Update to OT schema 1.7.5

EBIvariation · Jan 20, 2021 · a2fd920 · a2fd920
1 parent b1f78a1
commit a2fd920
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Showing 9 changed files with 8 additions and 8 deletions.
diff --git a/docs/generate-evidence-strings.md b/docs/generate-evidence-strings.md
@@ -19,8 +19,8 @@ export OT_RELEASE=YYYY-MM
 export CLINVAR_RELEASE_YEAR=YYYY
 export CLINVAR_RELEASE_MONTH=MM
 
-# Open Targets JSON schema version
-export OT_SCHEMA_VERSION=1.7.3
+# Open Targets JSON schema version.
+export OT_SCHEMA_VERSION=1.7.5
 
 # Open Targets validator schema version
 export OT_VALIDATOR_VERSION=0.6.0

diff --git a/eva_cttv_pipeline/evidence_string_generation/resources/CTTVGeneticsEvidenceString.json b/eva_cttv_pipeline/evidence_string_generation/resources/CTTVGeneticsEvidenceString.json
@@ -6,7 +6,7 @@
     "type": null,
     "id": []
   },
-  "validated_against_schema_version": "1.7.3",
+  "validated_against_schema_version": "1.7.5",
   "disease": {
     "id": []
   },

diff --git a/eva_cttv_pipeline/evidence_string_generation/resources/CTTVSomaticEvidenceString.json b/eva_cttv_pipeline/evidence_string_generation/resources/CTTVSomaticEvidenceString.json
@@ -2,7 +2,7 @@
   "type": "somatic_mutation",
   "access_level": "public",
   "sourceID": "eva_somatic",
-  "validated_against_schema_version": "1.7.3",
+  "validated_against_schema_version": "1.7.5",
   "disease": {
     "id": []
   },

diff --git a/tests/evidence_string_generation/config.py b/tests/evidence_string_generation/config.py
@@ -4,6 +4,6 @@
 
 snp_2_gene_file = os.path.join(test_dir, 'resources/snp2gene_extract.tsv')
 test_clinvar_record_file = os.path.join(test_dir, 'resources/test_clinvar_record.json')
-open_targets_schema_gz = os.path.join(test_dir, 'resources/opentargets.1.7.3.json.gz')
+open_targets_schema_gz = os.path.join(test_dir, 'resources/opentargets.1.7.5.json.gz')
 expected_genetics_evidence_string = os.path.join(test_dir, 'resources/expected_genetics_evidence_string.json')
 expected_somatic_evidence_string = os.path.join(test_dir, 'resources/expected_somatic_evidence_string.json')
diff --git a/tests/evidence_string_generation/resources/expected_genetics_evidence_string.json b/tests/evidence_string_generation/resources/expected_genetics_evidence_string.json
@@ -128,7 +128,7 @@
     "phenotype": "http://www.orpha.net/ORDO/Orphanet_88991",
     "variant_id": "rs28940313"
   },
-  "validated_against_schema_version": "1.7.3",
+  "validated_against_schema_version": "1.7.5",
   "variant": {
     "id": "http://identifiers.org/dbsnp/rs28940313",
     "type": "snp single"

diff --git a/tests/evidence_string_generation/resources/expected_somatic_evidence_string.json b/tests/evidence_string_generation/resources/expected_somatic_evidence_string.json
@@ -100,5 +100,5 @@
     "phenotype": "http://www.orpha.net/ORDO/Orphanet_88991",
     "variant_id": "rs28940313"
   },
-  "validated_against_schema_version": "1.7.3"
+  "validated_against_schema_version": "1.7.5"
 }
diff --git a/tests/evidence_string_generation/resources/opentargets.1.7.3.json.gz b/tests/evidence_string_generation/resources/opentargets.1.7.3.json.gz
diff --git a/tests/evidence_string_generation/resources/opentargets.1.7.5.json.gz b/tests/evidence_string_generation/resources/opentargets.1.7.5.json.gz
diff --git a/tests/evidence_string_generation/test_evidence_strings.py b/tests/evidence_string_generation/test_evidence_strings.py
@@ -214,7 +214,7 @@ def setUp(self):
         test_args = get_input_data_for_evidence_string_generation()
         self.test_ses = evidence_strings.CTTVSomaticEvidenceString(*test_args)
         ot_schema_path = os.path.join(
-            os.path.dirname(__file__), 'resources', 'opentargets.1.7.3.json.gz')
+            os.path.dirname(__file__), 'resources', 'opentargets.1.7.5.json.gz')
         self.ot_schema_contents = json.loads(gzip.open(ot_schema_path).read().decode('utf-8'))
 
     def test_db_xref_url(self):