From fd55ecfdefeb8ffb7096312bd9832b40b6644865 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Thu, 14 Mar 2024 20:08:46 +0100
Subject: [PATCH 01/33] MAINT: remove error when comparing different roles
---
src/linkahead/apiutils.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/linkahead/apiutils.py b/src/linkahead/apiutils.py
index e2ed0fac..06547198 100644
--- a/src/linkahead/apiutils.py
+++ b/src/linkahead/apiutils.py
@@ -215,9 +215,9 @@ def compare_entities(old_entity: Entity, new_entity: Entity, compare_referenced_
if old_entity is new_entity:
return (olddiff, newdiff)
- if type(old_entity) is not type(new_entity):
- raise ValueError(
- "Comparison of different Entity types is not supported.")
+ #if type(old_entity) is not type(new_entity):
+ # raise ValueError(
+ # "Comparison of different Entity types is not supported.")
for attr in SPECIAL_ATTRIBUTES:
try:
--
GitLab
From 5f1b683541119becabfffb44a0dd7be3b58f5458 Mon Sep 17 00:00:00 2001
From: Daniel Hornung <d.hornung@indiscale.com>
Date: Mon, 25 Mar 2024 10:13:51 +0100
Subject: [PATCH 02/33] DOC: Typo
---
src/linkahead/common/models.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index 6f6e4c8f..d7bc7a47 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -2286,7 +2286,7 @@ class _Properties(list):
class _ParentList(list):
- # TODO unclear why this class is private. Isn't it use full for users?
+ # TODO unclear why this class is private. Isn't it useful for users?
def _get_entity_by_cuid(self, cuid):
'''
--
GitLab
From 6a39b7348ef05682e98e2aa6a7a7506c63d66bcf Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Thu, 2 May 2024 14:22:22 +0200
Subject: [PATCH 03/33] WIP: Plain json serialization for high level api.
---
src/linkahead/high_level_api.py | 91 ++++++++++++++++++++-------------
1 file changed, 56 insertions(+), 35 deletions(-)
diff --git a/src/linkahead/high_level_api.py b/src/linkahead/high_level_api.py
index 18d219c7..5b1682f3 100644
--- a/src/linkahead/high_level_api.py
+++ b/src/linkahead/high_level_api.py
@@ -471,8 +471,7 @@ class CaosDBPythonEntity(object):
if isinstance(att, list):
return att
- else:
- return [att]
+ return [att]
def add_parent(self, parent: Union[
CaosDBPythonUnresolvedParent, "CaosDBPythonRecordType", str]):
@@ -679,53 +678,68 @@ class CaosDBPythonEntity(object):
return entity
- def serialize(self, without_metadata: bool = False, visited: dict = None):
- """
- Serialize necessary information into a dict.
-
- without_metadata: bool
- If True don't set the metadata field in order to increase
- readability. Not recommended if deserialization is needed.
+ def serialize(self, without_metadata: bool = None, plain_json: bool = False,
+ visited: dict = None):
+ """Serialize necessary information into a dict.
+
+Parameters
+----------
+without_metadata: bool, optional
+ If True don't set the metadata field in order to increase
+ readability. Not recommended if deserialization is needed.
+plain_json: bool, optional
+ If True, serialize to a plain dict without any additional information besides the property values,
+ name and id. This should conform to the format as specified by the json schema generated by the
+ advanced user tools. This implies ``without_metadata = True``.
"""
+ if plain_json:
+ if without_metadata is None:
+ without_metadata = True
+ if not without_metadata:
+ raise ValueError("`plain_json` implies `without_metadata`.")
+ if without_metadata is None:
+ without_metadata = False
if visited is None:
- visited = dict()
+ visited = {}
if self in visited:
return visited[self]
- metadata: Dict[str, Any] = dict()
- properties = dict()
- parents = list()
+ metadata: Dict[str, Any] = {}
+ properties = {}
+ parents = []
# The full information to be returned:
- fulldict = dict()
+ fulldict = {}
visited[self] = fulldict
- # Add CaosDB role:
- fulldict["role"] = standard_type_for_high_level_type(self, True)
-
for parent in self._parents:
if isinstance(parent, CaosDBPythonEntity):
- parents.append(parent.serialize(without_metadata, visited))
+ parents.append(parent.serialize(without_metadata=without_metadata,
+ plain_json=plain_json,
+ visited=visited))
elif isinstance(parent, CaosDBPythonUnresolvedParent):
parents.append({"name": parent.name, "id": parent.id,
"unresolved": True})
else:
raise RuntimeError("Incompatible class used as parent.")
- for baseprop in ("name", "id", "description", "version"):
- val = self.__getattribute__(baseprop)
- if val is not None:
- fulldict[baseprop] = val
+ if not plain_json:
+ # Add LinkAhead role:
+ fulldict["role"] = standard_type_for_high_level_type(self, True)
+ for baseprop in ("name", "id", "description", "version"):
+ val = self.__getattribute__(baseprop)
+ if val is not None:
+ fulldict[baseprop] = val
- if type(self) == CaosDBPythonFile:
- fulldict["file"] = self.file
- fulldict["path"] = self.path
+ if isinstance(self, CaosDBPythonFile):
+ fulldict["file"] = self.file
+ fulldict["path"] = self.path
for p in self.get_properties():
m = self.get_property_metadata(p)
- metadata[p] = dict()
+ metadata[p] = {}
for f in fields(m):
val = m.__getattribute__(f.name)
if val is not None:
@@ -735,30 +749,37 @@ class CaosDBPythonEntity(object):
if isinstance(val, CaosDBPythonUnresolvedReference):
properties[p] = {"id": val.id, "unresolved": True}
elif isinstance(val, CaosDBPythonEntity):
- properties[p] = val.serialize(without_metadata, visited)
+ properties[p] = val.serialize(without_metadata=without_metadata,
+ plain_json=plain_json,
+ visited=visited)
elif isinstance(val, list):
serializedelements = []
for element in val:
if isinstance(element, CaosDBPythonUnresolvedReference):
- elm = dict()
+ elm = {}
elm["id"] = element.id
elm["unresolved"] = True
serializedelements.append(elm)
elif isinstance(element, CaosDBPythonEntity):
serializedelements.append(
- element.serialize(without_metadata,
- visited))
+ element.serialize(without_metadata=without_metadata,
+ plain_json=plain_json,
+ visited=visited))
else:
serializedelements.append(element)
properties[p] = serializedelements
else:
properties[p] = val
- fulldict["properties"] = properties
- fulldict["parents"] = parents
-
- if not without_metadata:
- fulldict["metadata"] = metadata
+ if plain_json:
+ fulldict["id"] = getattr(self, "id")
+ fulldict["name"] = getattr(self, "name")
+ fulldict.update(properties)
+ else:
+ fulldict["properties"] = properties
+ fulldict["parents"] = parents
+ if not without_metadata:
+ fulldict["metadata"] = metadata
return fulldict
def __str__(self):
--
GitLab
From da7a10d5124a02fee57ee86cef9fac4db626206f Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Fri, 3 May 2024 13:16:55 +0200
Subject: [PATCH 04/33] MAINT: Formatting.
