fix: Loading transcript mapping in lifespan (#14) (#15)

bihealth · Oct 16, 2023 · 62fdc32 · 62fdc32
1 parent 74b6199
commit 62fdc32
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Showing 2 changed files with 25 additions and 0 deletions.
diff --git a/dotty/main.py b/dotty/main.py
@@ -43,8 +43,24 @@ async def lifespan(app: FastAPI):  # pragma: no cover
                 assembly.value
                 not in driver.data_providers[assembly]
                 ._get_transcript(transcript)["genome_builds"]
+                .keys()  # genome build is not in the transcript data
+                or "hgnc" not in driver.data_providers[assembly]._get_transcript(transcript)
+                or "cds_start"
+                not in driver.data_providers[assembly]
+                ._get_transcript(transcript)["genome_builds"][assembly.value]
+                .keys()
+                or "cds_end"
+                not in driver.data_providers[assembly]
+                ._get_transcript(transcript)["genome_builds"][assembly.value]
+                .keys()
+                or "exons"
+                not in driver.data_providers[assembly]
+                ._get_transcript(transcript)["genome_builds"][assembly.value]
                 .keys()
             ):
+                _logger.warning(
+                    f"Skipping transcript {transcript} as it does not have all required data"
+                )
                 continue
             hgnc_id = f"HGNC:{driver.data_providers[assembly]._get_transcript(transcript)['hgnc']}"
             hgnc_to_transcripts.setdefault(hgnc_id, []).append(

diff --git a/tests/test_main.py b/tests/test_main.py
@@ -71,6 +71,15 @@ def _setup_mock_transcript_data() -> typing.Dict[Assembly, typing.Any]:
     return assembly_to_hgnc_to_transcripts
 
 
+def test_lifespan(monkeypatch: MonkeyPatch):
+    monkeypatch.setattr(dotty_main, "driver", _setup_mock_driver("c", "NC_000017.10"))
+    dotty_main.lifespan(dotty_main.app)
+    assert dotty_main.driver is not None
+    assert dotty_main.hgnc_to_transcripts is not None
+    assert dotty_main.assembly_to_hgnc_to_transcripts is not None
+    assert dotty_main.contig_names is not None
+
+
 def test_to_spdi_c(test_client: TestClient, monkeypatch: MonkeyPatch):
     monkeypatch.setattr(dotty_main, "driver", _setup_mock_driver("c", "NC_000017.10"))
     response = test_client.get("/api/v1/to-spdi?q=NM_000059.3:c.274G>A")