diff --git a/CHANGELOG.md b/CHANGELOG.md
index e5a7f8f6690bd134422255d43d0b7e3bfba7c347..be44a47d1a0c79c8a4fa39f382d4d3a0e22439f6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Security ###
+## [0.4.1] - 2022-05-03 ##
+(Henrik tom Wörden)
+
+### Changed ###
+
+- `JsonSchemaParser` now identifies `name` properties in the schema with the
+ CaosDB name property.
+
+### Fixed ###
+
+- [#40](https://gitlab.com/caosdb/caosdb-advanced-user-tools/-/issues/40)
+ `assure_object_is_in_list` now handles adding objects to an initially empty list correctly.
+
## [0.4.0] - 2022-04-05 ##
### Added ###
diff --git a/RELEASE_GUIDELINES.md b/RELEASE_GUIDELINES.md
index e71234b8e2bc95f954ffbebdc26acf6edd8e0b2d..7592b02d8084d3a5e6419ae66b61331026f2766c 100644
--- a/RELEASE_GUIDELINES.md
+++ b/RELEASE_GUIDELINES.md
@@ -9,7 +9,7 @@ guidelines of the CaosDB Project
* All tests are passing.
* FEATURES.md is up-to-date and a public API is being declared in that document.
* CHANGELOG.md is up-to-date.
-* DEPENDENCIES.md is up-to-date.
+* dependencies in `setup.py` are up-to-date.
## Steps
diff --git a/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/README.md b/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/README.md
index d844a2ddf0d87d303c69b9107a366f2e34b6d03c..2057703d18dad94127037e05b3180603e9e37380 100644
--- a/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/README.md
+++ b/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/README.md
@@ -1,6 +1,6 @@
---
responsible: Responsible, Only
-description: A description of this example analysis.
+description: A description of another example analysis.
sources:
- file: "/ExperimentalData/2010_TestProject/2019-02-03/*.dat"
diff --git a/integrationtests/extroot/Software/2020NewProject0X/2020-02-03/README.md b/integrationtests/extroot/Software/2020NewProject0X/2020-02-03/README.md
index a47ea6e105c20d050ddf2fdc8cd29d4685ba30bf..bd57ffe2c43fe6406672db2dd18902b8269569d4 100644
--- a/integrationtests/extroot/Software/2020NewProject0X/2020-02-03/README.md
+++ b/integrationtests/extroot/Software/2020NewProject0X/2020-02-03/README.md
@@ -1,7 +1,7 @@
---
responsible:
- Only Responsible MPI DS
-description: A description of this example analysis.
+description: A description of another example analysis.
sources:
- file: "/ExperimentalData/2010_TestProject/2019-02-03/*.dat"
diff --git a/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/README.md b/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/README.md
index 97b7137af372c127ee01458c9844b5ff10fd464b..b55907aaa2bb3794dbe04484c025146c3c7cd101 100644
--- a/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/README.md
+++ b/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/README.md
@@ -2,7 +2,7 @@
responsible:
- Some Responsible
- Responsible, No, MPI DS
-description: A description of this example analysis.
+description: A description of another example analysis.
sources:
- file: "/ExperimentalData/2010_TestProject/2019-02-03/*.dat"
diff --git a/integrationtests/test.sh b/integrationtests/test.sh
index a142d917215eb7469faab9c66a581539ce867e4e..5bb013db6e70a3a8393e7e3b7c7993a6da6bf9b9 100755
--- a/integrationtests/test.sh
+++ b/integrationtests/test.sh
@@ -35,14 +35,17 @@ echo "Testing the crawler database"
python3 -m pytest test_crawler_with_cfoods.py
echo "make a change"
cd extroot
-egrep -liRZ 'A description of another example' . | xargs -0 -l sed -i -e 's/A description of another example/A description of this example/g'
+egrep -liRZ 'A description of another example' . \
+ | xargs -0 -l sed -i -e 's/A description of another example/A description of this example/g'
# remove a file to check that this does not lead to a crawler crash
-mv DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx_back
+mv DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx \
+ DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx_back
cd ..
echo "run crawler"
./crawl.py / | tee $OUT
# rename the moved file
-mv extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx_back extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx
+mv extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx_back \
+ extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx
# check whether there was something UNAUTHORIZED
grep "There where unauthorized changes" $OUT
# get the id of the run which is the last field of the output string
@@ -59,7 +62,8 @@ fi
set -e
echo "Undoing previous changes to extroot content..."
cd extroot
-egrep -liRZ 'A description of this example' . | xargs -0 -l sed -i -e 's/A description of this example/A description of another example/g'
+egrep -liRZ 'A description of this example' . \
+ | xargs -0 -l sed -i -e 's/A description of this example/A description of another example/g'
cd ..
echo "Done."
python3 test_table.py
diff --git a/integrationtests/test_assure_functions.py b/integrationtests/test_assure_functions.py
index 9f4e387d52f25382d18cfb21372a06346d2b5465..b1c731dbbf25f33b54fc3a005402f292525d2d05 100644
--- a/integrationtests/test_assure_functions.py
+++ b/integrationtests/test_assure_functions.py
@@ -1,26 +1,25 @@
#!/usr/bin/env python
# encoding: utf-8
#
-# ** header v3.0
# This file is a part of the CaosDB Project.
#
+# Copyright (C) 2022 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2021 University Medical Center Göttingen, Institute for Medical Informatics
# Copyright (C) 2021 Florian Spreckelsen <florian.spreckelsen@med.uni-goettingen.de>
+# Copyright (C) 2022 Florian Spreckelsen <f.spreckelsen@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
-# published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Affero General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU Affero General Public License for more details.
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
+# details.
#
-# 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
+# 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/>.
"""Integration tests for the `assure_...` functions from
`caosadvancedtools.cfood`. They mainly test the in-place updates when
no `to_be_updated` is specified.
@@ -90,3 +89,29 @@ def test_assure_list_in_place():
assert len(rec2.get_property(ref_rt.name).value) == 3
assert ref_rec2.id in rec2.get_property(ref_rt.name).value
assert ref_rec3.id in rec2.get_property(ref_rt.name).value
+
+
+def test_add_to_empty_list():
+ """See https://gitlab.com/caosdb/caosdb-advanced-user-tools/-/issues/40."""
+ # @author Florian Spreckelsen
+ # @date 2022-04-19
+ referenced_rt = db.RecordType(name="TestReferencedType").insert()
+ list_prop = db.Property(name="TestListProp",
+ datatype=db.LIST(referenced_rt)).insert()
+ referencing_rt = db.RecordType(
+ name="TestReferencingType").add_property(list_prop).insert()
+
+ db.Record(name="TestReferencedRecord").add_parent(referenced_rt).insert()
+ db.Record(name="TestReferencingRecord").add_parent(
+ referencing_rt).add_property(list_prop, value=[]).insert()
+
+ referenced_rec = db.execute_query("FIND TestReferencedRecord", unique=True)
+ referencing_rec = db.execute_query(
+ "FIND TestReferencingRecord", unique=True)
+
+ assure_object_is_in_list(referenced_rec, referencing_rec, list_prop.name)
+
+ referencing_rec = db.execute_query(
+ "FIND TestReferencingRecord", unique=True)
+ assert referencing_rec.get_property(list_prop.name).value == [
+ referenced_rec.id]
diff --git a/setup.py b/setup.py
index 6964fd9c15848efc95f788cd3b4c7476e636abe6..9988a3afc6f2afda29942af4569c5f32b74f40e6 100755
--- a/setup.py
+++ b/setup.py
@@ -47,9 +47,9 @@ from setuptools import find_packages, setup
MAJOR = 0
MINOR = 4
-MICRO = 0
+MICRO = 1
PRE = "" # e.g. rc0, alpha.1, 0.beta-23
-ISRELEASED = False
+ISRELEASED = True
if PRE:
VERSION = "{}.{}.{}-{}".format(MAJOR, MINOR, MICRO, PRE)
diff --git a/src/caosadvancedtools/cfood.py b/src/caosadvancedtools/cfood.py
index 0074d9a13ca8ab60314b59e2a52496cbacc441f7..4a9f955a17fc429deb6cdd10c3645700e579b4df 100644
--- a/src/caosadvancedtools/cfood.py
+++ b/src/caosadvancedtools/cfood.py
@@ -1,14 +1,13 @@
#!/usr/bin/env python
# encoding: utf-8
#
-# ** header v3.0
# This file is a part of the CaosDB Project.
#
# Copyright (C) 2018 Research Group Biomedical Physics,
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
-# Copyright (C) 2019,2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2019-2022 IndiScale GmbH <info@indiscale.com>
# Copyright (C) 2019,2020 Henrik tom Wörden
-# Copyright (C) 2020 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+# Copyright (C) 2020-2022 Florian Spreckelsen <f.spreckelsen@indiscale.com>
# Copyright (C) 2021 University Medical Center Göttingen, Institute for Medical Informatics
# Copyright (C) 2021 Florian Spreckelsen <florian.spreckelsen@med.uni-goettingen.de>
#
@@ -24,8 +23,6 @@
#
# 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
""" Defines how something that shall be inserted into CaosDB is treated.
CaosDB can automatically be filled with Records based on some structure, a file
@@ -415,11 +412,13 @@ def assure_object_is_in_list(obj, containing_object, property_name,
datatype=datatype)
# TODO: case where multiple times the same property exists is not treated
- if not isinstance(containing_object.get_property(property_name).value, list):
- containing_object.get_property(property_name).value = [
- containing_object.get_property(property_name).value]
- containing_object.get_property(property_name).datatype = datatype
- current_list = containing_object.get_property(property_name).value
+ list_prop = containing_object.get_property(property_name)
+ if list_prop.value is None:
+ list_prop.value = []
+ elif not isinstance(list_prop.value, list):
+ list_prop.value = [list_prop.value]
+ list_prop.datatype = datatype
+ current_list = list_prop.value
if not isinstance(obj, list):
objects = [obj]
@@ -674,7 +673,8 @@ def assure_has_property(entity, name, value, to_be_updated=None,
tmp_value = el.value.id
if isinstance(tmp_value, list):
- tmp_value = [i.id if isinstance(i, db.Entity) else i for i in tmp_value]
+ tmp_value = [i.id if isinstance(
+ i, db.Entity) else i for i in tmp_value]
if tmp_value == value:
contained = True
@@ -810,7 +810,9 @@ class RowCFood(AbstractCFood):
for key, value in self.item.iteritems():
if key in self.unique_cols:
continue
- rec.add_property(key, value)
+ assure_property_is(rec, key,
+ value,
+ to_be_updated=self.to_be_updated)
class CMeal():
diff --git a/src/caosadvancedtools/crawler.py b/src/caosadvancedtools/crawler.py
index 87b91a52a6034e906766a56ded787416e5c0027d..0159688c7c7d59e779d576aed54b176e802fca85 100644
--- a/src/caosadvancedtools/crawler.py
+++ b/src/caosadvancedtools/crawler.py
@@ -392,7 +392,6 @@ class Crawler(object):
for cfood in cfoods:
try:
cfood.create_identifiables()
-
self._cached_find_or_insert_identifiables(cfood.identifiables)
cfood.update_identifiables()
diff --git a/src/caosadvancedtools/models/parser.py b/src/caosadvancedtools/models/parser.py
index 48fc1e722c4ce9e888b8b80dbb5f29595c2f6b26..ad149222b5b90671a50943dc00bc9de8074a42f1 100644
--- a/src/caosadvancedtools/models/parser.py
+++ b/src/caosadvancedtools/models/parser.py
@@ -566,9 +566,11 @@ class Parser(object):
db.BOOLEAN]:
if is_list:
- value.datatype = db.LIST(db.__getattribute__(dtype)) # pylint: disable=no-member
+ value.datatype = db.LIST(db.__getattribute__( # pylint: disable=no-member
+ dtype))
else:
- value.datatype = db.__getattribute__(dtype) # pylint: disable=no-member
+ value.datatype = db.__getattribute__( # pylint: disable=no-member
+ dtype)
continue
@@ -632,8 +634,9 @@ class JsonSchemaParser(Parser):
return self._create_model_from_dict(model_dict)
def _create_model_from_dict(self, model_dict: [dict, List[dict]]):
- """Parse a dictionary read in from the model definition in a json schema and
- return the Datamodel created from it.
+ """Parse a dictionary and return the Datamodel created from it.
+
+ The dictionary was typically created from the model definition in a json schema file.
Parameters
----------
@@ -692,6 +695,15 @@ class JsonSchemaParser(Parser):
# Each element must have a specific type
raise JsonSchemaDefinitionError(
f"`type` is missing in element {name}.")
