Merge pull request #18 from MRCIEU/migration-v1

Changes related to v1.0 updates
MRCIEU · Mar 11, 2021 · 27edc44 · 27edc44
2 parents 2d6f9cb + bb5b148
commit 27edc44
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Showing 3 changed files with 24 additions and 14 deletions.
diff --git a/config/db_schema.yaml b/config/db_schema.yaml
@@ -995,7 +995,12 @@ meta_rels:
         type: float
       selection:
         doc: >-
-          TODO Ben
+          Instrument selection.
+
+          - DF: directionality filtering
+          - HF: heterogeneity filtering
+          - Tophits: no filtering
+          - DF + HF: both types of filtering
         type: string
     required:
       - source
@@ -1065,7 +1070,7 @@ meta_rels:
       - action_type
   PATHWAY_CHILD_OF:
     doc: >-
-      Parent/child relationship of pathways. 
+      Parent/child relationship of pathways.
     properties:
       source:
         doc: ''

diff --git a/epigraphdb_common_utils b/epigraphdb_common_utils
diff --git a/tests/graph_database/test_db_schema.py b/tests/graph_database/test_db_schema.py
@@ -4,7 +4,7 @@
 
 from workflow.scripts.utils.general import neo4j_connect
 
-from tests.utils.load_schema import meta_node_names, meta_rel_names
+from tests.utils.load_schema import meta_node_names, meta_rel_names, meta_node_dict
 
 
 def test_connect():
@@ -24,8 +24,8 @@ def test_meta_node_exist():
         CALL db.labels() YIELD label RETURN label
     """
     driver = neo4j_connect()
-    session = driver.session()
-    data = session.run(query).data()
+    with driver.session() as session:
+        data = session.run(query).data()
     db_meta_node_names = set([_["label"] for _ in data])
     if {"Meta"}.issubset(db_meta_node_names):
         db_meta_node_names.remove({"Meta"})
@@ -41,17 +41,22 @@ def test_meta_rel_exist():
         RETURN relationshipType AS label
     """
     driver = neo4j_connect()
-    session = driver.session()
-    data = session.run(query).data()
+    with driver.session() as session:
+        data = session.run(query).data()
     db_meta_rel_names = set([_["label"] for _ in data])
     logger.info(f"meta_rel_names: {meta_rel_names}")
     logger.info(f"db_meta_rel_names: {db_meta_rel_names}")
     assert set(meta_rel_names) == db_meta_rel_names
 
 
-def main():
-    pass
-
-
-if __name__ == "__main__":
-    main()
+def test_meta_node_index():
+    query = "CALL db.indexes()"
+    driver = neo4j_connect()
+    with driver.session() as session:
+        data = session.run(query).data()
+    actual_node_indexes = {(_["labelsOrTypes"][0], _["properties"][0]) for _ in data}
+    expected_node_indexes = {
+        (key, value["index"]) for key, value in meta_node_dict.items()
+    }
+    # We would expect expected_indexes to be a subset of current_indexes
+    assert len(expected_node_indexes.difference(actual_node_indexes)) == 0
+21 −2		api_env_configs.py
+0 −353		data-dict-meta-nodes.yml
+0 −620		data-dict-meta-rels.yml
+621 −252		db_schema.yaml
+72 −59		epigraphdb_data_dicts.py
+17 −11		tests/test_epigraphdb_data_dicts.py