feat: update make_diff_changelog

- reset entity counter for property graph nodes and relationships for each cypher statement to make them easier to test
- add _parent object attr to Tags
- handle generating match clauses for entities that rely on other entities for their uniqueness (props, edges, tags)
- add tests for diff changelog to test_014diff_changelog.py
- update versioning tests to turn entity versioning off at the end of test so it doesn't affect subsequent tests involving entities
- bump version from 0.2.4 to 0.2.5
- update dependency versions identified as security risks by dependabot

python/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "bento-meta"
-version = "0.2.4"
+version = "0.2.5"
 description = "Python drivers for Bento Metamodel Database"
 authors = [
   { name="Mark A. Jensen", email = "mark.jensen@nih.gov"},
@@ -20,7 +20,7 @@ classifiers = [
 
 [tool.poetry]
 name = "bento-meta"
-version = "0.2.4"
+version = "0.2.5"
 description = "Python drivers for Bento Metamodel Database"
 authors = [
     "Mark A. Jensen <mark.jensen@nih.gov>",
@@ -37,7 +37,7 @@ PyYAML = ">=6.0.1"
 delfick-project = "^0.7.9"
 neo4j = ">=4.0"
 nanoid = "^2.0.0"
-requests = "^2.28.1"
+requests = "2.31.0"
 tqdm = "^4.64.1"
 setuptools = "^65.4.1"
 numpy = {version = "^1.23.5", optional = true}
@@ -46,6 +46,10 @@ spacy = {version = "^3.4.3", optional = true}
 click = {version = "^8.1.3", optional = true}
 liquichange = "^0.2.1"
 bento-mdf = "^0.9.1"
+tornado = "6.3.3"
+cryptography = "41.0.3"
+certifi = "2023.7.22"
+markdown-it-py = "2.2.0"
 
 [tool.poetry.extras]
 Tools = ["click", "numpy", "pandas", "spacy", "liquichange"]

python/src/bento_meta/objects.py

@@ -91,7 +91,7 @@ class Property(Entity):
             "units": "units",
             "item_domain": "item_domain",
             "is_required": "is_required",
-            "parent_handle": "parent_handle",
+            "_parent_handle": "_parent_handle",
         },
         "relationship": {
             "concept": {"rel": ":has_concept>", "end_cls": "Concept"},
@@ -335,11 +335,12 @@ def __init__(self, init=None):
 class Tag(Entity):
     """Subclass that allows simple key-value tagging of a model at arbitrary points."""
 
-    attspec_ = {"key": "simple", "value": "simple"}
+    attspec_ = {"key": "simple", "value": "simple", "_parent": "object"}
     mapspec_ = {
         "label": "tag",
         "key": "key",
         "property": {"key": "key", "value": "value"},
+        "relationship": {"_parent": {"rel": "<:has_tag", "end_cls": "Entity"}},
     }
     (attspec, _mapspec) = mergespec("Tag", attspec_, mapspec_)
 

python/tests/test_007versioning.py

@@ -1,106 +1,112 @@
 import re
 import sys
-sys.path.insert(0,'.')
-sys.path.insert(0,'..')
+
+sys.path.insert(0, ".")
+sys.path.insert(0, "..")
+from pdb import set_trace
+
 import pytest
 from bento_meta.entity import *
 from bento_meta.objects import *
-from pdb import set_trace
+
 
