diff --git a/README_SETUP.md b/README_SETUP.md
index 374ea306100aff4cb4f6cbb37f4e9f1eee6f7abc..dc667da8aa5877132c1212d2ddd2827e85992118 100644
--- a/README_SETUP.md
+++ b/README_SETUP.md
@@ -103,7 +103,10 @@ like this, check out the "Authentication" section in the [configuration document
Now would be a good time to continue with the [tutorials](tutorials/index).
## Run Unit Tests
-tox
+
+- Run all tests: `tox` or `make unittest`
+- Run a specific test file: e.g. `tox -- unittests/test_schema.py`
+- Run a specific test function: e.g. `tox -- unittests/test_schema.py::test_config_files`
## Documentation ##
diff --git a/src/caosdb/apiutils.py b/src/caosdb/apiutils.py
index 12b2b32060aeece374f560f7be4fe7a741c07db6..a376068c372c1b6f460c7927467b8da8df328545 100644
--- a/src/caosdb/apiutils.py
+++ b/src/caosdb/apiutils.py
@@ -39,7 +39,9 @@ from caosdb.common.datatype import (BOOLEAN, DATETIME, DOUBLE, FILE, INTEGER,
REFERENCE, TEXT, is_reference)
from caosdb.common.models import (Container, Entity, File, Property, Query,
Record, RecordType, execute_query,
- get_config)
+ get_config, SPECIAL_ATTRIBUTES)
+
+import logging
def new_record(record_type, name=None, description=None,
@@ -186,10 +188,6 @@ def getCommitIn(folder):
return t.readline().strip()
-COMPARED = ["name", "role", "datatype", "description",
- "id", "path", "checksum", "size"]
-
-
def compare_entities(old_entity: Entity, new_entity: Entity):
"""
Compare two entites.
@@ -213,7 +211,7 @@ def compare_entities(old_entity: Entity, new_entity: Entity):
if old_entity is new_entity:
return (olddiff, newdiff)
- for attr in COMPARED:
+ for attr in SPECIAL_ATTRIBUTES:
try:
oldattr = old_entity.__getattribute__(attr)
old_entity_attr_exists = True
@@ -302,51 +300,25 @@ def compare_entities(old_entity: Entity, new_entity: Entity):
return (olddiff, newdiff)
-def copy_entity(entity: Entity):
- """
- Return a copy of entity.
-
- If deep == True return a deep copy, recursively copying all sub entities.
+def merge_entities(entity_a: Entity, entity_b: Entity):
"""
- print(entity)
- new: Optional[Entity] = None
- if entity.role == "File":
- new = File()
- elif entity.role == "Property":
- new = Property()
- elif entity.role == "RecordType":
- new = RecordType()
- elif entity.role == "Record":
- new = Record()
- elif entity.role == "Entity":
- new = Entity()
- else:
- raise RuntimeError("Unkonwn role.")
-
- # Copy special attributes:
- # TODO: this might rise an exception when copying
- # special file attributes like checksum and size.
- for attribute in COMPARED + ["value"]:
- val = getattr(entity, attribute)
- if val is not None:
- setattr(new, attribute, val)
-
- # Copy parents:
- for p in entity.parents:
- new.add_parent(p)
+ Merge entity_b into entity_a such that they have the same parents and properties.
- # Copy properties:
- for p in entity.properties:
- new.add_property(p, importance=entity.get_importance(p))
+ datatype, unit, value, name and description will only be changed in entity_a if they
+ are None for entity_a and set for entity_b. If there is a corresponding value
+ for entity_a different from None a RuntimeError will be raised informing of an
+ unresolvable merge conflict.
- return new
+ The merge operation is done in place.
+ Returns entity_a.
-def merge_entities(entity_a: Entity, entity_b: Entity):
- """
- Merge entity_b into entity_a such that they have the same parents and properties.
+ WARNING: This function is currently experimental and insufficiently tested. Use with care.
