diff --git a/.gitignore b/.gitignore
index bea8a04f8e93b7659fdc4d7b8d5246a19b8759ad..e2526574b37539d054397d49bbefcadcc9dce654 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,6 @@
# -*- mode:conf; -*-
+# generated
+src/caosadvancedtools/version.py
# compiled python and dist stuff
*.egg
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 9b573a53f424ccdbe3d47c426e497df15dbc1257..8ad682bf6bac6b50ed6a98ffe42b94f2c96aabb0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -109,9 +109,7 @@ style:
stage: style
image: $CI_REGISTRY_IMAGE
script:
- # For the moment, ignore type comparisons in datamodel_problems.py
- - autopep8 -ar --diff --exit-code --exclude ./src/caosadvancedtools/datamodel_problems.py .
- - autopep8 -ar --diff --exit-code --ignore E721 ./src/caosadvancedtools/datamodel_problems.py
+ - autopep8 -ar --diff --exit-code .
allow_failure: true
unittest:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f9519355322f23a30ed156b87b8688d29cbd6a20..3973a4b3f6b0098b871abf6394e5b9158b3e43c2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -40,6 +40,10 @@ 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`.
+- complies with new exception handling, i.e., TransactionErros with
+ children being raised in all cases of EntityErrors (see
+ [#32](https://gitlab.com/caosdb/caosdb-pylib/-/issues/32) in
+ caosdb-pylib)
- `caosadvancedtools.cfood.assure_object_is_in_list` conducts in-place
updates if no `to_be_updated` object is supplied.
diff --git a/integrationtests/test_datamodel_problems.py b/integrationtests/test_datamodel_problems.py
index d9af69c79007bae5212f16d18363ff18b4ba9d32..7d56f4da8eea34604ed1c820e14555f087c353bd 100644
--- a/integrationtests/test_datamodel_problems.py
+++ b/integrationtests/test_datamodel_problems.py
@@ -30,7 +30,8 @@ class in crawler.py and cfood.py can be found in full-tests.
import caosdb as db
import pytest
from caosadvancedtools.datamodel_problems import DataModelProblems
-from caosdb.exceptions import (UnqualifiedParentsError,
+from caosdb.exceptions import (TransactionError,
+ UnqualifiedParentsError,
UnqualifiedPropertiesError)
@@ -65,8 +66,9 @@ def test_missing_parent():
missing_name = "TestType"
rec = db.Record(name="TestRecord")
rec.add_parent(name=missing_name)
- with pytest.raises(UnqualifiedParentsError):
+ with pytest.raises(TransactionError) as te:
_insert_and_evaluate_exception(rec)
+ assert te.value.has_error(UnqualifiedParentsError)
assert missing_name in DataModelProblems.missing
@@ -74,8 +76,9 @@ def test_missing_property():
"""Test if missing Property is in datamodel problems."""
missing_name = "TestProp"
rec = db.Record(name="TestRecord").add_property(name=missing_name)
- with pytest.raises(UnqualifiedPropertiesError):
+ with pytest.raises(TransactionError) as te:
_insert_and_evaluate_exception(rec)
+ assert te.value.has_error(UnqualifiedPropertiesError)
assert missing_name in DataModelProblems.missing
@@ -89,8 +92,9 @@ def test_missing_property_existing_type():
db.RecordType(name=existing_rt).insert()
rec = db.Record(name="TestRecord").add_parent(name=existing_rt)
rec.add_property(name=missing_prop)
- with pytest.raises(UnqualifiedPropertiesError):
+ with pytest.raises(TransactionError) as te:
_insert_and_evaluate_exception(rec)
+ assert te.value.has_error(UnqualifiedPropertiesError)
assert missing_prop in DataModelProblems.missing
assert existing_rt not in DataModelProblems.missing
@@ -107,7 +111,8 @@ def test_wrong_property_value():
prop = db.Property(name=prop_name, datatype=prop_dtype).insert()
rec = db.Record(name="TestRecord").add_parent(
name=rt_name).add_property(name=prop_name, value="bla")
- with pytest.raises(UnqualifiedPropertiesError):
+ with pytest.raises(TransactionError) as te:
_insert_and_evaluate_exception(rec)
+ assert te.value.has_error(UnqualifiedPropertiesError)
# Should be empty
assert not DataModelProblems.missing
diff --git a/src/caosadvancedtools/cfood.py b/src/caosadvancedtools/cfood.py
index 680f592bdca62f7a0a31c54484568da99eea95dc..8ce1dced48ba12e62717fe5bd788178e1e5a9488 100644
--- a/src/caosadvancedtools/cfood.py
+++ b/src/caosadvancedtools/cfood.py
@@ -6,6 +6,7 @@
#
# 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) 2019,2020 Henrik tom Wörden
# Copyright (C) 2020 Florian Spreckelsen <f.spreckelsen@indiscale.com>
# Copyright (C) 2021 University Medical Center Göttingen, Institute for Medical Informatics
@@ -46,7 +47,8 @@ from abc import ABCMeta, abstractmethod
from datetime import datetime
import caosdb as db
-from caosdb.exceptions import AmbiguityException, EntityDoesNotExistError
+from caosdb.exceptions import (BadQueryError, EmptyUniqueQueryError,
+ QueryNotUniqueError, TransactionError)
from .datamodel_problems import DataModelProblems
from .guard import global_guard as guard
@@ -75,12 +77,12 @@ def get_entity(name):
def get_property(name):
- """Returns the record type with a given name, preferably from a local
+ """Returns the property with a given name, preferably from a local
cache.