---
src/linkahead/high_level_api.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/src/linkahead/high_level_api.py b/src/linkahead/high_level_api.py
index 5b1682f3..cdbd81e3 100644
--- a/src/linkahead/high_level_api.py
+++ b/src/linkahead/high_level_api.py
@@ -44,7 +44,8 @@ from .common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER,
REFERENCE, TEXT, get_list_datatype,
is_list_datatype, is_reference)
-warnings.warn("""EXPERIMENTAL! The high_level_api module is experimental and may be changed or
+warnings.warn("""
+EXPERIMENTAL! The high_level_api module is experimental and may be changed or
removed in the future. Its purpose is to give an impression on how the Python client user interface
might be changed.""")
--
GitLab
From fd0650aef3de47be12112937a09ca0380c8c1bb2 Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Wed, 22 May 2024 14:00:29 +0200
Subject: [PATCH 05/33] FIX: No infinite recursion for 1-character strings.
---
src/linkahead/common/models.py | 4 ++--
unittests/test_issues.py | 6 ++++++
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index 483c5231..9df9788e 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -1709,8 +1709,8 @@ def _parse_value(datatype, value):
return ret
# This is for a special case, where the xml parser could not differentiate
- # between single values and lists with one element. As
- if hasattr(value, "__len__") and len(value) == 1:
+ # between single values and lists with one element.
+ if hasattr(value, "__len__") and not isinstance(value, str) and len(value) == 1:
return _parse_value(datatype, value[0])
# deal with references
diff --git a/unittests/test_issues.py b/unittests/test_issues.py
index 7472f710..ba934009 100644
--- a/unittests/test_issues.py
+++ b/unittests/test_issues.py
@@ -64,3 +64,9 @@ def test_issue_156():
# </ParentList>
assert value is project
assert parents[0].name == "RTName"
+
+
+def test_parse_datatype():
+ """No infinite recursion."""
+ from linkahead.common.models import _parse_value
+ assert 1 == _parse_value("labels0", "1")
--
GitLab
From e7efcb316825a0b788cb8dc375792372aeaf7424 Mon Sep 17 00:00:00 2001
From: Daniel Hornung <d.hornung@indiscale.com>
Date: Wed, 18 Sep 2024 14:43:52 +0200
Subject: [PATCH 06/33] MAINT: Added deprecation warning to DropOffBox related
options.
---
src/linkahead/common/models.py | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index a8144286..0cc0f11e 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -2279,12 +2279,12 @@ class File(Record):
server's "caosroot" file system.
@param file: A local path or python file object. The file designated by
this argument will be uploaded to the server via HTTP.
- @param pickup: A file/folder in the DropOffBox (the server will move that
+ @param pickup: Deprecated: A file/folder in the DropOffBox (the server will move that
file into its "caosroot" file system).
@param thumbnail: (Local) filename to a thumbnail for this file.
@param properties: A list of properties for this file record. @todo is this
implemented?
- @param from_location: Deprecated, use `pickup` instead.
+ @param from_location: Deprecated x 2, use `pickup` instead.
"""
@@ -2311,10 +2311,12 @@ class File(Record):
self.thumbnail = thumbnail
self.pickup = pickup
+ if self.pickup is not None:
+ warn(DeprecationWarning("The DropOffBox is deprecated, do not use `pickup`."))
if from_location is not None:
warn(DeprecationWarning(
- "Param `from_location` is deprecated, use `pickup instead`."))
+ "Param `from_location` is deprecated, as everything DropOffBox related."))
if self.pickup is None:
self.pickup = from_location
--
GitLab
From 2600dacb6a3193f90d6174c84d29229a90bd2776 Mon Sep 17 00:00:00 2001
From: Daniel Hornung <d.hornung@indiscale.com>
Date: Wed, 18 Sep 2024 15:40:40 +0200
Subject: [PATCH 07/33] MAINT: Removced DropOffBox class.
---
src/linkahead/__init__.py | 2 +-
src/linkahead/common/models.py | 36 ----------------------------------
2 files changed, 1 insertion(+), 37 deletions(-)
diff --git a/src/linkahead/__init__.py b/src/linkahead/__init__.py
index cd54f8f4..2c34c252 100644
--- a/src/linkahead/__init__.py
+++ b/src/linkahead/__init__.py
@@ -42,7 +42,7 @@ from .common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER, LIST,
REFERENCE, TEXT)
# Import of the basic API classes:
from .common.models import (ACL, ALL, FIX, NONE, OBLIGATORY, RECOMMENDED,
- SUGGESTED, Container, DropOffBox, Entity, File,
+ SUGGESTED, Container, Entity, File,
Info, Message, Permissions, Property, Query,
QueryTemplate, Record, RecordType, delete,
execute_query, get_global_acl,
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index 0cc0f11e..c4b4d15e 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -4999,42 +4999,6 @@ def execute_query(
cache=cache, page_length=page_length)
-class DropOffBox(list):
- def __init__(self, *args, **kwargs):
- warn(DeprecationWarning("The DropOffBox is deprecated and will be removed in future."))
- super().__init__(*args, **kwargs)
-
- path = None
-
- def sync(self):
- c = get_connection()
- _log_request("GET: Info")
- http_response = c.retrieve(["Info"])
- body = http_response.read()
- _log_response(body)
-
- xml = etree.fromstring(body)
-
- for child in xml:
- if child.tag.lower() == "stats":
- infoelem = child
-
- break
-
- for child in infoelem:
- if child.tag.lower() == "dropoffbox":
- dropoffboxelem = child
-
- break
- del self[:]
- self.path = dropoffboxelem.get('path')
-
- for f in dropoffboxelem:
- self.append(f.get('path'))
-
- return self
-
-
class UserInfo():
"""User information from a server response.
--
GitLab
From 85d209eb825e8192c8e18527c0ea8777d1a79d8f Mon Sep 17 00:00:00 2001
From: Daniel Hornung <d.hornung@indiscale.com>
Date: Wed, 25 Sep 2024 16:09:55 +0200
Subject: [PATCH 08/33] WIP: DropOffBox removal
---
CHANGELOG.md | 2 ++
src/linkahead/common/models.py | 35 +---------------------------------
2 files changed, 3 insertions(+), 34 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5b792cc1..78b4b206 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Removed ###
+- `DropOffBox` class and related parameters (`pickup` for file uploading).
+
### Fixed ###
### Security ###
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index c4b4d15e..6683ed11 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -358,17 +358,6 @@ class Entity:
def file(self, new_file):
self.__file = new_file
- @property
- def pickup(self):
- if self.__pickup is not None or self._wrapped_entity is None:
- return self.__pickup
-
- return self._wrapped_entity.pickup
-
- @pickup.setter
- def pickup(self, new_pickup):
- self.__pickup = new_pickup
-
def grant(
self,
realm: Optional[str] = None,
@@ -2263,8 +2252,7 @@ class File(Record):
"""This class represents LinkAhead's file entities.
For inserting a new file to the server, `path` gives the new location, and
- (exactly?) one of `file` and `pickup` should (must?) be given to specify the
- source of the file.
+ `file` specifies the source of the file.
Symlinking from the "extroot" file system is not supported by this API yet,
it can be done manually using the `InsertFilesInDir` flag. For sample code,
@@ -2279,13 +2267,9 @@ class File(Record):
server's "caosroot" file system.
@param file: A local path or python file object. The file designated by
this argument will be uploaded to the server via HTTP.