 def test_object_versioning():
-  Entity.versioning(True)
-  assert Entity.versioning_on
-  Entity.set_version_count(3)
-  assert Entity.version_count==3
-  Entity.set_version_count(1)
-  #         r1                                                                    
-  #       /   \                                                                   
-  #    n1       n2                                                                
-  #            /|\                                                                
-  #          p1 p2 p3                
-  n1=Node({"handle":"n1"})
-  n2=Node({"handle":"n2"})  
-  r1=Edge({"handle":"r1","src":n1,"dst":n2})
-  p1=Property({"handle":"p1"})
-  p2=Property({"handle":"p2"})
-  p3=Property({"handle":"p3"})
-  n2.props['p1']=p1
-  n2.props['p2']=p2
-  n2.props['p3']=p3
-
-  assert r1.src == n1
-  assert r1.dst == n2
-  assert n2.props['p1'] == p1
-
-  for e in [n1,n2,r1,p1,p2,p3]:
-    assert e._from==1
-    assert not e._to
-
-  dup = n1.dup()
-  assert dup != n1
-  Entity.set_version_count(2) # bump version
-
-  #         r1       r21                                                          
-  #       /   \    /    \                                                         
-  #    n1       n2       n21                                                      
-  #            /|\        |                                                       
-  #          p1 p2 p3    p21                                                      
-
-  n21=Node({"handle":"n21"})
-  r21=Edge({"handle":"r21","src":n2,"dst":n21})
-  p21=Property({"handle":"p21"})
-  n21.props['p21']=p21
-  assert r1.dst == r21.src
-
-  for e in [r21,n21,p21]:
-    assert e._from == 2
-    assert not e._to
-
-  for e in [n1,n2,r1,p1,p2,p3]:
-    assert e._from == 1
-
-  Entity.set_version_count(3)
-
-  #         r1       r21                                                          
-  #       /   \    /    \                                                         
-  #    n1       n2       n21                                                      
-  #            /|\        |                                                       
-  #          p1 p2 p3    p21                                                      
-
-  n31=Node({"handle":"n31"})
-  n21.delete()
-  r21.dst=n31
-  assert r21.dst == n31
-  assert r21._prev
-  assert r21._prev._next == r21
-  assert r21._prev.handle == "r21"
-  assert r21._prev.dst == n21
-
-  n1._commit = "blarf"
-  assert n1._commit == "blarf"
-  assert not n1._prev._commit # prev version attr still empth
-  assert not n1._prev._prev # only two versions of n1
-  assert r1._prev # changing n1 induced a change on r1 (owner of n1)
-  assert r1.src._commit == "blarf" # latest r1 src is the latest n1
-  assert not r1._prev.src._commit # old r1 src, old n1, has empty category attr
-  assert not r1._prev._prev # only 2 versions of r1
-  prev = n1._prev
-  n1.model="test2" # change another attr shouldn't dup
-  assert n1._prev == prev # and it didn't dup
-  assert prev._next == n1 # yep
-
-  Entity.set_version_count(4)
-  #         r1       r21 --                                                       
-  #       /   \    /        \                                                     
-  #    n1*      n2 --       n31                                                   
-  #            /|\    \      /                                                    
-  #          p1 p2 p3 p41  p21                                                    
-
-  p41=Property({"handle":"p41"})
-  n2.props['p41']=p41
-  assert n2._prev
-  assert not 'p41' in n2._prev.props
-  assert n2.props['p41'] == p41
-
+    Entity.versioning(True)
+    assert Entity.versioning_on
+    Entity.set_version_count(3)
+    assert Entity.version_count == 3
+    Entity.set_version_count(1)
+    #         r1
+    #       /   \
+    #    n1       n2
+    #            /|\
+    #          p1 p2 p3
+    n1 = Node({"handle": "n1"})
+    n2 = Node({"handle": "n2"})
+    r1 = Edge({"handle": "r1", "src": n1, "dst": n2})
+    p1 = Property({"handle": "p1"})
+    p2 = Property({"handle": "p2"})
+    p3 = Property({"handle": "p3"})
+    n2.props["p1"] = p1
+    n2.props["p2"] = p2
+    n2.props["p3"] = p3
+
+    assert r1.src == n1
+    assert r1.dst == n2
+    assert n2.props["p1"] == p1
+
+    for e in [n1, n2, r1, p1, p2, p3]:
+        assert e._from == 1
+        assert not e._to
+
+    dup = n1.dup()
+    assert dup != n1
+    Entity.set_version_count(2)  # bump version
+
+    #         r1       r21
+    #       /   \    /    \
+    #    n1       n2       n21
+    #            /|\        |
+    #          p1 p2 p3    p21
+
+    n21 = Node({"handle": "n21"})
+    r21 = Edge({"handle": "r21", "src": n2, "dst": n21})
+    p21 = Property({"handle": "p21"})
+    n21.props["p21"] = p21
+    assert r1.dst == r21.src
+
+    for e in [r21, n21, p21]:
+        assert e._from == 2
+        assert not e._to
+
+    for e in [n1, n2, r1, p1, p2, p3]:
+        assert e._from == 1
+
+    Entity.set_version_count(3)
+
+    #         r1       r21
+    #       /   \    /    \
+    #    n1       n2       n21
+    #            /|\        |
+    #          p1 p2 p3    p21
+
+    n31 = Node({"handle": "n31"})
+    n21.delete()
+    r21.dst = n31
+    assert r21.dst == n31
+    assert r21._prev
+    assert r21._prev._next == r21
+    assert r21._prev.handle == "r21"
+    assert r21._prev.dst == n21
+
+    n1._commit = "blarf"
+    assert n1._commit == "blarf"
+    assert not n1._prev._commit  # prev version attr still empth
+    assert not n1._prev._prev  # only two versions of n1
+    assert r1._prev  # changing n1 induced a change on r1 (owner of n1)
+    assert r1.src._commit == "blarf"  # latest r1 src is the latest n1
+    assert not r1._prev.src._commit  # old r1 src, old n1, has empty category attr
+    assert not r1._prev._prev  # only 2 versions of r1
+    prev = n1._prev
+    n1.model = "test2"  # change another attr shouldn't dup
+    assert n1._prev == prev  # and it didn't dup
+    assert prev._next == n1  # yep
+
+    Entity.set_version_count(4)
+    #         r1       r21 --
+    #       /   \    /        \
+    #    n1*      n2 --       n31
+    #            /|\    \      /
+    #          p1 p2 p3 p41  p21
+
+    p41 = Property({"handle": "p41"})
+    n2.props["p41"] = p41
+    assert n2._prev
+    assert not "p41" in n2._prev.props
+    assert n2.props["p41"] == p41
+    Entity.versioning(False)
+    assert not Entity.versioning_on
+
+
 if __name__ == "__main__":
-  test_object_versioning()
+    test_object_versioning()