"""
+ logging.warning(
+ "This function is currently experimental and insufficiently tested. Use with care.")
+
# Compare both entities:
diff_r1, diff_r2 = compare_entities(entity_a, entity_b)
@@ -372,9 +344,17 @@ def merge_entities(entity_a: Entity, entity_b: Entity):
else:
raise RuntimeError("Merge conflict.")
else:
- entity_a.add_property(
- entity_b.get_property(key),
- importance=entity_b.get_importance(key))
+ # TODO: This is a temporary FIX for
+ # https://gitlab.indiscale.com/caosdb/src/caosdb-pylib/-/issues/105
+ entity_a.add_property(id=entity_b.get_property(key).id,
+ name=entity_b.get_property(key).name,
+ datatype=entity_b.get_property(key).datatype,
+ value=entity_b.get_property(key).value,
+ unit=entity_b.get_property(key).unit,
+ importance=entity_b.get_importance(key))
+ # entity_a.add_property(
+ # entity_b.get_property(key),
+ # importance=entity_b.get_importance(key))
for special_attribute in ("name", "description"):
sa_a = getattr(entity_a, special_attribute)
diff --git a/src/caosdb/common/models.py b/src/caosdb/common/models.py
index 181750aae6fd3e1aeab2c61b59f53d8b8111d5bd..6475bc99ec825e102d5eac1b38d506247c11ebcb 100644
--- a/src/caosdb/common/models.py
+++ b/src/caosdb/common/models.py
@@ -79,6 +79,10 @@ ALL = "ALL"
NONE = "NONE"
+SPECIAL_ATTRIBUTES = ["name", "role", "datatype", "description",
+ "id", "path", "checksum", "size"]
+
+
class Entity(object):
"""Entity is a generic CaosDB object.
@@ -121,6 +125,48 @@ class Entity(object):
self.id = id
self.state = None
+
+ def copy(self):
+ """
+ Return a copy of entity.
+
+ If deep == True return a deep copy, recursively copying all sub entities.
+
+ Standard properties are copied using add_property.
+ Special attributes, as defined by the global variable SPECIAL_ATTRIBUTES and additionaly
+ the "value" are copied using setattr.
+ """
+ if self.role == "File":
+ new = File()
+ elif self.role == "Property":
+ new = Property()
+ elif self.role == "RecordType":
+ new = RecordType()
+ elif self.role == "Record":
+ new = Record()
+ elif self.role == "Entity":
+ new = Entity()
+ else:
+ raise RuntimeError("Unkonwn role.")
+
+ # Copy special attributes:
+ # TODO: this might rise an exception when copying
+ # special file attributes like checksum and size.
+ for attribute in SPECIAL_ATTRIBUTES + ["value"]:
+ val = getattr(self, attribute)
+ if val is not None:
+ setattr(new, attribute, val)
+
+ # Copy parents:
+ for p in self.parents:
+ new.add_parent(p)
+
+ # Copy properties:
+ for p in self.properties:
+ new.add_property(p, importance=self.get_importance(p))
+
+ return new
+
@property
def version(self):
if self._version is not None or self._wrapped_entity is None:
diff --git a/unittests/test_apiutils.py b/unittests/test_apiutils.py
index fcedc380d15c06acaf93122922e513d025a1563e..2859a0ec529d5b1a5f51b57b1407320ba98f8d73 100644
--- a/unittests/test_apiutils.py
+++ b/unittests/test_apiutils.py
@@ -29,7 +29,9 @@
import caosdb as db
import caosdb.apiutils
from caosdb.apiutils import (apply_to_ids, compare_entities, create_id_query,
- resolve_reference, copy_entity, merge_entities)
+ resolve_reference, merge_entities)
+
+from caosdb.common.models import SPECIAL_ATTRIBUTES
def test_apply_to_ids():
@@ -221,15 +223,83 @@ def test_copy_entities():
r.add_property(name="D", value=[3, 4, 7], importance="OBLIGATORY")
r.description = "A fancy test record"
- c = copy_entity(r)
+ c = r.copy()
- assert c != r
+ assert c is not r
assert c.name == "A"
+ assert c.role == r.role
assert c.parents[0].name == "B"
- # Currently parents and properties are always individual to a copy:
- assert c.parents[0] != r.parents[0]
+ # parent and property objects are not shared among copy and original:
+ assert c.parents[0] is not r.parents[0]
for i in [0, 1]:
- assert c.properties[i] != r.properties[i]
- assert c.properties[i].value == r.properties[i].value
+ assert c.properties[i] is not r.properties[i]
+ for special in SPECIAL_ATTRIBUTES:
+ assert getattr(c.properties[i], special) == getattr(r.properties[i], special)
assert c.get_importance(c.properties[i]) == r.get_importance(r.properties[i])
+
+
+def test_merge_entities():
+ r = db.Record(name="A")
+ r.add_parent(name="B")
+ r.add_property(name="C", value=4, importance="OBLIGATORY")
+ r.add_property(name="D", value=[3, 4, 7], importance="OBLIGATORY")
+ r.description = "A fancy test record"
+
+ r2 = db.Record()
+ r2.add_property(name="F", value="text")
+ merge_entities(r2, r)
+ assert r2.get_parents()[0].name == "B"
+ assert r2.get_property("C").name == "C"
+ assert r2.get_property("C").value == 4
+ assert r2.get_property("D").name == "D"
+ assert r2.get_property("D").value == [3, 4, 7]
+
+ assert r2.get_property("F").name == "F"
+ assert r2.get_property("F").value == "text"
+
+
+def test_merge_bug_109():
+ rt = db.RecordType(name="TestBug")
+ p = db.Property(name="test_bug_property", datatype=db.LIST(db.INTEGER))
+
+ r_b = db.Record(name="TestRecord")
+ r_b.add_parent(rt)
+ r_b.add_property(p, value=[18, 19])
+
+ r_a = db.Record(name="TestRecord")
+ r_a.add_parent(rt)
+
+ merge_entities(r_a, r_b)
+
+ assert r_b.get_property("test_bug_property").value == [18, 19]
+ assert r_a.get_property("test_bug_property").value == [18, 19]
+
+ assert "<Value>18</Value>\n <Value>19</Value>" in str(r_b)
+ assert "<Value>18</Value>\n <Value>19</Value>\n <Value>18</Value>\n <Value>19</Value>" not in str(r_b)
+
+ assert "<Value>18</Value>\n <Value>19</Value>" in str(r_a)
+ assert "<Value>18</Value>\n <Value>19</Value>\n <Value>18</Value>\n <Value>19</Value>" not in str(r_a)
+
+
+@pytest.mark.xfail
+def test_bug_109():
+ rt = db.RecordType(name="TestBug")
+ p = db.Property(name="test_bug_property", datatype=db.LIST(db.INTEGER))
+
+ r_b = db.Record(name="TestRecord")
+ r_b.add_parent(rt)
+ r_b.add_property(p, value=[18, 19])
+
+ r_a = db.Record(name="TestRecord")
+ r_a.add_parent(rt)
+ r_a.add_property(r_b.get_property("test_bug_property"))
+
+ assert r_b.get_property("test_bug_property").value == [18, 19]
+ assert r_a.get_property("test_bug_property").value == [18, 19]
+
+ assert "<Value>18</Value>\n <Value>19</Value>" in str(r_b)
+ assert "<Value>18</Value>\n <Value>19</Value>\n <Value>18</Value>\n <Value>19</Value>" not in str(r_b)
+
+ assert "<Value>18</Value>\n <Value>19</Value>" in str(r_a)
+ assert "<Value>18</Value>\n <Value>19</Value>\n <Value>18</Value>\n <Value>19</Value>" not in str(r_a)