- @param pickup: Deprecated: A file/folder in the DropOffBox (the server will move that
- file into its "caosroot" file system).
@param thumbnail: (Local) filename to a thumbnail for this file.
@param properties: A list of properties for this file record. @todo is this
implemented?
- @param from_location: Deprecated x 2, use `pickup` instead.
-
"""
def __init__(
@@ -2295,9 +2279,7 @@ class File(Record):
description: Optional[str] = None, # @ReservedAssignment
path: Optional[str] = None,
file: Union[str, TextIO, None] = None,
- pickup: Optional[str] = None, # @ReservedAssignment
thumbnail: Optional[str] = None,
- from_location=None,
):
Record.__init__(self, id=id, name=name, description=description)
self.role = "File"
@@ -2310,17 +2292,6 @@ class File(Record):
self.file = file
self.thumbnail = thumbnail
- self.pickup = pickup
- if self.pickup is not None:
- warn(DeprecationWarning("The DropOffBox is deprecated, do not use `pickup`."))
-
- if from_location is not None:
- warn(DeprecationWarning(
- "Param `from_location` is deprecated, as everything DropOffBox related."))
-
- if self.pickup is None:
- self.pickup = from_location
-
def to_xml(
self,
xml: Optional[etree._Element] = None,
@@ -3975,8 +3946,6 @@ class Container(list):
if hasattr(entity, '_upload') and entity._upload is not None:
entity_xml.set("upload", entity._upload)
- elif hasattr(entity, 'pickup') and entity.pickup is not None:
- entity_xml.set("pickup", entity.pickup)
insert_xml.append(entity_xml)
@@ -4149,8 +4118,6 @@ class Container(list):
if hasattr(entity, '_upload') and entity._upload is not None:
entity_xml.set("upload", entity._upload)
- elif hasattr(entity, 'pickup') and entity.pickup is not None:
- entity_xml.set("pickup", entity.pickup)
insert_xml.append(entity_xml)
if len(self) > 0 and len(insert_xml) < 1:
--
GitLab
From b1a00123707c72e256f97fb7ca34aff7ee97401c Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Mon, 9 Dec 2024 16:59:32 +0100
Subject: [PATCH 09/33] WIP: Better diff in case of different types.
---
src/linkahead/apiutils.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/src/linkahead/apiutils.py b/src/linkahead/apiutils.py
index 1aa127d3..b0b65d8d 100644
--- a/src/linkahead/apiutils.py
+++ b/src/linkahead/apiutils.py
@@ -291,6 +291,7 @@ def compare_entities(entity0: Optional[Entity] = None,
if entity0 is entity1:
return diff
+ # FIXME Why not simply return a diff which says that the types are different?g
if type(entity0) is not type(entity1):
raise ValueError(
"Comparison of different Entity types is not supported.")
--
GitLab
From b70d0f98bce6f7accfaffb9a2f159605d5d710df Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Mon, 9 Dec 2024 17:04:46 +0100
Subject: [PATCH 10/33] WIP: Better diff in case of different types.
---
src/linkahead/apiutils.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/linkahead/apiutils.py b/src/linkahead/apiutils.py
index b0b65d8d..53336a4a 100644
--- a/src/linkahead/apiutils.py
+++ b/src/linkahead/apiutils.py
@@ -291,10 +291,10 @@ def compare_entities(entity0: Optional[Entity] = None,
if entity0 is entity1:
return diff
- # FIXME Why not simply return a diff which says that the types are different?g
+ # FIXME Why not simply return a diff which says that the types are different?
if type(entity0) is not type(entity1):
- raise ValueError(
- "Comparison of different Entity types is not supported.")
+ diff[0]["type"] = type(entity0)
+ diff[1]["type"] = type(entity1)
# compare special attributes
for attr in SPECIAL_ATTRIBUTES:
--
GitLab
From 0dbb1a1943ce1c6984ce296462db0578a7e0b4b9 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Tue, 14 Jan 2025 15:50:42 +0100
Subject: [PATCH 11/33] REL: Begin next release cycle
---
CHANGELOG.md | 16 ++++++++++++++++
setup.py | 4 ++--
src/doc/conf.py | 4 ++--
3 files changed, 20 insertions(+), 4 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f56bc3ab..e780ce25 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,22 @@ 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).
+## [Unreleased] ##
+
+### Added ###
+
+### Changed ###
+
+### Deprecated ###
+
+### Removed ###
+
+### Fixed ###
+
+### Security ###
+
+### Documentation ###
+
## [0.17.0] - 2025-01-14 ##
### Added ###
diff --git a/setup.py b/setup.py
index 75bcf0c7..ab8555b8 100755
--- a/setup.py
+++ b/setup.py
@@ -46,10 +46,10 @@ from setuptools import find_packages, setup
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
########################################################################
-ISRELEASED = True
+ISRELEASED = False
MAJOR = 0
MINOR = 17
-MICRO = 0
+MICRO = 1
# 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 65600678..ce1aa8ff 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -29,10 +29,10 @@ copyright = '2024, IndiScale GmbH'
author = 'Daniel Hornung'
# The short X.Y version
-version = '0.17.0'
+version = '0.17.1'
# The full version, including alpha/beta/rc tags
# release = '0.5.2-rc2'
-release = '0.17.0'
+release = '0.17.1-dev'
# -- General configuration ---------------------------------------------------
--
GitLab
From cc8c254e8145f45720a29f9fd58f3e4f6542100a Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Thu, 16 Jan 2025 13:05:55 +0100
Subject: [PATCH 12/33] DOC: Fix and extend docstrings of
linkahead.utils.register_tests
---
src/linkahead/utils/register_tests.py | 72 +++++++++++++++++----------
1 file changed, 47 insertions(+), 25 deletions(-)
diff --git a/src/linkahead/utils/register_tests.py b/src/linkahead/utils/register_tests.py
index 6909544f..66fd4553 100644
--- a/src/linkahead/utils/register_tests.py
+++ b/src/linkahead/utils/register_tests.py
@@ -18,44 +18,62 @@
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
-
-import linkahead as db
-from linkahead import administration as admin
-
-"""
-This module implements a registration procedure for integration tests which
+"""This module implements a registration procedure for integration tests which
need a running LinkAhead instance.
-It ensures that tests do not accidentally overwrite data in real LinkAhead
-instances, as it checks whether the running LinkAhead instance is actually the
-correct one, that
-should be used for these tests.
-
-The test files have to define a global variable TEST_KEY which must be unique
-for each test using
+It ensures that tests do not accidentally overwrite data in real
+LinkAhead instances, as it checks whether the running LinkAhead
+instance is actually the correct one, that should be used for these
+tests.
-set_test_key("ABCDE")
+The test files have to define a global variable ``TEST_KEY`` which
+must be unique for each test using
+:py:meth:`~linkahead.utils.register_tests.set_test_key`.
The test procedure (invoked by pytest) checks whether a registration
information is stored in one of the server properties or otherwise
-- offers to register this test in the currently running database ONLY if this
- is empty.
+
+- offers to register this test in the currently running database ONLY if this is
+ empty.
- fails otherwise with a RuntimeError
-NOTE: you probably need to use pytest with the -s option to be able to
- register the test interactively. Otherwise, the server property has to be
- set before server start-up in the server.conf of the LinkAhead server.