If the local cache does not contain the record type, try to
- retrieve it from CaosDB. If it does not exist, add it to the data
- model problems
+ retrieve it from CaosDB. If it does not exist, see whether it
+ could be a record type used as a property.
"""
@@ -89,7 +91,7 @@ def get_property(name):
prop = db.execute_query("FIND Property with name='{}'".format(
name),
unique=True)
- except (EntityDoesNotExistError, AmbiguityException):
+ except (EmptyUniqueQueryError, QueryNotUniqueError):
# Property might actually be a RecordTypes
prop = get_recordtype(name)
PROPERTIES[name] = prop
@@ -127,7 +129,7 @@ def get_recordtype(name):
try:
rec = db.execute_query("FIND RecordType WITH name='{}'".format(name),
unique=True)
- except (EntityDoesNotExistError, AmbiguityException) as e:
+ except (EmptyUniqueQueryError, QueryNotUniqueError) as e:
DataModelProblems.add(name)
raise e
RECORDTYPES[name] = rec
@@ -266,7 +268,7 @@ def get_entity_for_path(path):
FILES[path] = db.execute_query(q, unique=True)
return FILES[path]
- except EntityDoesNotExistError:
+ except BadQueryError:
path_prefix = "**"
if not path.startswith("/"):
diff --git a/src/caosadvancedtools/converter/labfolder_api.py b/src/caosadvancedtools/converter/labfolder_api.py
index 567ee5a8aa7fdb1176fcbcc9bff96dfb6a19b821..a29d965b1598285105a06871ee1017adfdf4e222 100644
--- a/src/caosadvancedtools/converter/labfolder_api.py
+++ b/src/caosadvancedtools/converter/labfolder_api.py
@@ -82,7 +82,7 @@ class Importer(object):
p = db.Property(name=element['title'], unit=element['unit'], datatype=db.DOUBLE)
try:
p.insert()
- except db.exceptions.EntityError as e:
+ except db.exceptions.TransactionError as e:
print(e)
return
diff --git a/src/caosadvancedtools/crawler.py b/src/caosadvancedtools/crawler.py
index 1083f8c0fa027d014842f4368d4e732c80cc2b48..5dccdd8ce04daf6b6c15c676d195ce02c8d6ae12 100644
--- a/src/caosadvancedtools/crawler.py
+++ b/src/caosadvancedtools/crawler.py
@@ -48,7 +48,7 @@ from datetime import datetime
from sqlite3 import IntegrityError
import caosdb as db
-from caosdb.exceptions import TransactionError
+from caosdb.exceptions import BadQueryError
from .cache import Cache, UpdateCache, get_pretty_xml
from .cfood import RowCFood, add_files, get_ids_for_entities_with_names
@@ -653,7 +653,8 @@ carefully and if the changes are ok, click on the following link:
# is using the unique keyword
try:
r = q.execute(unique=True)
- except TransactionError:
+ except BadQueryError:
+ # either empty or ambiguous response
r = None
# if r is not None:
diff --git a/src/caosadvancedtools/datamodel_problems.py b/src/caosadvancedtools/datamodel_problems.py
index 224744ea763de97b5710e81da93ad9f638c82ea5..df5b7e56dfcc939e2eabf6454cb6e81b22a37727 100644
--- a/src/caosadvancedtools/datamodel_problems.py
+++ b/src/caosadvancedtools/datamodel_problems.py
@@ -28,6 +28,7 @@ or updating entities with missing parents and/or properties.
