diff --git a/src/caosdb/apiutils.py b/src/caosdb/apiutils.py
index d90ef0d55bb081d71d6dd04784cc013c77e9fd3e..12b2b32060aeece374f560f7be4fe7a741c07db6 100644
--- a/src/caosdb/apiutils.py
+++ b/src/caosdb/apiutils.py
@@ -357,14 +357,14 @@ def merge_entities(entity_a: Entity, entity_b: Entity):
for key in diff_r2["properties"]:
if key in diff_r1["properties"]:
if ("importance" in diff_r1["properties"][key] and
- "importance" in diff_r2["properties"][key]):
+ "importance" in diff_r2["properties"][key]):
if (diff_r1["properties"][key]["importance"] !=
- diff_r2["properties"][key]["importance"]):
+ diff_r2["properties"][key]["importance"]):
raise NotImplementedError()
elif ("importance" in diff_r1["properties"][key] or
"importance" in diff_r2["properties"][key]):
raise NotImplementedError()
-
+
for attribute in ("datatype", "unit", "value"):
if diff_r1["properties"][key][attribute] is None:
setattr(entity_a.get_property(key), attribute,
@@ -503,7 +503,7 @@ def create_flat_list(ent_list: list[Entity], flat: list[Entity]):
if isinstance(el, Entity):
if el not in flat:
flat.append(el)
- create_flat_list([el], flat) # TODO: move inside if block?
+ create_flat_list([el], flat) # TODO: move inside if block?
elif isinstance(p.value, Entity):
if p.value not in flat:
flat.append(p.value)
diff --git a/src/caosdb/high_level_api.py b/src/caosdb/high_level_api.py
index 697ef2d38a828144d9f4f9ea7959e6ab43cbb4cf..03dd208e51cc5f2ed461ee156d935f71aba15bb3 100644
--- a/src/caosdb/high_level_api.py
+++ b/src/caosdb/high_level_api.py
@@ -90,7 +90,7 @@ def high_level_type_for_role(role: str):
if role == "Entity":
return CaosDBPythonEntity
raise RuntimeError("Unknown role.")
-
+
def high_level_type_for_standard_type(standard_record: db.Entity):
if not isinstance(standard_record, db.Entity):
@@ -273,7 +273,7 @@ class CaosDBPythonEntity(object):
if ent.name in self.get_properties():
raise RuntimeError("Multiproperty not implemented yet.")
-
+
val = self._type_converted_value(ent.value, ent.datatype,
references)
self.set_property(
@@ -281,7 +281,7 @@ class CaosDBPythonEntity(object):
val,
datatype=ent.datatype)
metadata = self.get_property_metadata(ent.name)
-
+
for prop_name in fields(metadata):
k = prop_name.name
if k == "importance":
@@ -302,7 +302,7 @@ class CaosDBPythonEntity(object):
prop_name: str
Name of the property to retrieve metadata for.
"""
-
+
if not self.property_exists(prop_name):
raise RuntimeError("The property with name {} does not exist.".format(prop_name))
@@ -331,10 +331,10 @@ class CaosDBPythonEntity(object):
name: str
Name of the property.
-
+
value: Any
Value of the property.
-
+
overwrite: bool
Use this if you definitely only want one property with
that name (set to True).
@@ -344,7 +344,7 @@ class CaosDBPythonEntity(object):
raise RuntimeError("Entity cannot be converted to a corresponding "
"Python representation. Name of property " +
name + " is forbidden!")
-
+
already_exists = self.property_exists(name)
if already_exists and not overwrite:
@@ -515,7 +515,7 @@ class CaosDBPythonEntity(object):
if isinstance(parent, int):
parent = CaosDBPythonUnresolvedParent(id=parent)
-
+
for p in self._parents:
if p.id is not None and p.id == parent.id:
return True
@@ -599,7 +599,7 @@ class CaosDBPythonEntity(object):
else:
resolvedelements.append(element)
self.__setattr__(prop, resolvedelements)
-
+
elif isinstance(propval, CaosDBPythonUnresolvedReference):
val = self._resolve_caosdb_python_unresolved_reference(propval, deep,
references, visited)
@@ -658,8 +658,7 @@ class CaosDBPythonEntity(object):
entity.deserialize(prop))
else:
entity.__setattr__(p, prop)
-
-
+
# if there is no metadata in the yaml file just initialize an empty metadata object
if "metadata" in serialization and p in serialization["metadata"]:
metadata = serialization["metadata"][p]
@@ -672,7 +671,6 @@ class CaosDBPythonEntity(object):
raise NotImplementedError()
return entity
-
def serialize(self, without_metadata: bool = False, visited: dict = None):
"""
@@ -688,7 +686,7 @@ class CaosDBPythonEntity(object):
if self in visited:
return visited[self]
-
+
metadata: dict[str, Any] = dict()
properties = dict()
parents = list()
@@ -713,7 +711,7 @@ class CaosDBPythonEntity(object):
val = self.__getattribute__(baseprop)
if val is not None:
fulldict[baseprop] = val
-
+
if type(self) == CaosDBPythonFile:
fulldict["file"] = self.file
fulldict["path"] = self.path
@@ -748,10 +746,10 @@ class CaosDBPythonEntity(object):
properties[p] = serializedelements
else:
properties[p] = val
-
+
fulldict["properties"] = properties
fulldict["parents"] = parents
-
+
if not without_metadata:
fulldict["metadata"] = metadata
return fulldict
@@ -782,7 +780,7 @@ class CaosDBMultiProperty:
"""
This implements a multi property using a python list.