+.. note::
+
+ you probably need to use pytest with the -s option to be able to
+ register the test interactively. Otherwise, the server property
+ has to be set before server start-up in the server.conf of the
+ LinkAhead server.
This module is intended to be used with pytest.
-There is a pytest fixture "clear_database" that performs the above mentioned
-checks and clears the database in case of success.
+There is a pytest fixture
+:py:meth:`~linkahead.utils.register_tests.clear_database` that
+performs the above mentioned checks and clears the database in case of
+success.
+
"""
+import linkahead as db
+from linkahead import administration as admin
+
TEST_KEY = None
-def set_test_key(KEY):
+def set_test_key(KEY: str):
+ """Set the global ``TEST_KEY`` variable to `KEY`. Afterwards, if
+ `KEY` matches the ``_CAOSDB_INTEGRATION_TEST_SUITE_KEY`` server
+ environment variable, mehtods like :py:meth:`clear_database` can
+ be used. Call this function in the beginning of your test file.
+
+ Parameters
+ ----------
+ KEY : str
+ key with which the test using this function is registered and
+ which is checked against the
+ ``_CAOSDB_INTEGRATION_TEST_SUITE_KEY`` server environment
+ variable.
+
+ """
global TEST_KEY
TEST_KEY = KEY
@@ -122,10 +140,14 @@ try:
@pytest.fixture
def clear_database():
- """Remove Records, RecordTypes, Properties, and Files ONLY IF the LinkAhead
- server the current connection points to was registered with the appropriate key.
+ """Remove Records, RecordTypes, Properties, and Files ONLY IF
+ the LinkAhead server the current connection points to was
+ registered with the appropriate key using
+ :py:meth:`set_test_key`.
+
+ PyTestInfo Records and the corresponding RecordType and
+ Property are preserved.
- PyTestInfo Records and the corresponding RecordType and Property are preserved.
"""
_assure_test_is_registered()
yield _clear_database() # called before the test function
--
GitLab
From 90a8df2132508069cb949cb40ba4f63e0254b4ce Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Thu, 16 Jan 2025 13:07:55 +0100
Subject: [PATCH 13/33] DOC: Update changelog
---
CHANGELOG.md | 3 +++
1 file changed, 3 insertions(+)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index e780ce25..23ddf860 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,6 +21,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Documentation ###
+* [#78](https://gitlab.com/linkahead/linkahead-pylib/-/issues/78) Fix
+ and extend test-registration docstrings.
+
## [0.17.0] - 2025-01-14 ##
### Added ###
--
GitLab
From 6b4062059f34c8cdc87172487f9604a9d7b5c42d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Thu, 16 Jan 2025 17:12:15 +0100
Subject: [PATCH 14/33] FIX: run linting on all linkahead
---
Makefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Makefile b/Makefile
index 21ea40ac..7490c5d5 100644
--- a/Makefile
+++ b/Makefile
@@ -40,7 +40,7 @@ style:
.PHONY: style
lint:
- pylint --unsafe-load-any-extension=y -d all -e E,F src/linkahead/common
+ pylint --unsafe-load-any-extension=y -d all -e E,F src/linkahead
.PHONY: lint
mypy:
--
GitLab
From f6c3fba01eaad2f2e282a423e775ea60b53477c4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Fri, 24 Jan 2025 10:52:05 +0100
Subject: [PATCH 15/33] ENH: add convenience functions
`value_matches_versionid`, `get_id_from_versionid` and `get_versionid`
---
CHANGELOG.md | 1 +
src/linkahead/common/models.py | 21 +++++++++++++++++++++
unittests/test_entity.py | 28 +++++++++++++++++++++++++++-
3 files changed, 49 insertions(+), 1 deletion(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 23ddf860..20f2498a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,6 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased] ##
### Added ###
+- convenience functions `value_matches_versionid`, `get_id_from_versionid` and `get_versionid`
### Changed ###
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index 75b03b70..0912647a 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -505,6 +505,9 @@ class Entity:
return self
+ def get_versionid(self):
+ return str(self.id)+"@"+str(self.version.id)
+
def get_importance(self, property): # @ReservedAssignment
"""Get the importance of a given property regarding this entity."""
@@ -1954,6 +1957,7 @@ class QueryTemplate():
return len(self.get_errors()) > 0
+
class Parent(Entity):
"""The parent entities."""
@@ -2126,6 +2130,12 @@ class Property(Entity):
return is_reference(self.datatype)
+ def value_matches_versionid(self):
+ return value_matches_versionid(self.value)
+
+ def get_id_from_versionid_value(self):
+ return get_id_from_versionid(self.value)
+
class Message(object):
def __init__(
@@ -5670,3 +5680,14 @@ def _filter_entity_list_by_identity(listobject: list[Entity],
if pid_none and name_match:
matches.append(candidate)
return matches
+
+def value_matches_versionid(value: Union[int, str]):
+ if isinstance(value, int):
+ return False
+ if not isinstance(value, str):
+ raise ValueError(f"A reference value needs to be int or str. It was {type(value)}. "
+ "Did you call value_matches_versionid on a non reference value?")
+ return "@" in value
+
+def get_id_from_versionid(versionid: str):
+ return versionid.split("@")[0]
diff --git a/unittests/test_entity.py b/unittests/test_entity.py
index 855e5a39..722930b2 100644
--- a/unittests/test_entity.py
+++ b/unittests/test_entity.py
@@ -30,7 +30,9 @@ import linkahead
from linkahead import (INTEGER, Entity, Parent, Property, Record, RecordType,
configure_connection)
import warnings
-from linkahead.common.models import SPECIAL_ATTRIBUTES
+from linkahead.common.models import (SPECIAL_ATTRIBUTES, get_id_from_versionid,
+value_matches_versionid)
+from linkahead.common.versioning import Version
from linkahead.connection.mockup import MockUpServerConnection
from lxml import etree
from pytest import raises
@@ -295,3 +297,27 @@ def test_filter_by_identity():
t.parents.filter(pid=234)
assert issubclass(w[-1].category, DeprecationWarning)
assert "This function was renamed" in str(w[-1].message)
+
+
+def test_value_matches_versionid():
+ assert value_matches_versionid(234) is False, "integer is no version id"
+ assert value_matches_versionid("234") is False, ("string that only contains an integer is no "
+ "version id")
+ assert value_matches_versionid("234@bfe1a42cb37aae8ac625a757715d38814c274158") is True, (
+ "integer is no version id") is True
+ with raises(ValueError):
+ value_matches_versionid(234.0)
+ p = Property(value=234)
+ assert p.value_matches_versionid() is False
+ p = Property(value="234@bfe1a42cb37aae8ac625a757715d38814c274158")
+ assert p.value_matches_versionid() is True
+
+def test_get_id_from_versionid():
+ assert get_id_from_versionid("234@bfe1a42cb37aae8ac625a757715d38814c274158") == "234"
+ p = Property(value="234@bfe1a42cb37aae8ac625a757715d38814c274158")
+ assert p.get_id_from_versionid_value() == "234"
+
+def test_get_versionid():
+ e = Entity(id=234)
+ e.version = Version(id="bfe1a42cb37aae8ac625a757715d38814c274158")
+ assert e.get_versionid() =="234@bfe1a42cb37aae8ac625a757715d38814c274158"
--
GitLab
From 85d807d332542485f12a3cdfd235a6b587f54c85 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Fri, 24 Jan 2025 11:05:06 +0100
Subject: [PATCH 16/33] DOC: add docstrings
---
src/linkahead/common/models.py | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index 0912647a..12d36179 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -506,6 +506,7 @@ class Entity:
return self
def get_versionid(self):
+ """Returns the concatenation of ID and version"""
return str(self.id)+"@"+str(self.version.id)
def get_importance(self, property): # @ReservedAssignment
@@ -2131,9 +2132,11 @@ class Property(Entity):
def value_matches_versionid(self):
+ """Returns True if the value matches the pattern <id>@<version>"""
return value_matches_versionid(self.value)
def get_id_from_versionid_value(self):
+ """Returns the ID part of the versionid with the pattern <id>@<version>"""
return get_id_from_versionid(self.value)
class Message(object):
@@ -5682,6 +5685,7 @@ def _filter_entity_list_by_identity(listobject: list[Entity],
return matches
def value_matches_versionid(value: Union[int, str]):
+ """Returns True if the value matches the pattern <id>@<version>"""
if isinstance(value, int):
return False
if not isinstance(value, str):
@@ -5690,4 +5694,5 @@ def value_matches_versionid(value: Union[int, str]):
return "@" in value
def get_id_from_versionid(versionid: str):
+ """Returns the ID part of the versionid with the pattern <id>@<version>"""
return versionid.split("@")[0]
--
GitLab
From 1a8c63724874076b633cce93e7d636c33ff0c125 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Fri, 24 Jan 2025 14:08:53 +0100
Subject: [PATCH 17/33] STY: autopep8'd
---
src/linkahead/common/models.py | 5 +++--
unittests/test_entity.py | 8 +++++---
2 files changed, 8 insertions(+), 5 deletions(-)
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index 12d36179..bfe43b01 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -1958,7 +1958,6 @@ class QueryTemplate():
return len(self.get_errors()) > 0
-
class Parent(Entity):
"""The parent entities."""
