Merge branch 'release-0.6.1' into 'main'

RELEASE: 0.6.1

See merge request !36

CHANGELOG.md

@@ -5,6 +5,13 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.6.1] - 2021-12-03 ##
+
+### Fixed ###
+
+- #50 keyring can be used as password input method again
+* #81 compare_entities from apiutils does not compare entity values
+
 ## [0.6.0] - 2021-10-19 ##
 
 ### Added ###

setup.py

@@ -47,7 +47,7 @@ from setuptools import find_packages, setup
 
 MAJOR = 0
 MINOR = 6
-MICRO = 0
+MICRO = 1
 PRE = ""  # e.g. rc0, alpha.1, 0.beta-23
 ISRELEASED = True
 

src/caosdb/apiutils.py

@@ -30,15 +30,15 @@ Some simplified functions for generation of records etc.
 
 import sys
 import tempfile
-from collections.abc import Iterable
 import warnings
+from collections.abc import Iterable
 from subprocess import call
 
 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, get_config,
-                                  execute_query)
+                                  Record, RecordType, execute_query,
+                                  get_config)
 
 
 def new_record(record_type, name=None, description=None,
@@ -561,7 +561,23 @@ def getCommitIn(folder):
 COMPARED = ["name", "role", "datatype", "description", "importance"]
 
 
-def compare_entities(old_entity, new_entity):
+def compare_entities(old_entity: Entity, new_entity: Entity):
+    """
+    Compare two entites.
+
+    Return a tuple of dictionaries, the first index belongs to additional information for old
+    entity, the second index belongs to additional information for new entity.
+
+    Additional information means in detail:
+    - Additional parents (a list under key "parents")
+    - Information about properties:
+      - Each property lists either an additional property or a property with a changed:
+        - ... datatype
+        - ... importance or
+        - ... value (not implemented yet)
+        In case of changed information the value listed under the respective key shows the
+        value that is stored in the respective entity.
+    """
     olddiff = {"properties": {}, "parents": []}
     newdiff = {"properties": {}, "parents": []}
 
@@ -616,13 +632,16 @@ def compare_entities(old_entity, new_entity):
                 newdiff["properties"][prop.name]["importance"] = \
                     new_entity.get_importance(prop.name)
 
-            if ((prop.datatype is not None and
-                    matching[0].datatype is not None) and
-                    (prop.datatype != matching[0].datatype)):
+            if (prop.datatype != matching[0].datatype):
                 olddiff["properties"][prop.name]["datatype"] = prop.datatype
                 newdiff["properties"][prop.name]["datatype"] = \
                     matching[0].datatype
 
+            if (prop.value != matching[0].value):
+                olddiff["properties"][prop.name]["value"] = prop.value
+                newdiff["properties"][prop.name]["value"] = \
+                    matching[0].value
+
             if (len(newdiff["properties"][prop.name]) == 0
                     and len(olddiff["properties"][prop.name]) == 0):
                 newdiff["properties"].pop(prop.name)
@@ -700,6 +719,7 @@ def apply_to_ids(entities, func):
     entities : list of Entity
     func : function with one parameter.
     """
+
     for entity in entities:
         _apply_to_ids_of_entity(entity, func)
 

src/caosdb/connection/authentication/keyring.py

@@ -28,7 +28,7 @@ retrieve the password.
 """
 
 import sys
-import imp
+import importlib
 from getpass import getpass
 from caosdb.exceptions import ConfigurationError
 from .external_credentials_provider import ExternalCredentialsProvider
@@ -52,17 +52,13 @@ def get_authentication_provider():
 
 def _get_external_keyring():
     try:
-        fil, pathname, desc = imp.find_module("keyring", sys.path[1:])
-        module = imp.load_module("external_keyring", fil, pathname, desc)
-        return module
+        return importlib.import_module("keyring")
     except ImportError:
         raise RuntimeError(
             "The keyring password method requires installation of the"
             "keyring python package. On linux with python < 3.5, "
             "this requires the installation of dbus-python as a "
             "system package.")
-    finally:
-        fil.close()
 
 
 def _call_keyring(**config):
@@ -74,7 +70,6 @@ def _call_keyring(**config):
     url = config.get("url")
     username = config.get("username")
     app = "caosdb — {}".format(url)
-    password = _call_keyring(app=app, username=username)
     external_keyring = _get_external_keyring()
     password = external_keyring.get_password(app, username)
     if password is None:

src/caosdb/yamlapi.py

@@ -98,7 +98,7 @@ def yaml_to_xml(yamlstr):
         The string to load the yaml document from.
 
     """
-    return dict_to_xml(yaml.safe_load(yamlstr))
+    return dict_to_xml(yaml.load(yamlstr, Loader=yaml.SafeLoader))
 
 
 def process(text):

unittests/test_apiutils.py

@@ -26,11 +26,14 @@
 # Test apiutils
 # A. Schlemmer, 02/2018
 
-import caosdb as db
 import pickle
 import tempfile
-from caosdb.apiutils import apply_to_ids, create_id_query, resolve_reference
+
+import caosdb as db
 import caosdb.apiutils
+from caosdb.apiutils import (apply_to_ids, compare_entities, create_id_query,
+                             resolve_reference)
+
 from .test_property import testrecord
 
 
@@ -67,7 +70,8 @@ def test_apply_to_ids():
 
 def test_id_query():
     ids = [1, 2, 3, 4, 5]
-    assert create_id_query(ids) == 'FIND ENTITY WITH ID=1 OR ID=2 OR ID=3 OR ID=4 OR ID=5'
+    assert create_id_query(ids) == 'FIND ENTITY WITH ID=1 OR ID=2 OR ID=3 OR '\
+        'ID=4 OR ID=5'
 
 
 def test_resolve_reference():
@@ -77,8 +81,10 @@ def test_resolve_reference():
     prop = db.Property(id=1, datatype=db.REFERENCE, value=100)
     prop.is_valid = lambda: True
     items = [200, 300, 400]
-    prop_list = db.Property(datatype=db.LIST(db.REFERENCE), value=items)
-    prop_list2 = db.Property(datatype=db.LIST(db.REFERENCE), value=[db.Record(id=500)])
+    prop_list = db.Property(datatype=db.LIST(db.REFERENCE),
+                            value=items)
+    prop_list2 = db.Property(datatype=db.LIST(db.REFERENCE),
+                             value=[db.Record(id=500)])
     resolve_reference(prop)
     resolve_reference(prop_list)
     resolve_reference(prop_list2)
@@ -86,6 +92,7 @@ def test_resolve_reference():
     assert isinstance(prop.value, db.Entity)
 
     prop_list_ids = []
+
     for i in prop_list.value:
         prop_list_ids.append(i.id)
         assert isinstance(i, db.Entity)
@@ -102,3 +109,38 @@ def test_resolve_reference():
 
     # restore retrive_entity_with_id
     caosdb.apiutils.retrieve_entity_with_id = original_retrieve_entity_with_id
+
+
+def test_compare_entities():
+    r1 = db.Record()
+    r2 = db.Record()
+    r1.add_parent("bla")
+    r2.add_parent("bla")
+    r1.add_parent("lopp")
+    r1.add_property("test", value=2)
+    r2.add_property("test", value=2)
+    r1.add_property("tests", value=3)
+    r2.add_property("tests", value=45)
+    r1.add_property("tester", value=3)
+    r2.add_property("tester", )
+    r1.add_property("tests_234234", value=45)
+    r2.add_property("tests_TT", value=45)
+
+    diff_r1, diff_r2 = compare_entities(r1, r2)
+
+    assert len(diff_r1["parents"]) == 1
+    assert len(diff_r2["parents"]) == 0
+    assert len(diff_r1["properties"]) == 3
+    assert len(diff_r2["properties"]) == 3
+
+    assert "test" not in diff_r1["properties"]
+    assert "test" not in diff_r2["properties"]
+
+    assert "tests" in diff_r1["properties"]
+    assert "tests" in diff_r2["properties"]
+
+    assert "tester" in diff_r1["properties"]
+    assert "tester" in diff_r2["properties"]
+
+    assert "tests_234234" in diff_r1["properties"]
+    assert "tests_TT" in diff_r2["properties"]

unittests/test_property.py

@@ -24,15 +24,18 @@
 # ** end header
 #
 """Tests for the Property class."""
+import os
+
 import caosdb as db
 from caosdb import Entity, Property, Record
 # pylint: disable=missing-docstring
 from lxml import etree
 
 parser = etree.XMLParser(remove_comments=True)
-testrecord = Record._from_xml(Record(),
-                              etree.parse("unittests/test_record.xml",
-                                          parser).getroot())
+testrecord = Record._from_xml(
+    Record(),
+    etree.parse(os.path.join(os.path.dirname(__file__), "test_record.xml"),
+                parser).getroot())
 
 
 def test_is_entity():
@@ -48,7 +51,8 @@ def test_instance_variables():
 
 
 def test_null_empty_text_value_1():
-    assert testrecord.get_property("LISTofTEXT").value == ["One", "Two", "Three", None, ""]
+    assert testrecord.get_property("LISTofTEXT").value == ["One", "Two",
+                                                           "Three", None, ""]
 
 
 def test_null_empty_text_value_2():