python/tests/test_014changelog.py

@@ -2,19 +2,19 @@
 import os
 import sys
 
-from bento_mdf.diff import diff_models
 from bento_mdf.mdf import MDF
 from bento_meta.objects import Property
 from bento_meta.util.changelog import update_config_changeset_id
-from scripts.make_diff_changelog import convert_diff_to_changelog
+from liquichange.changelog import Changeset
+
+sys.path.append("../")
+
 from scripts.make_mapping_changelog import convert_mappings_to_changelog
 from scripts.make_model_changelog import (
     convert_model_to_changelog,
     escape_quotes_in_attr,
 )
 
-sys.path.append("../")
-
 # define filepaths for sample MDFs
 CURRENT_DIRECTORY = os.path.dirname(os.path.abspath(__file__))
 TEST_MDF = os.path.join(CURRENT_DIRECTORY, "samples", "test_mdf.yml")
@@ -38,21 +38,6 @@ def test_make_model_changelog():
     assert len(changelog.subelements) == 46
 
 
-# make_diff_changelog
-def test_make_diff_changelog():
-    mdf_old = MDF(TEST_MDF, handle=MODEL_HDL, _commit=_COMMIT, raiseError=True)
-    mdf_new = MDF(TEST_MDF_DIFF, handle=MODEL_HDL, _commit=_COMMIT, raiseError=True)
-    diff = diff_models(mdl_a=mdf_old.model, mdl_b=mdf_new.model)
-    changelog = convert_diff_to_changelog(
-        diff=diff,
-        model_handle=MODEL_HDL,
-        author=AUTHOR,
-        config_file_path=TEST_CHANGELOG_CONFIG,
-    )
-    update_config_changeset_id(TEST_CHANGELOG_CONFIG, 1)
-    assert len(changelog.subelements) == 33
-
-
 # make_mapping_changelog
 def test_make_mapping_changelog():
     changelog = convert_mappings_to_changelog(
@@ -62,6 +47,9 @@ def test_make_mapping_changelog():
         _commit=_COMMIT,
     )
     update_config_changeset_id(TEST_CHANGELOG_CONFIG, 1)
+    sample_changeset = changelog.subelements[0]
+    assert isinstance(sample_changeset, Changeset)
+    assert sample_changeset.run_always is True
     assert len(changelog.subelements) == 6