@@ -2130,7 +2129,6 @@ class Property(Entity):
else:
return is_reference(self.datatype)
-
def value_matches_versionid(self):
"""Returns True if the value matches the pattern <id>@<version>"""
return value_matches_versionid(self.value)
@@ -2139,6 +2137,7 @@ class Property(Entity):
"""Returns the ID part of the versionid with the pattern <id>@<version>"""
return get_id_from_versionid(self.value)
+
class Message(object):
def __init__(
@@ -5684,6 +5683,7 @@ def _filter_entity_list_by_identity(listobject: list[Entity],
matches.append(candidate)
return matches
+
def value_matches_versionid(value: Union[int, str]):
"""Returns True if the value matches the pattern <id>@<version>"""
if isinstance(value, int):
@@ -5693,6 +5693,7 @@ def value_matches_versionid(value: Union[int, str]):
"Did you call value_matches_versionid on a non reference value?")
return "@" in value
+
def get_id_from_versionid(versionid: str):
"""Returns the ID part of the versionid with the pattern <id>@<version>"""
return versionid.split("@")[0]
diff --git a/unittests/test_entity.py b/unittests/test_entity.py
index 722930b2..2f413717 100644
--- a/unittests/test_entity.py
+++ b/unittests/test_entity.py
@@ -31,7 +31,7 @@ from linkahead import (INTEGER, Entity, Parent, Property, Record, RecordType,
configure_connection)
import warnings
from linkahead.common.models import (SPECIAL_ATTRIBUTES, get_id_from_versionid,
-value_matches_versionid)
+ value_matches_versionid)
from linkahead.common.versioning import Version
from linkahead.connection.mockup import MockUpServerConnection
from lxml import etree
@@ -302,7 +302,7 @@ def test_filter_by_identity():
def test_value_matches_versionid():
assert value_matches_versionid(234) is False, "integer is no version id"
assert value_matches_versionid("234") is False, ("string that only contains an integer is no "
- "version id")
+ "version id")
assert value_matches_versionid("234@bfe1a42cb37aae8ac625a757715d38814c274158") is True, (
"integer is no version id") is True
with raises(ValueError):
@@ -312,12 +312,14 @@ def test_value_matches_versionid():
p = Property(value="234@bfe1a42cb37aae8ac625a757715d38814c274158")
assert p.value_matches_versionid() is True
+
def test_get_id_from_versionid():
assert get_id_from_versionid("234@bfe1a42cb37aae8ac625a757715d38814c274158") == "234"
p = Property(value="234@bfe1a42cb37aae8ac625a757715d38814c274158")
assert p.get_id_from_versionid_value() == "234"
+
def test_get_versionid():
e = Entity(id=234)
e.version = Version(id="bfe1a42cb37aae8ac625a757715d38814c274158")
- assert e.get_versionid() =="234@bfe1a42cb37aae8ac625a757715d38814c274158"
+ assert e.get_versionid() == "234@bfe1a42cb37aae8ac625a757715d38814c274158"
--
GitLab
From 82ce5c08c7f35dedee7622660c28e211bf17db63 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Fri, 24 Jan 2025 14:34:35 +0100
Subject: [PATCH 18/33] FIX: remove value_matches_versionid and
get_id_from_versionid_value member functions
---
src/linkahead/common/models.py | 8 --------
unittests/test_entity.py | 6 ------
2 files changed, 14 deletions(-)
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index bfe43b01..8b8141be 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -2129,14 +2129,6 @@ class Property(Entity):
else:
return is_reference(self.datatype)
- def value_matches_versionid(self):
- """Returns True if the value matches the pattern <id>@<version>"""
- return value_matches_versionid(self.value)
-
- def get_id_from_versionid_value(self):
- """Returns the ID part of the versionid with the pattern <id>@<version>"""
- return get_id_from_versionid(self.value)
-
class Message(object):
diff --git a/unittests/test_entity.py b/unittests/test_entity.py
index 2f413717..f2164d96 100644
--- a/unittests/test_entity.py
+++ b/unittests/test_entity.py
@@ -307,16 +307,10 @@ def test_value_matches_versionid():
"integer is no version id") is True
with raises(ValueError):
value_matches_versionid(234.0)
- p = Property(value=234)
- assert p.value_matches_versionid() is False
- p = Property(value="234@bfe1a42cb37aae8ac625a757715d38814c274158")
- assert p.value_matches_versionid() is True
def test_get_id_from_versionid():
assert get_id_from_versionid("234@bfe1a42cb37aae8ac625a757715d38814c274158") == "234"
- p = Property(value="234@bfe1a42cb37aae8ac625a757715d38814c274158")
- assert p.get_id_from_versionid_value() == "234"
def test_get_versionid():
--
GitLab
From 1459d6c612da49d21aefb59f57ba3674626007c3 Mon Sep 17 00:00:00 2001
From: "i.nueske" <i.nueske@indiscale.com>
Date: Fri, 28 Feb 2025 11:12:49 +0100
Subject: [PATCH 19/33] CI: Add python 3.14 to tests
---
.gitlab-ci.yml | 15 ++++++++++++++-
1 file changed, 14 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index db600343..a773c677 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -101,13 +101,26 @@ unittest_py3.12:
script: *python_test_script
unittest_py3.13:
- allow_failure: true
tags: [ docker ]
stage: test
needs: [ ]
image: python:3.13
script: *python_test_script
+unittest_py3.14:
+ allow_failure: true # remove on release
+ tags: [ docker ]
+ stage: test
+ needs: [ ]
+ image: python:3.14-rc
+ script: # replace by '*python_test_script' on release
+ # Install cargo manually, source its env, and set it to accept 3.14 as interpreter
+ - curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+ - . "$HOME/.cargo/env"
+ - export PYO3_USE_ABI3_FORWARD_COMPATIBILITY=1
+ # Continue normally
+ - *python_test_script
+
# Trigger building of server image and integration tests
trigger_build:
stage: deploy
--
GitLab
From d1cf1b9e3b2853c0d353c582aff5f515ea2815ed Mon Sep 17 00:00:00 2001
From: "i.nueske" <i.nueske@indiscale.com>
Date: Tue, 11 Mar 2025 15:21:41 +0100
Subject: [PATCH 20/33] MNT: Change warnings.warn to logger.warning to enable
warning suppression, and add it to the module docstring
---
src/linkahead/high_level_api.py | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/src/linkahead/high_level_api.py b/src/linkahead/high_level_api.py
index 18d219c7..9aa59fb9 100644
--- a/src/linkahead/high_level_api.py
+++ b/src/linkahead/high_level_api.py
@@ -26,11 +26,12 @@
# type: ignore
"""
A high level API for accessing LinkAhead entities from within python.