"""
-
+
def __init__(self):
raise NotImplementedError()
@@ -832,6 +830,7 @@ def _single_convert_to_python_object(robj: CaosDBPythonEntity,
return robj
+
def _convert_property_value(propval):
if isinstance(propval, CaosDBPythonUnresolvedReference):
propval = propval.id
@@ -842,9 +841,10 @@ def _convert_property_value(propval):
propval = [_convert_property_value(element) for element in propval]
# TODO: test case for list missing
-
+
return propval
+
def _single_convert_to_entity(entity: db.Entity,
robj: CaosDBPythonEntity):
"""
@@ -864,9 +864,9 @@ def _single_convert_to_entity(entity: db.Entity,
# Skip version:
if base_attribute == "version":
continue
-
+
val = robj.__getattribute__(base_attribute)
-
+
if val is not None:
entity.__setattr__(base_attribute, val)
@@ -883,7 +883,7 @@ def _single_convert_to_entity(entity: db.Entity,
metadata = robj.get_property_metadata(prop)
propval = _convert_property_value(propval)
-
+
entity.add_property(
name=prop,
value=propval,
@@ -932,7 +932,7 @@ def convert_to_python_object(entity: Union[db.Container, db.Entity],
return _single_convert_to_python_object(
high_level_type_for_standard_type(entity)(), entity, references)
-
+
def new_high_level_entity(entity: db.RecordType,
importance_level: str,
@@ -967,8 +967,8 @@ def new_high_level_entity(entity: db.RecordType,
r.add_property(prop)
return convert_to_python_object(r)
-
-
+
+
def create_record(rtname: str, name: str = None, **kwargs):
"""
Create a new record based on the name of a record type. The new record is returned.
@@ -1006,11 +1006,11 @@ def create_entity_container(record: CaosDBPythonEntity):
lse: List[db.Entity] = [ent]
create_flat_list([ent], lse)
return db.Container().extend(lse)
-
+
def query(query: str, resolve_references: bool = True, references: db.Container = None):
"""
-
+
"""
res = db.execute_query(query)
objects = convert_to_python_object(res)
diff --git a/src/caosdb/utils/plantuml.py b/src/caosdb/utils/plantuml.py
index 2cc1bb53e50aca7b26dc2ade423f010f43f6a774..412d97d443c7561efdcc527b92b842d5416c1bd7 100644
--- a/src/caosdb/utils/plantuml.py
+++ b/src/caosdb/utils/plantuml.py
@@ -168,8 +168,6 @@ hide circle\n
else:
raise ValueError("Unknown style.")
-
-
if add_properties:
result += "package Properties #DDDDDD {\n"
for p in properties:
@@ -293,7 +291,7 @@ def retrieve_substructure(start_record_types, depth, result_id_set=None, result_
if is_reference(prop.datatype) and prop.datatype != db.FILE and depth > 0:
rt = db.RecordType(name=get_referenced_recordtype(prop.datatype)).retrieve()
retrieve_substructure([rt], depth-1, result_id_set, result_container, False)
-
+
# TODO: clean up this hack
# TODO: make it also work for files
if is_reference(prop.datatype) and prop.value is not None:
@@ -358,13 +356,13 @@ def to_graphics(recordtypes: list[db.Entity], filename: str,
if output_dirname is None:
output_dirname = os.getcwd()
-
+
allowed_formats = [
"tpng", "tsvg", "teps", "tpdf", "tvdx", "txmi",
"tscxml", "thtml", "ttxt", "tutxt", "tlatex", "tlatex:nopreamble"]
with tempfile.TemporaryDirectory() as td:
-
+
pu_filename = os.path.join(td, filename + ".pu")
with open(pu_filename, "w") as pu_file:
pu_file.write(pu)
@@ -373,7 +371,7 @@ def to_graphics(recordtypes: list[db.Entity], filename: str,
extension = format[1:]
if ":" in extension:
extension = extension[:extension.index(":")]
-
+
if format not in allowed_formats:
raise RuntimeError("Format not allowed.")
