diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 792ab22f1524f8d4dc1db90f2b65c7f8f28f90ed..0430a4f6b5ac08d4ab38f00bff78b845e11fb97e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -54,18 +54,25 @@ pylint:
allow_failure: true
# run unit tests
-unittest_py3.8:
+unittest_py3.7:
tags: [ docker ]
stage: test
needs: [ ]
- image: python:3.8
+ image: python:3.7
script: &python_test_script
# Python docker has problems with tox and pip so use plain pytest here
- touch ~/.pycaosdb.ini
- - pip install nose pytest pytest-cov python-dateutil jsonschema==4.0.1
+ - pip install nose pytest pytest-cov python-dateutil jsonschema>=4.4.0
- pip install .
- python -m pytest unittests
+unittest_py3.8:
+ tags: [ docker ]
+ stage: test
+ needs: [ ]
+ image: python:3.8
+ script: *python_test_script
+
# This needs to be changed once Python 3.9 isn't the standard Python in Debian
# anymore.
unittest_py3.9:
@@ -86,6 +93,13 @@ unittest_py3.10:
image: python:3.10
script: *python_test_script
+unittest_py3.11:
+ tags: [ docker ]
+ stage: test
+ needs: [ ]
+ image: python:3.11
+ script: *python_test_script
+
# Trigger building of server image and integration tests
trigger_build:
stage: deploy
diff --git a/.gitlab/issue_templates/Default.md b/.gitlab/issue_templates/Default.md
new file mode 100644
index 0000000000000000000000000000000000000000..aa1a65aca363b87aff50280e1a86824009d2098b
--- /dev/null
+++ b/.gitlab/issue_templates/Default.md
@@ -0,0 +1,28 @@
+## Summary
+
+*Please give a short summary of what the issue is.*
+
+## Expected Behavior
+
+*What did you expect how the software should behave?*
+
+## Actual Behavior
+
+*What did the software actually do?*
+
+## Steps to Reproduce the Problem
+
+*Please describe, step by step, how others can reproduce the problem. Please try these steps for yourself on a clean system.*
+
+1.
+2.
+3.
+
+## Specifications
+
+- Version: *Which version of this software?*
+- Platform: *Which operating system, which other relevant software versions?*
+
+## Possible fixes
+
+*Do you have ideas how the issue can be resolved?*
diff --git a/.gitlab/merge_request_templates/Default.md b/.gitlab/merge_request_templates/Default.md
new file mode 100644
index 0000000000000000000000000000000000000000..35c6d01c5904289b77fc7f1de9419ef91a1510e9
--- /dev/null
+++ b/.gitlab/merge_request_templates/Default.md
@@ -0,0 +1,54 @@
+# Summary
+
+*Insert a meaningful description for this merge request here: What is the new/changed behavior?
+Which bug has been fixed? Are there related issues?*
+
+
+# Focus
+
+*Point the reviewer to the core of the code change. Where should they start reading? What should
+they focus on (e.g. security, performance, maintainability, user-friendliness, compliance with the
+specs, finding more corner cases, concrete questions)?*
+
+
+# Test Environment
+
+*How to set up a test environment for manual testing?*
+
+
+# Check List for the Author
+
+Please, prepare your MR for a review. Be sure to write a summary and a focus and create gitlab
+comments for the reviewer. They should guide the reviewer through the changes, explain your changes
+and also point out open questions. For further good practices have a look at [our review
+guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md)
+
+- [ ] All automated tests pass
+- [ ] Reference related issues
+- [ ] Up-to-date CHANGELOG.md (or not necessary)
+- [ ] Up-to-date JSON schema (or not necessary)
+- [ ] Appropriate user and developer documentation (or not necessary)
+ - How do I use the software? Assume "stupid" users.
+ - How do I develop or debug the software? Assume novice developers.
+- [ ] Annotations in code (Gitlab comments)
+ - Intent of new code
+ - Problems with old code
+ - Why this implementation?
+
+
+# Check List for the Reviewer
+
+- [ ] I understand the intent of this MR
+- [ ] All automated tests pass
+- [ ] Up-to-date CHANGELOG.md (or not necessary)
+- [ ] Appropriate user and developer documentation (or not necessary)
+- [ ] The test environment setup works and the intended behavior is reproducible in the test
+ environment
+- [ ] In-code documentation and comments are up-to-date.
+- [ ] Check: Are there specifications? Are they satisfied?
+
+For further good practices have a look at [our review guidelines](https://gitlab.com/caosdb/caosdb/-/blob/dev/REVIEW_GUIDELINES.md).
+
+
+/assign me
+/target_branch dev
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0d63406b65c1d466c69cd6e90593bc8ce3095734..dfa9efbddabc8958845d33ac8e74c99da342e5e4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,7 +21,41 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Documentation ###
-* [Fixed](https://gitlab.com/caosdb/caosdb-pylib/-/issues/79) `{action}_entity_permissions` help line.
+## [0.11.1] - 2023-03-07 ##
+(Florian Spreckelsen)
+
+### Changed ###
+
+* Renamed `caosdb.common.models._Parents` to `caosdb.common.models._ParentList`.
+
+### Fixed ###
+
+* [caosdb-pylib#90](https://gitlab.com/caosdb/caosdb-pylib/-/issues/90): `Entity.get_parents_recursively()` did not work for unretrieved parents.
+
+## [0.11.0] - 2023-01-19 ##
+(Florian Spreckelsen)
+
+### Added ###
+
+* `apiutils.EntityMergeConflictError` class for unresesolvable merge conflicts
+ when merging two entities
+* Re-introduced support for Python 3.7
+
+### Changed ###
+
+* `apiutils.merge_entities` now raises an `EntityMergeConflictError` in case of
+ unresolvable merge conflicts.
+
+### Fixed ###
+
+* [#82](https://gitlab.com/caosdb/caosdb-pylib/-/issues/82) Merging an entity
+ with properties with missing datatype leads to Exception - The correct
+ exception is raised in case of a missing LIST datatype.
+
+### Documentation ###
+
+* [Fixed](https://gitlab.com/caosdb/caosdb-pylib/-/issues/79)
+ `{action}_entity_permissions` help line.
## [0.10.0] - 2022-11-14
(Florian Spreckelsen)
diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000000000000000000000000000000000000..910e40a2193d527fc8e4eb68c4ca6b10a28d3630
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,25 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+ - family-names: Fitschen
+ given-names: Timm
+ orcid: https://orcid.org/0000-0002-4022-432X
+ - family-names: Schlemmer
+ given-names: Alexander
+ orcid: https://orcid.org/0000-0003-4124-9649
+ - family-names: Hornung
+ given-names: Daniel
+ orcid: https://orcid.org/0000-0002-7846-6375
+ - family-names: tom Wörden
+ given-names: Henrik
+ orcid: https://orcid.org/0000-0002-5549-578X
+ - family-names: Parlitz
+ given-names: Ulrich
+ orcid: https://orcid.org/0000-0003-3058-1435
+ - family-names: Luther
+ given-names: Stefan
+ orcid: https://orcid.org/0000-0001-7214-8125
+title: CaosDB - Pylib
+version: 0.11.1
+doi: 10.3390/data4020083
+date-released: 2022-11-14
\ No newline at end of file
diff --git a/README.md b/README.md
index 602df33cecfc8ec37fd791e3257221e66f120cb3..7215591a4f31f1946029442de291eb9ccf9beea1 100644
--- a/README.md
+++ b/README.md
@@ -39,7 +39,7 @@ By participating, you are expected to uphold our [Code of Conduct](https://gitla
* If you have a suggestion for the [documentation](https://docs.indiscale.com/caosdb-pylib/),
the preferred way is also a merge request as describe above (the documentation resides in `src/doc`).
However, you can also create an issue for it.
-* You can also contact us at **info (AT) caosdb.de** and join the
+* You can also contact us at **info (AT) caosdb.org** and join the
CaosDB community on
[#caosdb:matrix.org](https://matrix.to/#/!unwwlTfOznjEnMMXxf:matrix.org).
diff --git a/README_SETUP.md b/README_SETUP.md
index 48928d6c3f2c878a8d8b268b36ed2cdeba7f8014..01eea85188078ae6f2fe226e89e5c227497b4bd0 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -109,6 +109,8 @@ Now would be a good time to continue with the [tutorials](tutorials/index).
- Run a specific test function: e.g. `tox -- unittests/test_schema.py::test_config_files`
## Documentation ##
+We use sphinx to create the documentation. Docstrings in the code should comply
+with the Googly style (see link below).
Build documentation in `build/` with `make doc`.
@@ -118,5 +120,11 @@ Build documentation in `build/` with `make doc`.
- `sphinx-autoapi`
- `recommonmark`
+### How to contribute ###
+
+- [Google Style Python Docstrings](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html)
+- [Google Style Python Docstrings 2nd reference](https://github.com/google/styleguide/blob/gh-pages/pyguide.md#38-comments-and-docstrings)
+- [References to other documentation](https://www.sphinx-doc.org/en/master/usage/extensions/intersphinx.html#role-external)
+
### Troubleshooting ###
If the client is to be executed directly from the `/src` folder, an initial `.\setup.py install --user` must be called.
diff --git a/RELEASE_GUIDELINES.md b/RELEASE_GUIDELINES.md
index 863afb8f3ac7d6770c372620523638b900785227..95ee8e314871153476c30790a456242e38dcaf9e 100644
--- a/RELEASE_GUIDELINES.md
+++ b/RELEASE_GUIDELINES.md
@@ -24,6 +24,7 @@ guidelines of the CaosDB Project
- `version` variables in `src/doc/conf.py`
- Version on [setup.py](./setup.py): Check the `MAJOR`, `MINOR`, `MICRO`, `PRE` variables and set
`ISRELEASED` to `True`. Use the possibility to issue pre-release versions for testing.
+ - `CITATION.cff` (update version and date)
5. Merge the release branch into the main branch.
diff --git a/pytest.ini b/pytest.ini
deleted file mode 100644
index ca6aad829a3e0607292cf69b8b1d4b7f7758993e..0000000000000000000000000000000000000000
--- a/pytest.ini
+++ /dev/null
@@ -1,3 +0,0 @@
-[pytest]
-testpaths=unittests
-addopts=-x -vv --cov=caosdb
diff --git a/setup.py b/setup.py
index 35d6d69a83338a0dc543b4b6438b56c1372b7237..a6d3594c7f37820cd4f5e66cb9761651d0c47907 100755
--- a/setup.py
+++ b/setup.py
@@ -47,8 +47,8 @@ from setuptools import find_packages, setup
ISRELEASED = False
MAJOR = 0
-MINOR = 10
-MICRO = 1
+MINOR = 11
+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
@@ -171,10 +171,10 @@ def setup_package():
"Topic :: Scientific/Engineering :: Information Analysis",
],
packages=find_packages('src'),
- python_requires='>=3.8',
+ python_requires='>=3.7',
package_dir={'': 'src'},
install_requires=['lxml>=4.6.3',
- "requests[socks]>=2.28.1",
+ "requests[socks]>=2.26",
"python-dateutil>=2.8.2",
'PyYAML>=5.4.1',
'future',
diff --git a/src/caosdb/apiutils.py b/src/caosdb/apiutils.py
index 0862cf9f32575b9773bc16d845bb459d67b0140c..f3195b8e152f0cb13e5dab3e3a449b7bb36623b4 100644
--- a/src/caosdb/apiutils.py
+++ b/src/caosdb/apiutils.py
@@ -27,12 +27,13 @@
Some simplified functions for generation of records etc.
"""
+import logging
import sys
import tempfile
import warnings
+
from collections.abc import Iterable
from subprocess import call
-
from typing import Optional, Any, Dict, List
from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER,
@@ -40,8 +41,13 @@ from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER,
from caosdb.common.models import (Container, Entity, File, Property, Query,
Record, RecordType, execute_query,
get_config, SPECIAL_ATTRIBUTES)
+from caosdb.exceptions import CaosDBException
-import logging
+
+class EntityMergeConflictError(CaosDBException):
+ """An error that is raised in case of an unresolvable conflict when merging
+ two entities.
+ """
def new_record(record_type, name=None, description=None,
@@ -365,14 +371,15 @@ def empty_diff(old_entity: Entity, new_entity: Entity, compare_referenced_record
return True
-def merge_entities(entity_a: Entity, entity_b: Entity, merge_references_with_empty_diffs=True, force=False):
- """
- Merge entity_b into entity_a such that they have the same parents and properties.
+def merge_entities(entity_a: Entity, entity_b: Entity, merge_references_with_empty_diffs=True,
+ force=False):
+ """Merge entity_b into entity_a such that they have the same parents and properties.
- datatype, unit, value, name and description will only be changed in entity_a if they
- are None for entity_a and set for entity_b. If there is a corresponding value
- for entity_a different from None a RuntimeError will be raised informing of an
- unresolvable merge conflict.
+ datatype, unit, value, name and description will only be changed in entity_a
+ if they are None for entity_a and set for entity_b. If there is a
+ corresponding value for entity_a different from None, an
+ EntityMergeConflictError will be raised to inform about an unresolvable merge
+ conflict.
The merge operation is done in place.
@@ -392,13 +399,18 @@ def merge_entities(entity_a: Entity, entity_b: Entity, merge_references_with_emp
force : bool, optional
If True, in case `entity_a` and `entity_b` have the same properties, the
values of `entity_a` are replaced by those of `entity_b` in the merge.
- If `False`, a RuntimeError is raised instead. Default is False.
+ If `False`, an EntityMergeConflictError is raised instead. Default is False.
Returns
-------
entity_a : Entity
The initial entity_a after the in-place merge
+ Raises
+ ------
+ EntityMergeConflictError
+ In case of an unresolvable merge conflict.
+
"""
logging.warning(
@@ -433,8 +445,8 @@ def merge_entities(entity_a: Entity, entity_b: Entity, merge_references_with_emp
setattr(entity_a.get_property(key), attribute,
diff_r2["properties"][key][attribute])
else:
- raise RuntimeError(
- f"Merge conflict:\nEntity a ({entity_a.id}, {entity_a.name}) "
+ raise EntityMergeConflictError(
+ f"Entity a ({entity_a.id}, {entity_a.name}) "
f"has a Property '{key}' with {attribute}="
f"{diff_r2['properties'][key][attribute]}\n"
f"Entity b ({entity_b.id}, {entity_b.name}) "
@@ -463,7 +475,9 @@ def merge_entities(entity_a: Entity, entity_b: Entity, merge_references_with_emp
# force overwrite
setattr(entity_a, special_attribute, sa_b)
else:
- raise RuntimeError("Merge conflict.")
+ raise EntityMergeConflictError(
+ f"Conflict in special attribute {special_attribute}:\n"
+ f"A: {sa_a}\nB: {sa_b}")
return entity_a
diff --git a/src/caosdb/common/models.py b/src/caosdb/common/models.py
index 7000ede917995c6c01b78a822c2d39ac626fcc23..08fcd0206b9df22902e80277d0e57b5f67c76db5 100644
--- a/src/caosdb/common/models.py
+++ b/src/caosdb/common/models.py
@@ -34,6 +34,7 @@ All additional classes are either important for the entities or the
transactions.
"""
from __future__ import print_function, unicode_literals
+from __future__ import annotations # Can be removed with 3.10.
import re
import sys
@@ -62,7 +63,6 @@ from caosdb.exceptions import (AmbiguousEntityError, AuthorizationError,
EntityDoesNotExistError, EntityError,
EntityHasNoDatatypeError, HTTPURITooLongError,
MismatchingEntitiesError, QueryNotUniqueError,
- ServerConfigurationException,
TransactionError, UniqueNamesError,
UnqualifiedParentsError,
UnqualifiedPropertiesError)
@@ -83,7 +83,7 @@ SPECIAL_ATTRIBUTES = ["name", "role", "datatype", "description",
"id", "path", "checksum", "size"]
-class Entity(object):
+class Entity:
"""Entity is a generic CaosDB object.
