From a389b54f86e5c499534a8c1bf5ea57fec074e9d7 Mon Sep 17 00:00:00 2001
From: SeriousHorncat <ange.unoantonison@gmail.com>
Date: Wed, 11 Dec 2024 16:07:30 -0600
Subject: [PATCH] Fixed linting and added gnomad to be added as annotations;
 even though not visualizing yet.  Some additional linkout datasets included
 also.

---
 backend/tests/unit/core/test_annotation_task.py   |  5 +++--
 etc/fixtures/initial-seed/annotations-config.json | 10 ++++++++++
 frontend/src/models/analyses.js                   |  4 ++--
 3 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/backend/tests/unit/core/test_annotation_task.py b/backend/tests/unit/core/test_annotation_task.py
index f19b18f7..bb303029 100644
--- a/backend/tests/unit/core/test_annotation_task.py
+++ b/backend/tests/unit/core/test_annotation_task.py
@@ -51,7 +51,7 @@ def test_extraction_forge_hgvs_variant_without_transcript_version(hgvs_without_t
     """Verifies the jq query used to forge create the transcript without a version dataset for a variant"""
     forge_annotation = hgvs_without_transcript_version_annotation_task.annotate()
     actual_extractions = hgvs_without_transcript_version_annotation_task.extract(forge_annotation)
-    assert(actual_extractions, "NM_170707:c.745C>T")
+    assert actual_extractions == "NM_170707:c.745C>T"
 
 
 def test_annotation_extraction_for_transcript_id_dataset(http_annotation_transcript_id, transcript_annotation_response):
@@ -258,13 +258,14 @@ def fixture_transcript_id_dataset():
 
 @pytest.fixture(name="hgvs_without_transcript_version_annotation_task")
 def fixture_hgvs_without_transcript_version(hgvs_variant_genomic_unit):
+    """An Annotation Unit to experiment with jq parsing and rebuilding a string in a result."""
     annotation_unit = AnnotationUnit(hgvs_variant_genomic_unit, {
         "data_set": "hgvs_variant_without_transcript_version",
         "data_source": "Rosalution",
         "annotation_source_type": "forge",
         "genomic_unit_type": "hgvs_variant",
         "base_string": "{hgvs_variant}",
-        "attribute": ".hgvs_variant_without_transcript_version | split(\":\") as $transcript_split | $transcript_split[0] | split(\".\")[0] | . + \":\" + $transcript_split[1] | {\"hgvs_variant_without_transcript_version\": .}",
+        "attribute": ".hgvs_variant_without_transcript_version | split(\":\") as $transcript_split | $transcript_split[0] | split(\".\")[0] | . + \":\" + $transcript_split[1] | {\"hgvs_variant_without_transcript_version\": .}", # pylint: disable=line-too-long 
         "versioning_type": "rosalution"
     })
     task = ForgeAnnotationTask(annotation_unit)
diff --git a/etc/fixtures/initial-seed/annotations-config.json b/etc/fixtures/initial-seed/annotations-config.json
index a95dddd4..802a3e9d 100644
--- a/etc/fixtures/initial-seed/annotations-config.json
+++ b/etc/fixtures/initial-seed/annotations-config.json
@@ -238,6 +238,16 @@
     "dependencies": ["ensembl_vep_vcf_string"],
     "versioning_type": "rosalution"
   },
+  {
+    "data_set": "gnomAD4",
+    "data_source": "OpenCravat",
+    "genomic_unit_type": "hgvs_variant",
+    "annotation_source_type": "http",
+    "base_string": "https://run.opencravat.org/submit/annotate?{opencravat_search_variant_vcf_string}&annotators=gnomad4",
+    "attribute": "{ \"gnomad4\": .gnomad4 }",
+    "dependencies": ["opencravat_search_variant_vcf_string"],
+    "versioning_type": "date"
+  },
   {
     "data_set": "COSMIC_gene_url",
     "data_source": "Rosalution",
diff --git a/frontend/src/models/analyses.js b/frontend/src/models/analyses.js
index 855360a6..0d05c5ee 100644
--- a/frontend/src/models/analyses.js
+++ b/frontend/src/models/analyses.js
@@ -323,7 +323,7 @@ const annotationRenderingTemporary = [
         'imageFilename': 'cosmic_logo.png',
         'altText': 'Catalogue Of Somatic Mutations In Cancer, COSMIC',
       },
-    },{
+    }, {
       'dataset': 'gnomAD_gene_url',
       'type': 'icon-linkout-dataset',
       'props': {
@@ -451,7 +451,7 @@ const annotationRenderingTemporary = [
               'set': [
                 {'value': 'likely_benign', 'classification': 'Likely Benign', 'colour': 'Blue'},
                 {'value': 'ambiguous', 'classification': 'Ambiguous', 'colour': 'Yellow'},
-                {'value': 'likely_pathogenic', 'classification': 'Likely Pathogenic', 'colour': 'Red'}
+                {'value': 'likely_pathogenic', 'classification': 'Likely Pathogenic', 'colour': 'Red'},
               ],
             },
           },