cmd = "plantuml -{} {}".format(format, pu_filename)
diff --git a/unittests/test_apiutils.py b/unittests/test_apiutils.py
index bc747f8ed67d5310a4bcd26af9de3a66958e1fd3..fcedc380d15c06acaf93122922e513d025a1563e 100644
--- a/unittests/test_apiutils.py
+++ b/unittests/test_apiutils.py
@@ -32,7 +32,6 @@ from caosdb.apiutils import (apply_to_ids, compare_entities, create_id_query,
resolve_reference, copy_entity, merge_entities)
-
def test_apply_to_ids():
parent = db.RecordType(id=3456)
rec = db.Record(id=23)
@@ -234,4 +233,3 @@ def test_copy_entities():
assert c.properties[i] != r.properties[i]
assert c.properties[i].value == r.properties[i].value
assert c.get_importance(c.properties[i]) == r.get_importance(r.properties[i])
-
diff --git a/unittests/test_high_level_api.py b/unittests/test_high_level_api.py
index bca279cd49bf75a622c033dba2fd559657c7c201..a9e55c9c2a79f7ead8bbb3fb652c1b81427e69e9 100644
--- a/unittests/test_high_level_api.py
+++ b/unittests/test_high_level_api.py
@@ -23,7 +23,6 @@
# A. Schlemmer, 02/2022
-
import caosdb as db
from caosdb.high_level_api import (convert_to_entity, convert_to_python_object,
new_high_level_entity)
@@ -46,7 +45,10 @@ import os
import tempfile
import pickle
-import sys, traceback, pdb
+import sys
+import traceback
+import pdb
+
@pytest.fixture
def testrecord():
@@ -115,7 +117,7 @@ def test_convert_record():
def test_convert_with_references():
r_ref = db.Record()
r_ref.add_property(name="a", value=42)
-
+
r = db.Record()
r.add_property(name="ref", value=r_ref)
@@ -131,7 +133,7 @@ def test_convert_with_references():
r_ref = db.Record()
r_ref.add_parent("bla")
r_ref.add_property(name="a", value=42)
-
+
r = db.Record()
r.add_property(name="ref", value=r_ref)
@@ -145,7 +147,7 @@ def test_convert_with_references():
r_ref = db.Record()
r_ref.add_parent("bla")
r_ref.add_property(name="a", value=42)
-
+
r = db.Record()
r.add_property(name="ref", value=r_ref, datatype="bla")
@@ -237,6 +239,7 @@ def test_resolve_references():
obj.resolve_references(True, references)
assert obj.ref.ref.ref == obj.ref
+
def equal_entities(r1, r2):
res = compare_entities(r1, r2)
if len(res) != 2:
@@ -245,7 +248,8 @@ def equal_entities(r1, r2):
if len(res[i]["parents"]) != 0 or len(res[i]["properties"]) != 0:
return False
return True
-
+
+
def test_conversion_to_entity():
r = db.Record()
r.add_parent("bla")
@@ -255,12 +259,11 @@ def test_conversion_to_entity():
rconv = convert_to_entity(obj)
assert equal_entities(r, rconv)
-
# With a reference:
r_ref = db.Record()
r_ref.add_parent("bla")
r_ref.add_property(name="a", value=42)
-
+
r = db.Record()
r.add_property(name="ref", value=r_ref)
obj = convert_to_python_object(r)
@@ -269,6 +272,7 @@ def test_conversion_to_entity():
== r.get_property("ref").value.get_property("a").value)
# TODO: add more tests here
+
def test_base_properties():
r = db.Record(id=5, name="test", description="ok")
r.add_property(name="v", value=15, datatype=db.INTEGER, unit="kpx",
@@ -295,6 +299,7 @@ def test_base_properties():
assert prop.description == "description"
assert rconv.get_importance("v") == "RECOMMENDED"
+
def test_empty():
r = db.Record()
obj = convert_to_python_object(r)
@@ -305,6 +310,7 @@ def test_empty():
rconv = convert_to_entity(obj)
assert len(rconv.properties) == 0
+
def test_wrong_entity_for_file():
r = db.Record()
r.path = "test.dat"
@@ -422,7 +428,7 @@ def test_record_generator():
print(obj)
assert False
-
+
def test_list_types():
r = db.Record()
r.add_property(name="a", value=[1, 2, 4])
@@ -495,7 +501,7 @@ def test_list_types():
r2.add_property(name="a", value=4)
r3 = db.Record()
r3.add_property(name="b", value=8)
-
+
r = db.Record()
r.add_property(name="a", value=[r2, r3])
@@ -572,7 +578,6 @@ def test_deserialization():
assert obj_des.file == "bla.test"
assert obj_des.path == "/test/n/bla.test"
-
r = db.Record(id=17, name="test")
r.add_parent("bla")
r.add_property(name="a", value=42)
@@ -591,6 +596,7 @@ def test_deserialization():
obj_des = CaosDBPythonEntity.deserialize(serial)
assert obj.serialize() == obj_des.serialize()
+
@pytest.fixture
def get_record_container():
record_xml = """
@@ -612,6 +618,7 @@ def get_record_container():
c = db.Container.from_xml(record_xml)
return c
+
def test_recursion(get_record_container):
r = convert_to_python_object(get_record_container[0])
r.resolve_references(r, get_record_container)
@@ -623,7 +630,8 @@ def test_recursion(get_record_container):
d = r.serialize(True)
assert r.sources[0] == r.sources[0].sources[0]
-
+
+
@pytest.mark.xfail
def test_recursion_advanced(get_record_container):
# TODO: