diff --git a/CHANGELOG.md b/CHANGELOG.md
index f4aa6af88b000c0a5452bfe8e7171fe89e473491..f9519355322f23a30ed156b87b8688d29cbd6a20 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -40,6 +40,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- instead of `get_entity`, type-specific functions are used in
`cfood.py` when the type of the entity in question is known.
- Logger is used instead of `print` for errors in `crawler.py`.
+- `caosadvancedtools.cfood.assure_object_is_in_list` conducts in-place
+ updates if no `to_be_updated` object is supplied.
### Deprecated ###
diff --git a/integrationtests/test.sh b/integrationtests/test.sh
index 74ca823f59d2f12fa1352fb51e890a20f63a016e..a56b758421a059a0cc3461c08600c13ffd93705c 100755
--- a/integrationtests/test.sh
+++ b/integrationtests/test.sh
@@ -11,6 +11,8 @@ echo "Testing caching"
python3 -m pytest test_cache.py
echo "Testing models"
python3 -m pytest test_data_model.py
+echo "Testing cfood functionality"
+python3 -m pytest test_assure_functions.py
echo "Filling the database"
./filldb.sh
@@ -34,7 +36,7 @@ RUN_ID=$(grep "run id:" $OUT | awk '{ print $NF }')
echo $RUN_ID
echo "run crawler again"
echo "./crawl.py -a $RUN_ID /"
-./crawl.py -a $RUN_ID / > $OUT
+./crawl.py -a $RUN_ID / | tee $OUT
set +e
if grep "There where unauthorized changes" $OUT
then
diff --git a/integrationtests/test_assure_functions.py b/integrationtests/test_assure_functions.py
new file mode 100644
index 0000000000000000000000000000000000000000..56f9767a0f436201ab6003ffd88f631bdb089544
--- /dev/null
+++ b/integrationtests/test_assure_functions.py
@@ -0,0 +1,93 @@
+#!/usr/bin/env python
+# encoding: utf-8
+#
+# ** header v3.0
+# This file is a part of the CaosDB Project.
+#
+# Copyright (C) 2021 University Medical Center Göttingen, Institute for Medical Informatics
+# Copyright (C) 2021 Florian Spreckelsen <florian.spreckelsen@med.uni-goettingen.de>
+#
+# 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.
+#
+# 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
+"""Integration tests for the `assure_...` functions from
+`caosadvancedtools.cfood`. They mainly test the in-place updates when
+no `to_be_updated` is specified.
+
+"""
+import caosdb as db
+
+from caosadvancedtools.cfood import (assure_object_is_in_list)
+from caosadvancedtools.guard import (global_guard, RETRIEVE, UPDATE)
+
+
+def setup_module():
+ """Delete all test entities."""
+ db.execute_query("FIND Test*").delete(raise_exception_on_error=False)
+
+
+def setup():
+ """Allow all updates and delete test data"""
+ global_guard.level = UPDATE
+ setup_module()
+
+
+def teardown():
+ """Reset guard level and delete test data."""
+ global_guard.level = RETRIEVE
+ setup_module()
+
+
+def test_assure_list_in_place():
+ """Test an in-place update with `assure_object_is_in_list`."""
+
+ int_list_prop = db.Property(name="TestIntListProperty",
+ datatype=db.LIST(db.INTEGER)).insert()
+ rt1 = db.RecordType(name="TestType1").add_property(
+ name=int_list_prop.name).insert()
+ rec1 = db.Record(name="TestRecord1").add_parent(rt1)
+ rec1.add_property(name=int_list_prop.name, value=[1]).insert()
+
+ # Nothing should happen:
+ assure_object_is_in_list(1, rec1, int_list_prop.name, to_be_updated=None)
+ assert len(rec1.get_property(int_list_prop.name).value) == 1
+ assert 1 in rec1.get_property(int_list_prop.name).value
+
+ # Insertion should happen in-place
+ assure_object_is_in_list(2, rec1, int_list_prop.name, to_be_updated=None)
+ assert len(rec1.get_property(int_list_prop.name).value) == 2
+ assert 2 in rec1.get_property(int_list_prop.name).value
+
+ # Better safe than sorry -- test for reference properties, too.