+ if name == "name":
+ # This is identified with the CaosDB name property as long as the
+ # type is correct.
+ if not elt["type"] == "string":
+ raise JsonSchemaDefinitionError(
+ "The 'name' property must be string-typed, otherwise it cannot "
+ "be identified with CaosDB's name property."
+ )
+ return None, force_list
if "enum" in elt:
ent = self._treat_enum(elt, name)
elif elt["type"] in JSON_SCHEMA_ATOMIC_TYPES:
@@ -726,6 +738,10 @@ class JsonSchemaParser(Parser):
else:
name = self._stringify(key)
prop_ent, force_list = self._treat_element(prop, name)
+ if prop_ent is None:
+ # Nothing to be appended since the property has to be
+ # treated specially.
+ continue
importance = db.OBLIGATORY if key in required else db.RECOMMENDED
if not force_list:
rt.add_property(prop_ent, importance=importance)
diff --git a/src/doc/conf.py b/src/doc/conf.py
index 5f62cac4bb61282c755cd069aba9b04aa077360b..c7f82a99d3b287ca72ca57430b2d4b868539d39e 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -27,9 +27,9 @@ copyright = '2021, IndiScale GmbH'
author = 'Daniel Hornung'
# The short X.Y version
-version = '0.4.0'
+version = '0.4.1'
# The full version, including alpha/beta/rc tags
-release = '0.4.0'
+release = '0.4.1'
# -- General configuration ---------------------------------------------------
diff --git a/unittests/json-schema-models/datamodel_name.schema.json b/unittests/json-schema-models/datamodel_name.schema.json
new file mode 100644
index 0000000000000000000000000000000000000000..c0e86028c36172d27a4523f2c08db1b413b5c19f
--- /dev/null
+++ b/unittests/json-schema-models/datamodel_name.schema.json
@@ -0,0 +1,12 @@
+{
+ "title": "Dataset",
+ "type": "object",
+ "properties": {
+ "name": { "type": "string", "description": "Name of this dataset" },
+ "date_time": { "type": "string", "format": "date-time" },
+ "date": { "type": "string", "format": "date" },
+ "integer": { "type": "integer", "description": "Some integer property" },
+ "boolean": { "type": "boolean" },
+ "number_prop": { "type": "number", "description": "Some float property" }
+ }
+}
diff --git a/unittests/json-schema-models/datamodel_name_wrong_type.schema.json b/unittests/json-schema-models/datamodel_name_wrong_type.schema.json
new file mode 100644
index 0000000000000000000000000000000000000000..1988ad3d8cd613def36df69f5ad30fedd0a26e48
--- /dev/null
+++ b/unittests/json-schema-models/datamodel_name_wrong_type.schema.json
@@ -0,0 +1,12 @@
+{
+ "title": "Dataset",
+ "type": "object",
+ "properties": {
+ "name": { "type": "boolean", "description": "Name of this dataset" },
+ "date_time": { "type": "string", "format": "date-time" },
+ "date": { "type": "string", "format": "date" },
+ "integer": { "type": "integer", "description": "Some integer property" },
+ "boolean": { "type": "boolean" },
+ "number_prop": { "type": "number", "description": "Some float property" }
+ }
+}
diff --git a/unittests/test_json_schema_model_parser.py b/unittests/test_json_schema_model_parser.py
index 4b44f6efa1cda19c04ee13a6a50b04cefbff9177..7f47890f413dce5511cd498fe802e03a1af3be70 100644
--- a/unittests/test_json_schema_model_parser.py
+++ b/unittests/test_json_schema_model_parser.py
@@ -340,3 +340,19 @@ def test_list():
assert model[name].name == name
assert len(model[name].parents) == 1
assert model[name].has_parent(model["license"])
+
+
+def test_name_property():
+ model = parse_model_from_json_schema(os.path.join(
+ FILEPATH, "datamodel_name.schema.json"))
+
+ dataset_rt = model["Dataset"]
+ assert dataset_rt.get_property("name") is None
+ assert "name" not in model
+
+ with pytest.raises(JsonSchemaDefinitionError) as err:
+ broken = parse_model_from_json_schema(os.path.join(
+ FILEPATH, "datamodel_name_wrong_type.schema.json"))
+ assert str(err.value).startswith(
+ "The 'name' property must be string-typed, otherwise it cannot be identified with CaosDB's "
+ "name property.")