@@ -102,6 +102,8 @@ class Entity(object):
self._checksum = None
self._size = None
self._upload = None
+ # If an entity is used (e.g. as parent), it is wrapped instead of being used directly.
+ # see Entity._wrap()
self._wrapped_entity = None
self._version = None
self._cuid = None
@@ -112,7 +114,7 @@ class Entity(object):
self.value = value
self.messages = _Messages()
self.properties = _Properties()
- self.parents = _Parents()
+ self.parents = _ParentList()
self.path = None
self.file = None
self.unit = None
@@ -531,7 +533,7 @@ class Entity(object):
value=value, unit=unit)
if abstract_property is not None:
- new_property._wrap(property)
+ new_property._wrap(abstract_property)
# FIXME: this really necessary?
@@ -622,26 +624,46 @@ class Entity(object):
return self
- def has_parent(self, parent, recursive=True,
- check_name=True, check_id=False):
- """Checks if this entity has a given parent.
+ def has_parent(self, parent: Entity, recursive: bool = True, retrieve: bool = True,
+ check_name: bool = True, check_id: bool = False):
+ """Check if this entity has a given parent.
If 'check_name' and 'check_id' are both False, test for identity
on the Python level. Otherwise use the name and/or ID for the
check. Note that, if checked, name or ID should not be None,
lest the check fail.
- @param parent: Check for this parent.
- @param recursive: Whether to check recursively.
- @param check_name: Whether to use the name for ancestry check.
- @param check_id: Whether to use the ID for ancestry check.
- @return: True if 'parent' is a true parent, False otherwise.
- """
+Parameters
+----------
+
+parent: Entity
+ Check for this parent.
+
+recursive: bool, optional
+ Whether to check recursively.
+
+check_name: bool, optional
+ Whether to use the name for ancestry check.
+
+check_id: bool, optional
+ Whether to use the ID for ancestry check.
+
+retrieve: bool, optional
+ If False, do not retrieve parents from the server.
+
+Returns
+-------
+out: bool
+ True if ``parent`` is a true parent, False otherwise.
+"""
if recursive:
- parents = self.get_parents_recursively()
+ parents = self.get_parents_recursively(retrieve=retrieve)
else:
- parents = [pp._wrapped_entity for pp in self.parents]
+ if retrieve:
+ parents = [pp.retrieve()._wrapped_entity for pp in self.parents]
+ else:
+ parents = [pp._wrapped_entity for pp in self.parents]
if not (check_name or check_id):
return parent in parents
@@ -660,39 +682,61 @@ class Entity(object):
def get_parents(self):
"""Get all parents of this entity.
- @return: _Parents(list)
+ @return: _ParentList(list)
"""
return self.parents
- def get_parents_recursively(self):
+ def get_parents_recursively(self, retrieve: bool = True):
"""Get all ancestors of this entity.
- @return: list of Entities
- """
+Parameters
+----------
- all_parents = _Parents()
- self._get_parent_recursively(all_parents)
+retrieve: bool, optional
+ If False, do not retrieve parents from the server.
+
+Returns
+-------
+out: List[Entity]
+ The parents of this Entity
+"""
+
+ all_parents = []
+ self._get_parent_recursively(all_parents, retrieve=retrieve)
return all_parents
- def _get_parent_recursively(self, all_parents):
+ def _get_parent_recursively(self, all_parents: list, retrieve: bool = True):
"""Get all ancestors with a little helper.
As a side effect of this method, the ancestors are added to
all_parents.
- @param all_parents: The added parents so far.
+ @param all_parents: list, The added parents so far.
@return: None, but see side effects.
"""
for parent in self.parents:
+ # TODO:
+ # Comment on _wrap and _wrapped_entity
+ # Currently, I (henrik) do not why the wrapping is necessary (and it is not
+ # documented). However, the following illustrates, why I think, it is a bad idea.
