New annotations from opencravat (#188)

* Rendering some of the new linkouts and datasets, with some fixture updates * Fixed linting and added gnomad to be added as annotations; even though not visualizing yet. Some additional linkout datasets included also.
uab-cgds-worthey · Dec 11, 2024 · 95499a8 · 95499a8
1 parent bc739b6
commit 95499a8
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diff --git a/backend/src/core/annotation_unit.py b/backend/src/core/annotation_unit.py
@@ -100,10 +100,10 @@ def increment_delay_count(self):
 
     def delay_count_exceeds(self):
         """
-        Checks if the annotation unit has exceeded the delay count within the queue.
+        Checks if the annotation unit has exceeded the delay count within the queue
         Delay count is set as a magic number (10).
         """
-        if self.dataset['delay_count'] < 10:
+        if self.dataset['delay_count'] < 15:
             return False
         return True
 

diff --git a/backend/tests/unit/core/test_annotation_task.py b/backend/tests/unit/core/test_annotation_task.py
@@ -47,6 +47,13 @@ def test_extraction_forge_gene_linkout_dataset(forge_annotation_task_gene):
     assert extracted_annotations[0]['value'] == 'https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=45614'
 
 
+def test_extraction_forge_hgvs_variant_without_transcript_version(hgvs_without_transcript_version_annotation_task):
+    """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[0]['value'] == "NM_170707:c.745C>T"
+
+
 def test_annotation_extraction_for_transcript_id_dataset(http_annotation_transcript_id, transcript_annotation_response):
     """Verifying genomic unit extraction for a transcript using the the transcript ID dataset"""
     actual_extractions = http_annotation_transcript_id.extract(transcript_annotation_response)
@@ -250,6 +257,26 @@ 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\": .}",  # pylint: disable=line-too-long 
+            "versioning_type": "rosalution"
+        }
+    )
+    task = ForgeAnnotationTask(annotation_unit)
+    return task
+
+
 @pytest.fixture(name="hgvs_variant_annotation_unit")
 def fixture_hgvs_variant_annotation_unit(hgvs_variant_genomic_unit, transcript_id_dataset):
     """

diff --git a/backend/tests/unit/core/test_annotation_unit.py b/backend/tests/unit/core/test_annotation_unit.py
@@ -64,5 +64,5 @@ def fixture_annotation_unit_lmna_has_dependencies(annotation_unit_lmna):
 @pytest.fixture(name="annotation_unit_lmna_exceeded_delay_count")
 def fixture_annotation_unit_lmna_with_annotated_dependency(annotation_unit_lmna):
     """Returns the annotation unit for the genomic unit LMNA and the dataset Clingen gene url"""
-    annotation_unit_lmna.dataset['delay_count'] = 10
+    annotation_unit_lmna.dataset['delay_count'] = 20
     return annotation_unit_lmna
diff --git a/etc/fixtures/initial-seed/annotations-config.json b/etc/fixtures/initial-seed/annotations-config.json
@@ -1,24 +1,37 @@
 [
+  {
+      "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\": .}",
+      "versioning_type": "rosalution"
+  },
   {
     "data_set": "transcript_id",
     "data_source": "Ensembl",
     "genomic_unit_type": "hgvs_variant",
     "transcript": true,
     "annotation_source_type": "http",
-    "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
+    "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
     "attribute": ".[].transcript_consequences[] | { transcript_id: .transcript_id }",
+    "dependencies": ["hgvs_variant_without_transcript_version"],
     "versioning_type": "rest",
     "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
     "version_attribute": ".releases[]"
-   },
+  },
   {
-    "data_set": "HPO_NCBI_GENE_ID",
-    "data_source": "HPO",
-    "genomic_unit_type": "gene",
+    "data_set": "ensembl_vep_vcf_string",
+    "data_source": "Ensembl",
+    "genomic_unit_type": "hgvs_variant",
     "annotation_source_type": "http",
-    "url": "https://ontology.jax.org/api/network/search/GENE?q={gene}&page=0&limit=10",
