From a2fd920322d03d5b4213077467ee440a92148823 Mon Sep 17 00:00:00 2001 From: Kirill Tsukanov Date: Wed, 20 Jan 2021 10:01:59 +0000 Subject: [PATCH] Update to OT schema 1.7.5 --- docs/generate-evidence-strings.md | 4 ++-- .../resources/CTTVGeneticsEvidenceString.json | 2 +- .../resources/CTTVSomaticEvidenceString.json | 2 +- tests/evidence_string_generation/config.py | 2 +- .../expected_genetics_evidence_string.json | 2 +- .../expected_somatic_evidence_string.json | 2 +- .../resources/opentargets.1.7.3.json.gz | Bin 6104 -> 0 bytes .../resources/opentargets.1.7.5.json.gz | Bin 0 -> 6118 bytes .../test_evidence_strings.py | 2 +- 9 files changed, 8 insertions(+), 8 deletions(-) delete mode 100644 tests/evidence_string_generation/resources/opentargets.1.7.3.json.gz create mode 100644 tests/evidence_string_generation/resources/opentargets.1.7.5.json.gz diff --git a/docs/generate-evidence-strings.md b/docs/generate-evidence-strings.md index 439d34fb..da0f4329 100644 --- 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 index 529ffe95..c8dbadb6 100644 --- 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 index b6129d55..2fc6e545 100644 --- 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 index d1ddb34d..1760c96b 100644 --- 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 index a3fcd6cb..fb3a5b9b 100644 --- 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 index b9a35be7..0e6c81d2 100644 --- 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" } \ No newline at end of file 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 deleted file mode 100644 index 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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):