Merge pull request #674 from alliance-genome/add_xenbase_phenotype

Add XBXL and XBXT to PHENOTYPE data class.

src/config/default.yml

@@ -4,7 +4,7 @@ BGI: [FB, SGD, WB, ZFIN, RGD, MGI, HUMAN, XBXL, XBXT, SARS-CoV-2]
 CONSTRUCT: [ZFIN, WB, FB, MGI]
 ALLELE: [FB, WB, ZFIN, RGD, MGI, SGD]
 EXPRESSION: [FB, SGD, WB, ZFIN, RGD, MGI, XBXL, XBXT]
-PHENOTYPE: [FB, SGD, WB, ZFIN, RGD, MGI, HUMAN]
+PHENOTYPE: [FB, SGD, WB, ZFIN, RGD, MGI, HUMAN, XBXL, XBXT]
 DAF: [FB, SGD, WB, ZFIN, RGD, MGI, HUMAN]
 GAF: [FB, SGD, WB, ZFIN, RGD, MGI, XB, HUMAN]
 GEOXREF: [FB, SGD, WB, ZFIN, RGD, MGI, HUMAN]

src/config/validation.yml

@@ -21,7 +21,7 @@ DAF:
   allowed: [FB, SGD, WB, ZFIN, RGD, MGI, HUMAN]
 PHENOTYPE:
   type: list
-  allowed: [FB, SGD, WB, ZFIN, RGD, MGI, HUMAN]
+  allowed: [FB, SGD, WB, ZFIN, RGD, MGI, HUMAN, XBXL, XBXT]
 EXPRESSION:
   type: list
   allowed: [FB, SGD, WB, ZFIN, RGD, MGI, XBXL, XBXT]

src/test/specific_tests.py

@@ -304,7 +304,7 @@ def test_phenotype_for_all_species_exists():
                RETURN count(distinct s) AS counter"""
     with Neo4jHelper.run_single_query(query) as result:
         for record in result:
-            assert record["counter"] == 7
+            assert record["counter"] == 8
 
 
 def test_variant_for_expected_species_exists():