-    "attribute": "{ \"HPO_NCBI_GENE_ID\": .results[] | select( .name == \"{gene}\") | .id }",
-    "versioning_type": "date" 
+    "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;vcf_string=1;",
+    "attribute": ".[] | {\"ensembl_vep_vcf_string\": .vcf_string} ",
+    "versioning_type": "rest",
+    "dependencies": ["hgvs_variant_without_transcript_version"],
+    "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
+    "version_attribute": ".releases[]"
   },
   {
     "data_set": "Ensembl Gene Id",
@@ -48,8 +61,9 @@
     "genomic_unit_type": "hgvs_variant",
     "annotation_source_type": "http",
     "attribute": ".[] | select(.colocated_variants != null) | .colocated_variants[] | select(.var_synonyms != null) | .var_synonyms | select( .ClinVar != null ) | select(.ClinVar != []) | .ClinVar[] | select(contains(\"VCV\")) | sub(\"VCV0+\"; \"\") | {\"ClinVar_Variantion_Id\": . } ",
-    "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;clinvar=1;",
-    "versioning_type": "rosalution"
+    "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;clinvar=1;",
+    "versioning_type": "rosalution",
+    "dependencies": ["hgvs_variant_without_transcript_version"]
   },
   {
     "data_set": "OMIM_gene_search_url",
@@ -214,6 +228,44 @@
     "dependencies": ["Ensembl Gene Id"],
     "versioning_type": "rosalution"
   },
+  {
+    "data_set": "gnomAD_variant_url",
+    "data_source": "Rosalution",
+    "genomic_unit_type": "hgvs_variant",
+    "annotation_source_type": "forge",
+    "base_string": "https://gnomad.broadinstitute.org/variant/{ensembl_vep_vcf_string}?dataset=gnomad_r4",
+    "attribute": "{ \"gnomAD_variant_url\": .gnomAD_variant_url }",
+    "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",
+    "genomic_unit_type": "gene",
+    "annotation_source_type": "forge",
+    "base_string": "https://cancer.sanger.ac.uk/cosmic/gene/analysis?ln={gene}",
+    "attribute": "{ \"COSMIC_gene_url\": .COSMIC_gene_url }",
+    "versioning_type": "rosalution"
+  },
+  {
+    "data_set": "HPO_NCBI_GENE_ID",
+    "data_source": "HPO",
+    "genomic_unit_type": "gene",
+    "annotation_source_type": "http",
+    "url": "https://ontology.jax.org/api/network/search/GENE?q={gene}&page=0&limit=10",
+    "attribute": "{ \"HPO_NCBI_GENE_ID\": .results[] | select( .name == \"{gene}\") | .id }",
+    "versioning_type": "date"
+  },
   {
     "data_set": "OMIM",
     "data_source": "HPO",
@@ -384,9 +436,10 @@
      "genomic_unit_type": "hgvs_variant",
      "transcript": true,
      "annotation_source_type": "http",
-     "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
+     "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
      "attribute": ".[].transcript_consequences[] | { polyphen_prediction: .polyphen_prediction, transcript_id: .transcript_id }",
      "versioning_type": "rest",
+     "dependencies": ["hgvs_variant_without_transcript_version"],
      "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
      "version_attribute": ".releases[]"
    },
@@ -396,9 +449,10 @@
      "genomic_unit_type": "hgvs_variant",
      "transcript": true,
      "annotation_source_type": "http",
-     "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
+     "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
      "attribute": ".[].transcript_consequences[] | { polyphen_score: .polyphen_score, transcript_id: .transcript_id }",
      "versioning_type": "rest",
+     "dependencies": ["hgvs_variant_without_transcript_version"],
      "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
      "version_attribute": ".releases[]"
    },
@@ -408,9 +462,10 @@
      "genomic_unit_type": "hgvs_variant",
      "transcript": true,
      "annotation_source_type": "http",
-     "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
+     "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
      "attribute": ".[].transcript_consequences[] | { sift_prediction: .sift_prediction, transcript_id: .transcript_id }",
      "versioning_type": "rest",
+     "dependencies": ["hgvs_variant_without_transcript_version"],
      "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
      "version_attribute": ".releases[]"
    },
@@ -420,9 +475,11 @@
      "genomic_unit_type": "hgvs_variant",
      "transcript": true,
      "annotation_source_type": "http",
-     "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
+     "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
      "attribute": ".[].transcript_consequences[] | { sift_score: .sift_score, transcript_id: .transcript_id }",
      "versioning_type": "rest",
+     "dependencies": ["hgvs_variant_without_transcript_version"],
+
      "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
      "version_attribute": ".releases[]"
    },
@@ -432,20 +489,57 @@
      "genomic_unit_type": "hgvs_variant",
      "transcript": true,
      "annotation_source_type": "http",
-     "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
+     "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
      "attribute": ".[].transcript_consequences[] | { consequence_terms: .consequence_terms, transcript_id: .transcript_id }",
+     "dependencies": ["hgvs_variant_without_transcript_version"],
      "versioning_type": "rest",
-     "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
+    "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
      "version_attribute": ".releases[]"
    },
    {
     "data_set": "CADD",
     "data_source": "Ensembl",
     "genomic_unit_type": "hgvs_variant",
     "annotation_source_type": "http",
-    "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;CADD=1;refseq=1;",
+    "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;CADD=1;refseq=1;",
     "attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { CADD: .cadd_phred }",
-    "dependencies": ["transcript"],
+    "dependencies": ["transcript","hgvs_variant_without_transcript_version"],
+    "versioning_type": "rest",
+    "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
+    "version_attribute": ".releases[]"
+  },
+  {
+    "data_set": "alphamissense_pathogenicity",
+    "data_source": "Ensembl",
+    "genomic_unit_type": "hgvs_variant",
+    "annotation_source_type": "http",
+    "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;AlphaMissense=1;refseq=1;",
+    "attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { alphamissense: .alphamissense.am_pathogenicity }",
+    "dependencies": ["transcript","hgvs_variant_without_transcript_version"],
+    "versioning_type": "rest",
+    "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
+    "version_attribute": ".releases[]"
+  },
+  {
+    "data_set": "alphamissense_classification",
+    "data_source": "Ensembl",
+    "genomic_unit_type": "hgvs_variant",
+    "annotation_source_type": "http",
+    "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;AlphaMissense=1;refseq=1;",
+    "attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { alphamissense: .alphamissense.am_class }",
+    "dependencies": ["transcript","hgvs_variant_without_transcript_version"],
+    "versioning_type": "rest",
+    "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
+    "version_attribute": ".releases[]"
+  },
+  {
+    "data_set": "revel",
+    "data_source": "Ensembl",
+    "genomic_unit_type": "hgvs_variant",
+    "annotation_source_type": "http",
+    "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;AlphaMissense=1;refseq=1;",
+    "attribute": ".[].transcript_consequences[] | select( .transcript_id | contains(\"{transcript}\") ) | { revel: .revel }",
+    "dependencies": ["transcript","hgvs_variant_without_transcript_version"],
     "versioning_type": "rest",
     "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
     "version_attribute": ".releases[]"
@@ -456,9 +550,10 @@
     "genomic_unit_type": "hgvs_variant",
     "transcript": true,
     "annotation_source_type": "http",
-    "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant}?content-type=application/json;refseq=1;",
