Merge 6059d5c into e80ac65

Jenkinsfile

@@ -100,6 +100,14 @@ pipeline {
             }
         }
 
+        stage('QC'){
+            steps {
+                dir('./gitrepo') {
+                    sh '. venv/bin/activate && python3.7 queries/qc/ensmallen_report.py'
+                }
+            }
+        }
+
         stage('Make blazegraph journal'){
             steps {
                 dir('./gitrepo/blazegraph') {

queries/qc/ensmallen_report.py

@@ -0,0 +1,26 @@
+from ensmallen_graph import EnsmallenGraph
+import tarfile
+import compress_json
+
+tar = tarfile.open("kg-covid-19.tar.gz")
+
+tar.extractall()
+graph = EnsmallenGraph.from_csv(
+    edge_path="merged-kg_edges.tsv",
+    sources_column="subject",
+    destinations_column="object",
+    directed=False,
+    edge_types_column="edge_label",
+    default_edge_type="biolink:association",
+    node_path="merged-kg_nodes.tsv",
+    nodes_column="id",
+    node_types_column="category",
+    default_node_type="biolink:NamedThing",
+    ignore_duplicated_edges=True,
+    ignore_duplicated_nodes=True,
+    force_conversion_to_undirected=True
+)
+
+json_report = graph.report()
+compress_json.dump(json_report, "kg-covid-19-ensmallen-report.json")
+

queries/qc/ensmallen_report_expected_values.yaml

@@ -0,0 +1,12 @@
+degrees_mode
+bidirectional_rate
+strongly_connected_components_number
+nodes_number
+edges_number
+density
+singleton_nodes
+unique_edge_types_number
+connected_components_number
+unique_node_types_number
+degrees_median
+