+ # First you add a parent with rec.add_parent(parent), but then you cannot access
+ # attributes of parent when you use rec.parents[0] for example becasue you do not get
+ # the same object but a wrapping object and you need to know that you only get the
+ # original by accessing the private (!) _wrapped_entity object.
w_parent = parent._wrapped_entity
+ if retrieve:
+ parent.retrieve()
+ for next_parent in parent.parents:
+ w_parent.add_parent(next_parent)
- if w_parent not in all_parents:
+ if (w_parent.id, w_parent.name) not in [
+ (all_p.id, all_p.name) for all_p in all_parents]:
all_parents.append(w_parent)
- w_parent._get_parent_recursively(all_parents)
+ w_parent._get_parent_recursively(all_parents, retrieve=retrieve)
def get_parent(self, key):
"""Return the first parent matching the key or None if no match exists.
@@ -1136,7 +1180,7 @@ class Entity(object):
else:
raise TypeError(
'Child was neither a Property, nor a Parent, nor a Message.\
- Was ' + str(type(child)))
+ Was ' + str(type(child)) + "\n" + str(child))
# add VALUE
value = None
@@ -1297,6 +1341,12 @@ class Entity(object):
flags=flags)[0]
def _wrap(self, entity):
+ """
+ When entity shall be used as parent or property it is not added to the corresponding list
+ (such as the parent list) directly, but another Entity object is created and the original
+ Entity is wrapped using this function
+ TODO: document here and in dev docs why this is done.
+ """
self._wrapped_entity = entity
return self
@@ -1381,12 +1431,15 @@ def _parse_value(datatype, value):
# reference via name
return str(value)
- except TypeError:
+ except TypeError as te:
# deal with invalid XML: List of values without appropriate datatype
if isinstance(value, list):
- raise ServerConfigurationException(
- "The server sent an invalid XML: List valued properties must be announced by "
+ raise TypeError(
+ "Invalid datatype: List valued properties must be announced by "
"the datatype.\n" + f"Datatype: {datatype}\nvalue: {value}")
+ else:
+ # Everything else that's not related to wrong list assignments
+ raise te
def _log_request(request, xml_body=None):
@@ -2092,7 +2145,8 @@ class _Properties(list):
raise KeyError(str(prop) + " not found.")
-class _Parents(list):
+class _ParentList(list):
+ # TODO unclear why this class is private. Isn't it use full for users?
def _get_entity_by_cuid(self, cuid):
'''
@@ -2695,9 +2749,11 @@ class Container(list):
elif isinstance(entity, QueryTemplate):
super().append(entity)
else:
- raise TypeError(
- "Entity was neither an id nor a name nor an entity." +
- " (was " + str(type(entity)) + ")")
+ warn("Entity was neither an id nor a name nor an entity." +
+ " (was " + str(type(entity)) + ":\n" + str(entity) + ")")
+ # raise TypeError(
+ # "Entity was neither an id nor a name nor an entity." +
+ # " (was " + str(type(entity)) + "\n" + str(entity) + ")")
return self
@@ -3645,6 +3701,7 @@ class Container(list):
for p in e.get_properties():
if p.id is None:
if p.name is not None:
+ # TODO using try except for normal execution flow is bad style
try:
w = self.get_entity_by_name(p.name)
p._wrap(w)
@@ -3656,6 +3713,7 @@ class Container(list):
for p in e.get_parents():
if p.id is None:
if p.name is not None:
+ # TODO using try except for normal execution flow is bad style
try:
p._wrap(self.get_entity_by_name(p.name))
except KeyError:
diff --git a/src/caosdb/connection/connection.py b/src/caosdb/connection/connection.py
index a2802848af7bae8fb65378532156d8469f31a9b8..46dadea9dfcfa6e614493b75d709f604aa188ef6 100644
--- a/src/caosdb/connection/connection.py
+++ b/src/caosdb/connection/connection.py