+This module is experimental, and may be changed or removed in the future.
This is refactored from apiutils.
"""
-import warnings
+import logging
from dataclasses import dataclass, fields
from datetime import datetime
from typing import Any, Dict, List, Optional, Union
@@ -44,7 +45,10 @@ from .common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER,
REFERENCE, TEXT, get_list_datatype,
is_list_datatype, is_reference)
-warnings.warn("""EXPERIMENTAL! The high_level_api module is experimental and may be changed or
+logger = logging.getLogger(__name__)
+
+
+logger.warning("""EXPERIMENTAL! The high_level_api module is experimental and may be changed or
removed in the future. Its purpose is to give an impression on how the Python client user interface
might be changed.""")
--
GitLab
From dc339849eaedfd911ce2fd321dbd09df8a2d5f07 Mon Sep 17 00:00:00 2001
From: "i.nueske" <i.nueske@indiscale.com>
Date: Tue, 1 Apr 2025 13:15:09 +0200
Subject: [PATCH 21/33] FIX: Always import CredentialsAuthenticator, ignore
linting errors on version import
---
src/linkahead/__init__.py | 2 +-
src/linkahead/connection/connection.py | 5 +++--
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/src/linkahead/__init__.py b/src/linkahead/__init__.py
index 567748e3..97203a20 100644
--- a/src/linkahead/__init__.py
+++ b/src/linkahead/__init__.py
@@ -55,7 +55,7 @@ from .utils.get_entity import (get_entity_by_id, get_entity_by_name,
get_entity_by_path)
try:
- from .version import version as __version__
+ from .version import version as __version_ # pylint: disable=import-error
except ModuleNotFoundError:
version = "uninstalled"
__version__ = version
diff --git a/src/linkahead/connection/connection.py b/src/linkahead/connection/connection.py
index 74dd2317..1bee0b77 100644
--- a/src/linkahead/connection/connection.py
+++ b/src/linkahead/connection/connection.py
@@ -47,7 +47,7 @@ from ..exceptions import (ConfigurationError, HTTPClientError,
LoginFailedError)
try:
- from ..version import version
+ from ..version import version # pylint: disable=import-error
except ModuleNotFoundError:
version = "uninstalled"
@@ -56,11 +56,12 @@ from .interface import CaosDBHTTPResponse, CaosDBServerConnection
from .utils import make_uri_path, urlencode
from typing import TYPE_CHECKING
+from .authentication.interface import CredentialsAuthenticator
if TYPE_CHECKING:
from typing import Optional, Any, Iterator, Union
from requests.models import Response
from ssl import _SSLMethod
- from .authentication.interface import AbstractAuthenticator, CredentialsAuthenticator
+ from .authentication.interface import AbstractAuthenticator
_LOGGER = logging.getLogger(__name__)
--
GitLab
From dfc66218e2d5c213344093d84f376a7116eb8521 Mon Sep 17 00:00:00 2001
From: "i.nueske" <i.nueske@indiscale.com>
Date: Tue, 1 Apr 2025 13:34:33 +0200
Subject: [PATCH 22/33] FIX: Ignore false positive linting warnings
---
src/linkahead/connection/connection.py | 2 +-
src/linkahead/connection/encode.py | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/linkahead/connection/connection.py b/src/linkahead/connection/connection.py
index 1bee0b77..fe99b421 100644
--- a/src/linkahead/connection/connection.py
+++ b/src/linkahead/connection/connection.py
@@ -60,7 +60,7 @@ from .authentication.interface import CredentialsAuthenticator
if TYPE_CHECKING:
from typing import Optional, Any, Iterator, Union
from requests.models import Response
- from ssl import _SSLMethod
+ from ssl import _SSLMethod # pylint: disable=no-name-in-module
from .authentication.interface import AbstractAuthenticator
diff --git a/src/linkahead/connection/encode.py b/src/linkahead/connection/encode.py
index a7619780..0cbb0b69 100644
--- a/src/linkahead/connection/encode.py
+++ b/src/linkahead/connection/encode.py
@@ -384,7 +384,7 @@ class MultipartYielder(object):
# since python 3
def __next__(self):
- return self.next()
+ return self.next() # pylint: disable=not-callable
def next(self):
"""generator function to yield multipart/form-data representation of
--
GitLab
From d3b90636156c8d99bf9e6357387bf42e1bd3b1e2 Mon Sep 17 00:00:00 2001
From: "i.nueske" <i.nueske@indiscale.com>
Date: Tue, 1 Apr 2025 13:45:35 +0200
Subject: [PATCH 23/33] FIX: Revert accidental rename
---
src/linkahead/__init__.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/linkahead/__init__.py b/src/linkahead/__init__.py
index 97203a20..ac8df123 100644
--- a/src/linkahead/__init__.py
+++ b/src/linkahead/__init__.py
@@ -55,7 +55,7 @@ from .utils.get_entity import (get_entity_by_id, get_entity_by_name,
get_entity_by_path)
try:
- from .version import version as __version_ # pylint: disable=import-error
+ from .version import version as __version__ # pylint: disable=import-error
except ModuleNotFoundError:
version = "uninstalled"
__version__ = version
--
GitLab
From 49382a8fa5f0be460fd3fe34b7718021d25cf336 Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Tue, 8 Apr 2025 11:13:20 +0200
Subject: [PATCH 24/33] STYLE: Whitespace only.
---
src/linkahead/high_level_api.py | 2 ++
1 file changed, 2 insertions(+)
diff --git a/src/linkahead/high_level_api.py b/src/linkahead/high_level_api.py
index 44686a42..a835fbb3 100644
--- a/src/linkahead/high_level_api.py
+++ b/src/linkahead/high_level_api.py
@@ -688,9 +688,11 @@ class CaosDBPythonEntity(object):
Parameters
----------
+
without_metadata: bool, optional
If True don't set the metadata field in order to increase
readability. Not recommended if deserialization is needed.
