Merge remote-tracking branch 'origin/master' into new-data-source-format

biothings · Feb 8, 2024 · f262209 · f262209
2 parents 85eb4b2 + 238fcc9
commit f262209
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Showing 3 changed files with 11 additions and 1 deletion.
diff --git a/src/hub/dataload/sources/clinvar/clinvar_upload.py b/src/hub/dataload/sources/clinvar/clinvar_upload.py
@@ -159,6 +159,14 @@ def get_mapping(klass):
                                             "human_phenotype_ontology": {
                                                 "type": "text",
                                                 "analyzer": "string_lowercase"
+                                            },
+                                            "mondo": {
+                                                "type": "text",
+                                                "analyzer": "string_lowercase"
+                                            },
+                                            "mesh": {
+                                                "type": "text",
+                                                "analyzer": "string_lowercase"
                                             }
                                         }
                                     },

diff --git a/src/tests/data/test_annotation.py b/src/tests/data/test_annotation.py
@@ -91,7 +91,7 @@ def test_043_annotation_post(self):
         # TODO redo this test, doesn't test much really....
         res = self.request("variant", method='POST',
                            data={'ids': 'chr16:g.28883241A>G,chr8:g.19813529A>G',
-                                 'filter': 'dbsnp.chrom'}).json()
+                                 'fields': 'dbsnp.chrom'}).json()
         assert len(res) == 2
         for _g in res:
             assert set(_g) == set(['_id', 'query', 'dbsnp', '_version'])

diff --git a/static/context/context.json b/static/context/context.json
@@ -10,6 +10,8 @@
         "clinvar.rcv.conditions.identifiers.omim": "http://identifiers.org/omim/",
         "clinvar.rcv.conditions.identifiers.efo": "http://identifiers.org/efo/",
         "clinvar.rcv.conditions.identifiers.orphanet": "http://identifiers.org/orphanet/",
+        "clinvar.rcv.conditions.identifiers.mesh": "http://identifiers.org/mesh/",
+        "clinvar.rcv.conditions.identifiers.mondo": "http://identifiers.org/mondo/",
         "clinvar.gene.symbol": "http://identifiers.org/hgnc.symbol/",
         "clinvar.gene.id": "http://identifiers.org/ncbigene/",
         "dbnsfp.rsid": "http://identifiers.org/dbsnp/",