@@ -287,6 +287,8 @@ class _DefaultCaosDBServerConnection(CaosDBServerConnection):
"Insecure SSL mode, certificate will not be checked! "
"Please consider removing the `ssl_insecure` configuration option.\n"
"****************")
+ warnings.filterwarnings(action="ignore", module="urllib3",
+ message="Unverified HTTPS request is being made")
verify = False
if verify is not None:
self._session.verify = verify
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 15fa844e546a40efa99f577944c377f0a6a0c19a..292aa7a2a427da7044c9d6acf7b000cd2fa82a32 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -29,10 +29,10 @@ copyright = '2022, IndiScale GmbH'
author = 'Daniel Hornung'
# The short X.Y version
-version = '0.10.1'
+version = '0.11.2'
# The full version, including alpha/beta/rc tags
# release = '0.5.2-rc2'
-release = '0.10.1-dev'
+release = '0.11.2-dev'
# -- General configuration ---------------------------------------------------
diff --git a/src/doc/tutorials/basic_analysis.rst b/src/doc/tutorials/basic_analysis.rst
index cc185e0ee08f9e5ee0f890c0ab55f52972882d17..c40cad28b8c9a3be537c641b9614da2eb4df8dd9 100644
--- a/src/doc/tutorials/basic_analysis.rst
+++ b/src/doc/tutorials/basic_analysis.rst
@@ -34,7 +34,7 @@ Often we are interested in table like data for our processing. And the disentang
>>> from caosadvancedtools.table_converter import to_table
>>> # Let us retrieve the data in a table like form using `SELECT`
->>> data = db.execute_query("SELECT quality_factor FROM RECORD Analysis with quality_factor" )
+>>> data = db.execute_query("SELECT quality_factor FROM Analysis with quality_factor" )
>>> table = to_table(data)
>>> print(table)
quality_factor
diff --git a/tox.ini b/tox.ini
index 50c22d5716769ef2ec818f6c8fb94491ea372434..8212226eef2759c1864a86b8a3ad8f926480db4a 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,5 +1,5 @@
[tox]
-envlist=py38, py39, py310
+envlist=py37, py38, py39, py310, py311
skip_missing_interpreters = true
[testenv]
@@ -7,8 +7,13 @@ deps = .
nose
pytest
pytest-cov
- jsonschema==4.0.1
+ jsonschema>=4.4.0
commands=py.test --cov=caosdb -vv {posargs}
[flake8]
max-line-length=100
+
+[pytest]
+testpaths = unittests
+xfail_strict = True
+addopts = -x -vv --cov=caosdb
diff --git a/unittests/test_apiutils.py b/unittests/test_apiutils.py
index f9de6d1a037667d0ead0f02439bde13ac4f14f60..bda381cf6427377194e272dfa14b83399b6f012f 100644
--- a/unittests/test_apiutils.py
+++ b/unittests/test_apiutils.py
@@ -3,6 +3,7 @@
#
# Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
# Copyright (C) 2022 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+# Copyright (C) 2022 Daniel Hornung <d.hornung@indiscale.com>
# Copyright (C) 2020-2022 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
@@ -29,7 +30,8 @@ import pytest
import caosdb as db
import caosdb.apiutils
from caosdb.apiutils import (apply_to_ids, compare_entities, create_id_query,
- empty_diff, resolve_reference, merge_entities)
+ empty_diff, EntityMergeConflictError,
+ resolve_reference, merge_entities)
from caosdb.common.models import SPECIAL_ATTRIBUTES
@@ -306,7 +308,7 @@ def test_merge_bug_conflict():
r3 = db.Record()
r3.add_property(name="C", value=4, datatype="INTEGER")
- with pytest.raises(RuntimeError) as excinfo:
+ with pytest.raises(EntityMergeConflictError):
merge_entities(r3, r2)
@@ -401,15 +403,13 @@ def test_wrong_merge_conflict_reference():
rec_a.add_property(name=title_prop.name, value="Some dataset title")
# this does not compare referenced records, so it will fail
- with pytest.raises(RuntimeError) as re:
+ with pytest.raises(EntityMergeConflictError):
merge_entities(rec_a, rec_b, merge_references_with_empty_diffs=False)
