Added another unit test to verify that 'deprecate' value is propagate…

…d. Seems to work. Issue perhaps resolved?

tests/resources/phenio.json

@@ -0,0 +1,53 @@
+{
+  "graphs": [
+    {
+      "nodes": [
+        {
+          "id": "http://purl.obolibrary.org/obo/GO_0051370",
+          "lbl": "obsolete ZASP binding",
+          "type": "INDIVIDUAL",
+          "meta": {
+            "definition": {
+              "val": "OBSOLETE. Binding to Z-band alternatively spliced PDZ motif protein (ZASP). ZASP is a Z-band protein specifically expressed in heart and skeletal muscle. This protein contains N-terminal PDZ domain and C-terminal LIM domain.",
+              "xrefs": [
+                "PMID:10427098",
+                "PMID:11699871"
+              ]
+            },
+            "comments": [
+              "This term was made obsolete because it represents binding to an individual protein."
+            ],
+            "synonyms": [
+              {
+                "pred": "hasExactSynonym",
+                "val": "Z-band alternatively spliced PDZ-motif protein binding"
+              },
+              {
+                "pred": "hasExactSynonym",
+                "val": "ZASP binding"
+              }
+            ],
+            "basicPropertyValues": [
+              {
+                "pred": "http://purl.obolibrary.org/obo/IAO_0100001",
+                "val": "GO:0008092"
+              },
+              {
+                "pred": "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace",
+                "val": "molecular_function"
+              }
+            ],
+            "deprecated": true
+          }
+        }
+      ],
+      "edges": [],
+      "id": "http://purl.obolibrary.org/obo/phenio.owl",
+      "meta": {
+        "subsets": [],
+        "xrefs": [],
+        "basicPropertyValues": []
+      }
+    }
+  ]
+}

tests/unit/test_source/test_obograph_source.py

@@ -2,9 +2,10 @@
 
 import pytest
 
-from kgx.source import ObographSource
+from kgx.cli import transform
+from kgx.source import ObographSource, TsvSource
 from kgx.transformer import Transformer
-from tests import RESOURCE_DIR
+from tests import RESOURCE_DIR, TARGET_DIR
 
 
 def test_read_obograph1():
@@ -130,6 +131,29 @@ def test_read_deprecated_term():
     assert n1["deprecated"] is True
 
 
+def test_read_deprecated_term_phenio():
+    """
+    Read from a Phenio JSON using ObographSource,
+    to validate capture of "deprecate" status
+    """
+    t = Transformer()
+    s = ObographSource(t)
+    g = s.parse(
+        os.path.join(RESOURCE_DIR, "phenio.json"),
+        knowledge_source="Phenomics Integrative Ontology",
+    )
+    nodes = {}
+    for rec in g:
+        if rec:
+            if len(rec) != 4:
+                nodes[rec[0]] = rec[1]
+
+    n1 = nodes["GO:0051370"]
+    assert n1["id"] == "GO:0051370"
+    assert n1["name"] == "obsolete ZASP binding"
+    assert n1["deprecated"] is True
+
+
 @pytest.mark.parametrize(
     "query",
     [
@@ -228,3 +252,34 @@ def test_error_detection():
         t.write_report(None, "Error")
     if len(t.get_errors("Warning")) > 0:
         t.write_report(None, "Warning")
+
+
+def test_phenio_obojson_to_tsv():
+    """
+    Testing transitive propagation of node properties
+    (mainly node 'deprecated' status)
+    from a Phenio JSON to TSV file format
+    """
+    transform(
+        inputs=[os.path.join(RESOURCE_DIR, "phenio.json")],
+        input_format="obojson",
+        output=os.path.join(TARGET_DIR, "phenio"),
+        output_format="tsv",
+        stream=False
+    )
+
+    tin = Transformer()
+    s = TsvSource(tin)
+
+    g = s.parse(filename=os.path.join(TARGET_DIR, "phenio_nodes.tsv"), format="tsv")
+
+    nodes = {}
+    for rec in g:
+        if rec:
+            if len(rec) != 4:
+                nodes[rec[0]] = rec[1]
+
+    n1 = nodes["GO:0051370"]
+    assert n1["id"] == "GO:0051370"
+    assert n1["name"] == "obsolete ZASP binding"
+    assert n1["deprecated"] is True