+
plain_json: bool, optional
If True, serialize to a plain dict without any additional information besides the property values,
name and id. This should conform to the format as specified by the json schema generated by the
--
GitLab
From af843d65c6de11fea91f01728d2659c18d312b8f Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Tue, 8 Apr 2025 14:36:30 +0200
Subject: [PATCH 25/33] TEST: Added unit test for high level api serialization.
---
unittests/test_high_level_api.py | 29 +++++++++++++++++++++++++++++
1 file changed, 29 insertions(+)
diff --git a/unittests/test_high_level_api.py b/unittests/test_high_level_api.py
index 82c1a5ca..e35dc678 100644
--- a/unittests/test_high_level_api.py
+++ b/unittests/test_high_level_api.py
@@ -322,6 +322,7 @@ def test_wrong_entity_for_file():
def test_serialization():
+ # With ID
r = db.Record(id=5, name="test", description="ok")
r.add_property(name="v", value=15, datatype=db.INTEGER, unit="kpx",
importance="RECOMMENDED")
@@ -333,6 +334,22 @@ def test_serialization():
for teststr in teststrs:
assert teststr in text
+ serialized = convert_to_python_object(r).serialize()
+ assert serialized == {'role': 'Record',
+ 'name': 'test',
+ 'id': 5,
+ 'description': 'ok',
+ 'properties': {'v': 15},
+ 'parents': [],
+ 'metadata': {'v': {'unit': 'kpx',
+ 'datatype': 'INTEGER',
+ 'importance': 'RECOMMENDED'}}}
+
+ serialized_plain = convert_to_python_object(r).serialize(plain_json=True)
+ assert serialized_plain == {'id': 5, 'name': 'test', 'v': 15}
+
+ # Without ID
+
r = db.Record(description="ok")
r.add_property(name="v", value=15, datatype=db.INTEGER, unit="kpx",
importance="RECOMMENDED")
@@ -341,6 +358,18 @@ def test_serialization():
assert "name" not in text
assert "id" not in text
+ serialized = convert_to_python_object(r).serialize()
+ assert serialized == {'role': 'Record',
+ 'description': 'ok',
+ 'properties': {'v': 15},
+ 'parents': [],
+ 'metadata': {'v': {'unit': 'kpx',
+ 'datatype': 'INTEGER',
+ 'importance': 'RECOMMENDED'}}}
+
+ serialized_plain = convert_to_python_object(r).serialize(plain_json=True)
+ assert serialized_plain == {'id': None, 'name': None, 'v': 15}
+
def test_files():
# empty file:
--
GitLab
From 70588ba60165370b1262581b1fc620e3bbde3d94 Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Tue, 8 Apr 2025 14:40:34 +0200
Subject: [PATCH 26/33] DOCS: More documentation for the high level api
serialization.
---
CHANGELOG.md | 2 ++
src/linkahead/high_level_api.py | 28 ++++++++++++++++++----------
2 files changed, 20 insertions(+), 10 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 20f2498a..33142766 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased] ##
### Added ###
+
- convenience functions `value_matches_versionid`, `get_id_from_versionid` and `get_versionid`
+- Parameter for high level API serialization to output a plain JSON.
### Changed ###
diff --git a/src/linkahead/high_level_api.py b/src/linkahead/high_level_api.py
index a835fbb3..a0137dac 100644
--- a/src/linkahead/high_level_api.py
+++ b/src/linkahead/high_level_api.py
@@ -683,20 +683,28 @@ class CaosDBPythonEntity(object):
return entity
def serialize(self, without_metadata: bool = None, plain_json: bool = False,
- visited: dict = None):
+ visited: dict = None) -> dict:
"""Serialize necessary information into a dict.
-Parameters
-----------
+ Parameters
+ ----------
-without_metadata: bool, optional
- If True don't set the metadata field in order to increase
- readability. Not recommended if deserialization is needed.
+ without_metadata: bool, optional
+ If True don't set the metadata field in order to increase
+ readability. Not recommended if deserialization is needed.
-plain_json: bool, optional
- If True, serialize to a plain dict without any additional information besides the property values,
- name and id. This should conform to the format as specified by the json schema generated by the
- advanced user tools. This implies ``without_metadata = True``.
+ plain_json: bool, optional
+ If True, serialize to a plain dict without any additional information besides the property values,
+ name and id. This should conform to the format as specified by the json schema generated by the
+ advanced user tools. It also sets all properties as top level items of the resulting dict. This
+ implies ``without_metadata = True
+
+ Returns
+ -------
+
+ out: dict
+ A dict corresponding to this entity.
+ ``.
"""
if plain_json:
if without_metadata is None:
--
GitLab
From 7934fb3a7a638fe2eb32ef36a421f7e51fd645b4 Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Wed, 9 Apr 2025 15:16:58 +0200
Subject: [PATCH 27/33] DOCS: Small docstring fix.
---
src/linkahead/common/models.py | 32 +++++++++++++++++---------------
1 file changed, 17 insertions(+), 15 deletions(-)
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index 6de27153..a3b4683a 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -2315,21 +2315,23 @@ class File(Record):
look at `test_files.py` in the Python integration tests of the
`load_files.py` script in the advanced user tools.
- @param name: A name for this file record (That's an entity name - not to be
- confused with the last segment of the files path).
- @param id: An ID.
- @param description: A description for this file record.
- @param path: The complete path, including the file name, of the file in the
- server's "caosroot" file system.
- @param file: A local path or python file object. The file designated by
- this argument will be uploaded to the server via HTTP.
- @param pickup: A file/folder in the DropOffBox (the server will move that
- file into its "caosroot" file system).
- @param thumbnail: (Local) filename to a thumbnail for this file.
- @param properties: A list of properties for this file record. @todo is this
- implemented?
- @param from_location: Deprecated, use `pickup` instead.
-
+ @param name
+ A name for this file *Record* (That's an entity name - not to be confused with the last
+ segment of the files path).
+ @param id
+ An ID.
+ @param description
+ A description for this file record.
+ @param path
+ The complete path, including the file name, of the file in the server's "caosroot" file
+ system.
+ @param file
+ A local path or python file object. The file designated by this argument will be uploaded
+ to the server via HTTP.
+ @param thumbnail
+ (Local) filename to a thumbnail for this file.
+ @param properties
+ A list of properties for this file record. @todo is this implemented?
"""
def __init__(
--
GitLab
From 9639455f558fbc0120c4ac9a58de6810b974d996 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Thu, 10 Apr 2025 09:24:11 +0200
Subject: [PATCH 28/33] FIX: treat None case in depenency search
---
src/linkahead/common/models.py | 2 ++
1 file changed, 2 insertions(+)
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index a3b4683a..69ac403b 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -3824,6 +3824,8 @@ class Container(list):
is_being_referenced.add(prop.value)
elif is_list_datatype(prop_dt):
for list_item in prop.value:
+ if list_item is None:
+ continue
if isinstance(list_item, int):
is_being_referenced.add(list_item)
else:
--
GitLab
From cdd23d0ca8a9ff54e0bd1d21f2b5b152cd222b46 Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Tue, 15 Apr 2025 17:52:13 +0200
Subject: [PATCH 29/33] FEAT: `resolve_references` parameter
In `high_level_api.convert_to_python_object()`
---
CHANGELOG.md | 3 ++-
src/linkahead/high_level_api.py | 28 ++++++++++++++++------------
2 files changed, 18 insertions(+), 13 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 33142766..35b6a480 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,7 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Added ###
- convenience functions `value_matches_versionid`, `get_id_from_versionid` and `get_versionid`
-- Parameter for high level API serialization to output a plain JSON.