- assert "Merge conflict" in str(re.value)
# ... as should this, of course
rec_b.get_property(license_rt.name).value.name = "Another license"
- with pytest.raises(RuntimeError) as re:
+ with pytest.raises(EntityMergeConflictError) as re:
merge_entities(rec_a, rec_b)
- assert "Merge conflict" in str(re.value)
def test_empty_diff():
@@ -483,9 +483,8 @@ def test_force_merge():
recA = db.Record(name="A")
recB = db.Record(name="B")
- with pytest.raises(RuntimeError) as re:
+ with pytest.raises(EntityMergeConflictError):
merge_entities(recA, recB)
- assert "Merge conflict" in str(re.value)
merge_entities(recA, recB, force=True)
assert "B" == recA.name
@@ -498,9 +497,11 @@ def test_force_merge():
recB = db.Record()
recB.description = "something else"
- with pytest.raises(RuntimeError) as re:
+ with pytest.raises(EntityMergeConflictError) as emce:
merge_entities(recA, recB)
- assert "Merge conflict" in str(re.value)
+ assert str(emce.value) == """Conflict in special attribute description:
+A: something
+B: something else"""
merge_entities(recA, recB, force=True)
assert recA.description == "something else"
@@ -513,9 +514,8 @@ def test_force_merge():
recB = db.Record()
recB.add_property(name="propA", value="something else")
- with pytest.raises(RuntimeError) as re:
+ with pytest.raises(EntityMergeConflictError):
merge_entities(recA, recB)
- assert "Merge conflict" in str(re.value)
merge_entities(recA, recB, force=True)
assert recA.get_property("propA").value == "something else"
@@ -539,9 +539,8 @@ def test_force_merge():
rtB = db.RecordType()
rtB.add_property(name="propA", datatype=db.TEXT)
- with pytest.raises(RuntimeError) as re:
+ with pytest.raises(EntityMergeConflictError):
merge_entities(rtA, rtB)
- assert "Merge conflict" in str(re.value)
merge_entities(rtA, rtB, force=True)
assert rtA.get_property("propA").datatype == db.TEXT
@@ -554,10 +553,24 @@ def test_force_merge():
recB = db.Record()
recB.add_property(name="propA", value=5, unit="cm")
- with pytest.raises(RuntimeError) as re:
+ with pytest.raises(EntityMergeConflictError):
merge_entities(recA, recB)
- assert "Merge conflict" in str(re.value)
merge_entities(recA, recB, force=True)
assert recA.get_property("propA").unit == "cm"
# unchanged
assert recB.get_property("propA").unit == "cm"
+
+
+def test_merge_missing_list_datatype_82():
+ """Merging two properties, where the list-valued one has no datatype."""
+
+ recA = db.Record().add_property("a", 5, datatype="B")
+ recB_with_DT = db.Record().add_property("a", [1, 2], datatype=f"LIST<{db.DOUBLE}>")
+ merge_entities(recA, recB_with_DT, force=True)
+ assert recA.get_property("a").datatype == f"LIST<{db.DOUBLE}>"
+
+ recA = db.Record().add_property("a", 5, datatype="B")
+ recB_without_DT = db.Record().add_property("a", [1, 2])
+ with pytest.raises(TypeError) as te:
+ merge_entities(recA, recB_without_DT, force=True)
+ assert "Invalid datatype: List valued properties" in str(te.value)
diff --git a/unittests/test_issues.py b/unittests/test_issues.py
index 1e649db4f23de67e55301e0a053fba70d14680b4..2c45a6d77ba61c3f948e403f708994c0fe31481a 100644
--- a/unittests/test_issues.py
+++ b/unittests/test_issues.py
@@ -34,6 +34,6 @@ def test_issue_100():
# Parse from (invalid) XML file
filename = os.path.join(os.path.dirname(__file__), "data", "list_in_value.xml")
xml_el = lxml.etree.parse(filename).getroot()
- with raises(db.ServerConfigurationException) as exc_info:
+ with raises(TypeError) as exc_info:
db.common.models._parse_single_xml_element(xml_el)
- assert "invalid XML: List valued properties" in exc_info.value.msg
+ assert "Invalid datatype: List valued properties" in str(exc_info.value)