBLE # fails
+ assert prop_a.unit == prop_b.unit # fails
+
+
def test_wrong_merge_conflict_reference():
"""Test a wrongly detected merge conflict in case of two records referencing
two different, but identical objects.
diff --git a/unittests/test_container.py b/unittests/test_container.py
index 113dd6223a9a8cd246b3b2998faa586fbae3da11..4cd8fefcaefee9fe6fdc5857805353227b493dfb 100644
--- a/unittests/test_container.py
+++ b/unittests/test_container.py
@@ -23,7 +23,7 @@
# ** end header
#
"""Tests for the Container class."""
-from __future__ import absolute_import
+import pytest
import linkahead as db
@@ -125,7 +125,7 @@ def test_container_dependencies_for_deletion():
record_with_parent,
record_with_property_which_is_not_a_record
])
- assert (db.Container()._test_dependencies_in_container(container)
+ assert (db.Container._find_dependencies_in_container(container)
== {2002, 1005, 1007})
@@ -143,4 +143,38 @@ def test_container_dependencies_for_deletion_with_lists():
container = db.Container()
container.extend([record_with_list, record_referenced])
- assert db.Container()._test_dependencies_in_container(container) == {2001}
+ assert db.Container._find_dependencies_in_container(container) == {2001}
+
+
+def test_container_deletion_with_references():
+ """Test if dependencies are checked correctly.
+ """
+
+ RT1 = db.RecordType(name="RT1")
+ RT2 = db.RecordType(name="RT2").add_property(name="prop2", datatype=RT1)
+ RT3 = db.RecordType(name="RT3").add_property(name="prop3", datatype="LIST<RT1>")
+ prop4a = db.Property(name="prop4a", datatype=RT1)
+ prop4b = db.Property(name="prop4b", datatype="RT1")
+ prop5 = db.Property(name="prop5", datatype="LIST<RT1>")
+ cont12 = db.Container().extend([RT1, RT2])
+ cont13 = db.Container().extend([RT1, RT3])
+ cont14a = db.Container().extend([RT1, prop4a])
+ cont14b = db.Container().extend([RT1, prop4b])
+ cont15 = db.Container().extend([RT1, prop5])
+ cont12.to_xml()
+ cont13.to_xml()
+ cont14a.to_xml()
+ cont14b.to_xml()
+ cont15.to_xml()
+
+ deps12 = db.Container._find_dependencies_in_container(cont12)
+ deps13 = db.Container._find_dependencies_in_container(cont13)
+ deps14a = db.Container._find_dependencies_in_container(cont14a)
+ deps14b = db.Container._find_dependencies_in_container(cont14b)
+ deps15 = db.Container._find_dependencies_in_container(cont15)
+
+ assert len(deps12) == 1 and deps12.pop() == -1
+ assert len(deps13) == 1 and deps13.pop() == -1
+ assert len(deps14a) == 1 and deps14a.pop() == -1
+ assert len(deps14b) == 1 and deps14b.pop() == -1
+ assert len(deps15) == 1 and deps15.pop() == -1
diff --git a/unittests/test_datatype.py b/unittests/test_datatype.py
index 5a5e82cc5bfba9ac46a91b4baf4fe45665049c84..838edc120755e564cd6d237193a354c20652d492 100644
--- a/unittests/test_datatype.py
+++ b/unittests/test_datatype.py
@@ -33,6 +33,17 @@ def test_list_utilites():
"""Test for example if get_list_datatype works."""
dtype = db.LIST(db.INTEGER)
assert datatype.get_list_datatype(dtype) == db.INTEGER
+ assert datatype.get_list_datatype("LIST(Person)") == "Person"
+ assert datatype.get_list_datatype("Person") is None
+ assert datatype.get_list_datatype("LIST[]") is None
+ with raises(ValueError):
+ datatype.get_list_datatype("LIST[]", strict=True)
+ with raises(ValueError):
+ datatype.get_list_datatype("Person", strict=True)
+ with raises(ValueError):
+ datatype.get_list_datatype(5, strict=True)
+ with raises(ValueError):
+ datatype.get_list_datatype("listlol", strict=True)
def test_parsing_of_intger_list_values():