+ ref_rt = db.RecordType(name="TestRefType").insert()
+ ref_rec1 = db.Record(name="TestRefRec1").add_parent(ref_rt).insert()
+ ref_rec2 = db.Record(name="TestRefRec2").add_parent(ref_rt).insert()
+ ref_rec3 = db.Record(name="TestRefRec3").add_parent(ref_rt).insert()
+ rt2 = db.RecordType(name="TestType2").add_property(
+ name=ref_rt.name, datatype=db.LIST(ref_rt.name)).insert()
+ rec2 = db.Record(name="TestRecord2").add_parent(rt2)
+ rec2.add_property(name=ref_rt.name, value=[ref_rec1],
+ datatype=db.LIST(ref_rt.name)).insert()
+
+ # Again, nothing should happen
+ assure_object_is_in_list(ref_rec1, rec2, ref_rt.name, to_be_updated=None)
+ assert len(rec2.get_property(ref_rt.name).value) == 1
+ assert ref_rec1.id in rec2.get_property(ref_rt.name).value
+
+ # In-place update with two additional references
+ assure_object_is_in_list([ref_rec2, ref_rec3],
+ rec2, ref_rt.name, to_be_updated=None)
+ 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
diff --git a/src/caosadvancedtools/cfood.py b/src/caosadvancedtools/cfood.py
index 54a6b8093748a2e9ee5986bf5efe2e9f0dbdb078..680f592bdca62f7a0a31c54484568da99eea95dc 100644
--- a/src/caosadvancedtools/cfood.py
+++ b/src/caosadvancedtools/cfood.py
@@ -8,6 +8,8 @@
# Max-Planck-Institute for Dynamics and Self-Organization Göttingen
# Copyright (C) 2019,2020 Henrik tom Wörden
# Copyright (C) 2020 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>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -349,19 +351,22 @@ class AbstractFileCFood(AbstractCFood):
def assure_object_is_in_list(obj, containing_object, property_name,
- to_be_updated, datatype=None):
- """
- Checks whether `obj` is one of the values in the list property
+ to_be_updated=None, datatype=None):
+ """Checks whether `obj` is one of the values in the list property
`property_name` of the supplied entity containing_object`.
- If this is the case this function returns. Otherwise the entity is added to
- the property `property_name` and the entity `containing_object` is added to
- the supplied list to_be_updated in order to indicate, that the entity
- `containing_object` should be updated.
+ If this is the case this function returns. Otherwise the entity is
+ added to the property `property_name` and the entity
+ `containing_object` is added to the supplied list to_be_updated in
+ order to indicate, that the entity `containing_object` should be
+ updated. If none is submitted the update will be conducted
+ in-place.
- If the property is missing, it is added first and then the entity is added.
+ If the property is missing, it is added first and then the entity
+ is added/updated.
If obj is a list, every element is added
+
"""
if datatype is None:
@@ -409,7 +414,12 @@ def assure_object_is_in_list(obj, containing_object, property_name,
update = True
if update:
- to_be_updated.append(containing_object)
+ if to_be_updated is not None:
+ to_be_updated.append(containing_object)
+ else:
+ get_ids_for_entities_with_names([containing_object])
+
+ guard.safe_update(containing_object)
def assure_special_is(entity, value, kind, to_be_updated=None, force=False):
diff --git a/src/caosadvancedtools/scifolder/utils.py b/src/caosadvancedtools/scifolder/utils.py
index 3241764fd08b7bdd8509f9b0a11239996a1995fb..afa671af85506a57a06ad5198bec4495823c76f1 100644
--- a/src/caosadvancedtools/scifolder/utils.py
+++ b/src/caosadvancedtools/scifolder/utils.py
@@ -17,6 +17,7 @@
# 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/>.
+import logging
import os
from itertools import chain
@@ -28,6 +29,8 @@ from caosadvancedtools.utils import (find_records_that_reference_ids,
return_field_or_property,
string_to_person)
+logger = logging.getLogger("caosadvancedtools")
+
def parse_responsibles(header):
"""
@@ -71,6 +74,7 @@ def get_files_referenced_by_field(globs, prefix="", final_glob=None):
glob = os.path.normpath(glob)
query_string = "FIND file which is stored at {}".format(glob)
+ logger.debug(query_string)
el = db.execute_query(query_string)
@@ -126,13 +130,15 @@ def reference_records_corresponding_to_files(record, recordtypes, globs, path,
files_in_folders = list(chain(*get_files_referenced_by_field(
globs,
prefix=os.path.dirname(path),
- final_glob="**")))
+ final_glob="/**")))
files = [f for f in directly_named_files + files_in_folders if
is_filename_allowed(f.path, recordtype=recordtype)]
+ logger.debug("Referenced files:\n" + str(files))
entities = find_records_that_reference_ids(
list(set([
fi.id for fi in files])),
rt=recordtype)
+ logger.debug("Referencing entities:\n" + str(entities))
if len(entities) == 0:
continue
diff --git a/src/caosadvancedtools/scifolder/withreadme.py b/src/caosadvancedtools/scifolder/withreadme.py
index b3eb1095f9af74f11d7045a6096f5ca372913b4a..c36fb736c399724fe62e5f95dfa08b4bfe1a0f81 100644
--- a/src/caosadvancedtools/scifolder/withreadme.py
+++ b/src/caosadvancedtools/scifolder/withreadme.py
@@ -86,6 +86,9 @@ def get_glob(field):
if it is a dict, it must have either an include or a file key"""
globs = []
+ if not isinstance(field, list):
+ field = [field]
+
for value in field:
if isinstance(value, dict) and INCLUDE.key in value: