Merge pull request #575 from biolink/gocamgen-issue-90-modeltitle-fmt

Gocamgen issue 90 modeltitle fmt
biolink · Jun 10, 2021 · 2066457 · 2066457
2 parents 4def878 + dc5aaa3
commit 2066457
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Showing 2 changed files with 26 additions and 2 deletions.
diff --git a/ontobio/rdfgen/gocamgen/gocam_builder.py b/ontobio/rdfgen/gocamgen/gocam_builder.py
@@ -50,8 +50,12 @@ def __init__(self, parser_config: AssocParserConfig, modelstate=None):
         self.modelstate = modelstate
 
     def translate_to_model(self, gene, assocs: List[GoAssociation]):
+        if gene not in self.gpi_entities:
+            error_msg = "Gene ID '{}' missing from provided GPI. Skipping model translation.".format(gene)
+            raise GocamgenException(error_msg)
         model_id = gene.replace(":", "_")
-        model = AssocGoCamModel(gene,
+        model_title = self.model_title(gene)
+        model = AssocGoCamModel(model_title,
                                 assocs,
                                 config=self.config,
                                 store=self.store,
@@ -115,6 +119,14 @@ def write_report(self, report_filepath):
                 for ex in errs:
                     reportf.write(f"{type(ex).__name__} - {gene}: {ex}\n")
 
+    def model_title(self, gene_id: str) -> str:
+        entity = self.gpi_entities.get(gene_id)
+        if entity:
+            model_title = "{} ({})".format(entity["label"], gene_id)
+        else:
+            model_title = gene_id
+        return model_title
+
     @staticmethod
     def extract_relations_ontology(ontology_graph):
         # TODO: This is probably all wrong - trying to reconstruct RO from broader ontology_graph

diff --git a/tests/test_gocamgen.py b/tests/test_gocamgen.py
@@ -4,7 +4,9 @@
 from ontobio.ontol_factory import OntologyFactory
 from ontobio.rdfgen.gocamgen import collapsed_assoc, gocam_builder, gocamgen
 
-GO_ONTO = OntologyFactory().create("tests/resources/go-binding.json")
+GO_ONTO = OntologyFactory().create("tests/resources/go-binding.json")  # Placeholder ontology to instantiate models
+PARSER_CONFIG = assocparser.AssocParserConfig(ontology=GO_ONTO,
+                                              gpi_authority_path="tests/resources/mgi2.test_entities.gpi")
 
 
 def test_evidence_max_date():
@@ -83,3 +85,13 @@ def test_ref_picker():
     test_refs = ["ZFIN:ZDB-PUB-170709-3"]
     result = gocamgen.ReferencePreference.pick(test_refs)
     assert result == "ZFIN:ZDB-PUB-170709-3"
+
+
+def test_model_title():
+    builder = gocam_builder.GoCamBuilder(parser_config=PARSER_CONFIG, modelstate="test")
+    title = builder.model_title(gene_id="MGI:MGI:1915834")
+    assert title == "1110020C17Rik (MGI:MGI:1915834)"
+
+    # Fallback to gene_id as title if not found in GPI
+    title = builder.model_title(gene_id="FAKE:1915834")
+    assert title == "FAKE:1915834"