+- High level API: Parameter for serialization to output a plain JSON.
+- High level API: Parameter to resolve references when converting to Python object.
### Changed ###
diff --git a/src/linkahead/high_level_api.py b/src/linkahead/high_level_api.py
index a0137dac..45839d9b 100644
--- a/src/linkahead/high_level_api.py
+++ b/src/linkahead/high_level_api.py
@@ -4,9 +4,10 @@
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
+# Copyright (C) 2020-2022,2025 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2020 Timm Fitschen <t.fitschen@indiscale.com>
-# Copyright (C) 2020-2022 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2022 Alexander Schlemmer <alexander.schlemmer@ds.mpg.de>
+# Copyright (C) 2025 Daniel Hornung <d.hornung@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -21,8 +22,7 @@
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
#
-# ** end header
-#
+
# type: ignore
"""
A high level API for accessing LinkAhead entities from within python.
@@ -974,26 +974,32 @@ def convert_to_entity(python_object):
def convert_to_python_object(entity: Union[db.Container, db.Entity],
references: Optional[db.Container] = None,
visited: Optional[Dict[int,
- "CaosDBPythonEntity"]] = None):
+ "CaosDBPythonEntity"]] = None,
+ resolve_references: Optional[bool] = False,
+ ):
"""
Convert either a container of CaosDB entities or a single CaosDB entity
into the high level representation.
- The optional second parameter can be used
+ The optional ``references`` parameter can be used
to resolve references that occur in the converted entities and resolve them
to their correct representations. (Entities that are not found remain as
- CaosDBPythonUnresolvedReferences.)
+ CaosDBPythonUnresolvedReferences, unless ``resolve_references`` is given and True.)
"""
if isinstance(entity, db.Container):
# Create a list of objects:
- return [convert_to_python_object(i, references, visited) for i in entity]
+ return [convert_to_python_object(ent, references=references, visited=visited,
+ resolve_references=resolve_references) for ent in entity]
# TODO: recursion problems?
- return _single_convert_to_python_object(
+ converted = _single_convert_to_python_object(
high_level_type_for_standard_type(entity)(),
entity,
references,
visited)
+ if resolve_references:
+ converted.resolve_references(True, references)
+ return converted
def new_high_level_entity(entity: db.RecordType,
@@ -1077,8 +1083,6 @@ def query(query: str,
"""
res = db.execute_query(query)
- objects = convert_to_python_object(res)
- if resolve_references:
- for obj in objects:
- obj.resolve_references(True, references)
+ objects = convert_to_python_object(res, references=references,
+ resolve_references=resolve_references)
return objects
--
GitLab
From 34f72e35e1f4a6d9c30877360552a45b919e7b8f Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Thu, 24 Apr 2025 08:58:32 +0200
Subject: [PATCH 30/33] FIX: Reverted some changes.
---
src/linkahead/common/models.py | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index 0985d8f0..da46c563 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -338,6 +338,17 @@ class Entity:
def file(self, new_file):
self.__file = new_file
+ # FIXME Add test.
+ @property # getter for _cuid
+ def cuid(self):
+ # Set if None?
+ return self._cuid
+
+ # FIXME Add test.
+ @property # getter for _flags
+ def flags(self):
+ return self._flags.copy() # for dict[str, str] shallow copy is enough
+
def grant(
self,
realm: Optional[str] = None,
--
GitLab
From 10db17e97bc78d0183c87f23f9d4b082388c4981 Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Wed, 7 May 2025 09:34:46 +0200
Subject: [PATCH 31/33] DOCS: Added note to docstring.
---
src/linkahead/common/models.py | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/src/linkahead/common/models.py b/src/linkahead/common/models.py
index da46c563..8d1afbac 100644
--- a/src/linkahead/common/models.py
+++ b/src/linkahead/common/models.py
@@ -3338,6 +3338,11 @@ class Container(list):
Returns
-------
xml_element : etree._Element
+
+ Note
+ ----
+ Calling this method has the side effect that all entities without ID will get a negative
+ integer ID.
"""
tmpid = 0
--
GitLab
From 17be5bafafc45084d5fd0dd131429de22af219ee Mon Sep 17 00:00:00 2001
From: Daniel <d.hornung@indiscale.com>
Date: Fri, 9 May 2025 13:35:28 +0200
Subject: [PATCH 32/33] DOCS: Fixed typo.
---
src/linkahead/exceptions.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/src/linkahead/exceptions.py b/src/linkahead/exceptions.py
index 7d4dc085..0904929c 100644
--- a/src/linkahead/exceptions.py
+++ b/src/linkahead/exceptions.py
@@ -190,7 +190,7 @@ class QueryNotUniqueError(BadQueryError):
class EmptyUniqueQueryError(BadQueryError):
- """A unique query or retrieve dound no result."""
+ """A unique query or retrieve found no result."""
# ######################### Transaction errors #########################
--
GitLab
From 8952c3a8ca7bdd92fba8f8e994f839002b29eb25 Mon Sep 17 00:00:00 2001
From: Florian Spreckelsen <f.spreckelsen@indiscale.com>
Date: Tue, 27 May 2025 17:37:28 +0200
Subject: [PATCH 33/33] BUILD: Bump versions for release
---
CHANGELOG.md | 10 +---------
CITATION.cff | 4 ++--
setup.py | 6 +++---
src/doc/conf.py | 4 ++--
4 files changed, 8 insertions(+), 16 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index bd0c7524..790b8aba 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,7 @@ 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).
-## [Unreleased] ##
+## [0.18.0] - 2025-05-27 ##
### Added ###
@@ -13,18 +13,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- High level API: Parameter for serialization to output a plain JSON.
- High level API: Parameter to resolve references when converting to Python object.
-### Changed ###
-
-### Deprecated ###
-
### Removed ###
- `DropOffBox` class and related parameters (`pickup` for file uploading).
-### Fixed ###
-
-### Security ###
-
### Documentation ###
* [#78](https://gitlab.com/linkahead/linkahead-pylib/-/issues/78) Fix
diff --git a/CITATION.cff b/CITATION.cff
index bcecc2fd..e685ff0c 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: 0.17.0
+version: 0.18.0
doi: 10.3390/data4020083
-date-released: 2025-01-14
+date-released: 2025-05-27
diff --git a/setup.py b/setup.py
index ab8555b8..9047cbd0 100755
--- a/setup.py
+++ b/setup.py
@@ -46,10 +46,10 @@ from setuptools import find_packages, setup
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
########################################################################
-ISRELEASED = False
+ISRELEASED = True
MAJOR = 0
-MINOR = 17
-MICRO = 1
+MINOR = 18
+MICRO = 0
# 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 ce1aa8ff..46c1645c 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -29,10 +29,10 @@ copyright = '2024, IndiScale GmbH'
author = 'Daniel Hornung'
# The short X.Y version
-version = '0.17.1'
+version = '0.18.0'
# The full version, including alpha/beta/rc tags
# release = '0.5.2-rc2'
-release = '0.17.1-dev'
+release = '0.18.0'
# -- General configuration ---------------------------------------------------
--
GitLab