"""
from caosdb.exceptions import (EntityDoesNotExistError,
+ TransactionError,
UnqualifiedParentsError,
UnqualifiedPropertiesError)
@@ -42,48 +43,51 @@ class DataModelProblems(object):
DataModelProblems.missing.add(ent)
@staticmethod
- def evaluate_exception(e):
- """Take an exception, see whether it was caused by datamodel problems,
- and update missing parents and/or properties if this was the
- case. Otherwise, raise the exception.
+ def _evaluate_unqualified(e):
+ """Evaluate all UnqualifiedParentsErrors and
+ UnqualifiedPropertiesErrors and check for possible datamodel
+ problems.
"""
- # type(e) == type(Exception()) seems to be necessary because
- # of EntityMultiErrors that are instances of (all? some of?)
- # theirchild errors. So isinstance doesn't show the desired
- # behavior.
+ # UnqualifiedParentsErrors are always possible problems:
+ if isinstance(e, UnqualifiedParentsError):
+ for err in e.errors:
+ DataModelProblems.add(err.entity.name)
+ elif isinstance(e, UnqualifiedPropertiesError):
+ # Only those UnqualifiedPropertiesErrors that were caused
+ # by (at least) an EntityDoesNotExistError are possible
+ # datamodel problems
+ for err in e.errors:
+ if isinstance(err, EntityDoesNotExistError):
+ DataModelProblems.add(err.entity.name)
+ # If there is at least one UnqualifiedParentsError or at least
+ # one UnqualifiedPropertiesError on some level below, go
+ # through the children.
+ elif (e.has_error(UnqualifiedParentsError) or
+ e.has_error(UnqualifiedPropertiesError)):
+ for err in e.errors:
+ DataModelProblems._evaluate_unqualified(err)
+
+ @staticmethod
+ def evaluate_exception(e):
+ """Take a TransactionError, see whether it was caused by datamodel
+ problems, and update missing parents and/or properties if this
+ was the case. Afterwards, raise the exception.
- if type(e) == type(UnqualifiedPropertiesError()):
- for err in e.get_errors():
- # Here, it doesn't matter if there is an actual
- # EntityDoesNotExistError or a MultiEntityError
- # including an EntityDoesNotExistError. The latter
- # case happens when a wrong entity with a value is
- # given since then, an EntityHasNoDatatypeError is
- # raised as well. Still, the problem is the missing
- # property, so this is okay.
+ Parameters
+ ----------
+ e : TransactionError
+ TransactionError, the children of which are checked for
+ possible datamodel problems.
- if isinstance(err, EntityDoesNotExistError):
- property_missing = True
- DataModelProblems.add(err.get_entity().name)
- raise e
- elif type(e) == type(UnqualifiedParentsError()):
- # This is always caused by missing/wrong parents
+ """
+ if not isinstance(e, TransactionError):
+ raise ValueError(
+ "Only TransactionErrors can be checked for datamodel problems")
+
+ if (e.has_error(UnqualifiedParentsError) or
+ e.has_error(UnqualifiedPropertiesError)):
+ for err in e.errors:
+ DataModelProblems._evaluate_unqualified(err)
- for err in e.get_errors():
- DataModelProblems.add(err.get_entity().name)
- raise e
- # This is the ugly workaround for a MultiEntityError that
- # stems from a UnqualifiedParentsError: an
- # EntityDoesNotExistError is raised AND the causing entity has
- # type PARENT.
- elif ((type(e) == type(EntityDoesNotExistError())) and
- ((str(type(e.get_entity()).__name__).upper() == "PARENT"))):
- DataModelProblems.add(e.get_entity().name)
- raise e
- # Evaluate children of real MultiEntityErrors:
- elif hasattr(e, "errors") and len(e.get_errors()) > 0:
- for err in e.get_errors():
- DataModelProblems.evaluate_exception(err)
- else:
- raise e
+ raise e