+    "url": "http://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;refseq=1;",
     "attribute": ".[].transcript_consequences[] | { impact: .impact, transcript_id: .transcript_id }",
     "versioning_type": "rest",
+    "dependencies": ["hgvs_variant_without_transcript_version"],
     "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
     "version_attribute": ".releases[]"
   },
@@ -538,6 +633,18 @@
     "version_url": "https://www.alliancegenome.org/api/releaseInfo",
     "version_attribute": ".releaseVersion"
   },
+  {
+    "data_set": "C-Elegens_Worm_Base_url",
+    "data_source": "Alliance Genome",
+    "annotation_source_type": "http",
+    "genomic_unit_type": "gene",
+    "url": "https://www.alliancegenome.org/api/gene/{C-Elegens Gene Identifier}",
+    "attribute": "{ \"C-Elegens_Worm_Base_url\": .modCrossRefCompleteUrl }",
+    "dependencies": ["C-Elegens Gene Identifier"],
+    "versioning_type": "rest",
+    "version_url": "https://www.alliancegenome.org/api/releaseInfo",
+    "version_attribute": ".releaseVersion"
+  },
   {
     "data_set": "C-Elegens_Alliance_Genome_url",
     "data_source": "Rosalution",
@@ -549,15 +656,15 @@
     "versioning_type": "rosalution"
   },
   {
-    "data_set": "C-Elegens_Worm_Base_url",
-    "data_source": "Alliance Genome",
+    "data_set": "opencravat_search_variant_vcf_string",
+    "data_source": "Ensembl",
+    "genomic_unit_type": "hgvs_variant",
     "annotation_source_type": "http",
-    "genomic_unit_type": "gene",
-    "url": "https://www.alliancegenome.org/api/gene/{C-Elegens Gene Identifier}",
-    "attribute": "{ \"C-Elegens_Worm_Base_url\": .modCrossRefCompleteUrl }",
-    "dependencies": ["C-Elegens Gene Identifier"],
+    "url": "https://rest.ensembl.org/vep/human/hgvs/{hgvs_variant_without_transcript_version}?content-type=application/json;CADD=1;refseq=1;vcf_string=1;",
+    "attribute": ".[] | .vcf_string | split(\"-\") | \"chrom=chr\" + .[0] + \"&pos=\" + .[1] + \"&ref_base=\" + .[2] + \"&alt_base=\" + .[3] | {\"opencravat_search_variant_vcf_string\": . }",
     "versioning_type": "rest",
-    "version_url": "https://www.alliancegenome.org/api/releaseInfo",
-    "version_attribute": ".releaseVersion"
+    "dependencies": ["hgvs_variant_without_transcript_version"],
+    "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",
+    "version_attribute": ".releases[]"
   }
 ]
diff --git a/etc/fixtures/initial-seed/genomic-units.json b/etc/fixtures/initial-seed/genomic-units.json
@@ -457,6 +457,34 @@
           }
         ]
       },
+      {
+        "alphamissense_classification": [
+          {
+            "data_source": "Ensembl",
+            "version": 112,
+            "value": "ambiguous"
+          }
+        ]
+      },
+      {
+        "alphamissense_pathogenicity": [
+          {
+            "data_source": "Ensembl",
+            "version": 112,
+            "value": 0.5303
+          }
+        ]
+      },
+      {
+        "alphamissense": [{
+            "data_source": "Ensembl",
+            "version": 112,
+            "value": {
+              "am_class": "ambiguous",
+              "am_pathogenicity": "0.5303"
+            }
+        }]
+      },
       {
         "ClinVar_variant_url": [
           {
@@ -465,6 +493,24 @@
             "value": "https://www.ncbi.nlm.nih.gov/clinvar/variation/581244"
           }
         ]
+      },
+      {
+        "ensembl_vep_vcf_string": [
+          {
+            "data_source": "Rosalution",
+            "version": "rosalution-manifest-00",
+            "value": "X-151404916-G-T"
+          }
+        ]
+      },
+      {
+        "gnomAD_variant_url": [
+          {
+            "data_source": "Rosalution",
+            "version": "rosalution-manifest-00",
+            "value": "https://gnomad.broadinstitute.org/variant/X-151404916-G-T?dataset=gnomad_r4"
+          }
+        ]
       }
     ]
   },

diff --git a/frontend/src/assets/cosmic_logo.png b/frontend/src/assets/cosmic_logo.png