Rendering some of the new linkouts and datasets, with some fixture up…

…dates
uab-cgds-worthey · Dec 11, 2024 · 55cbc0b · 55cbc0b
1 parent 2215466
commit 55cbc0b
Show file tree

Hide file tree

Showing 6 changed files with 101 additions and 6 deletions.
diff --git a/backend/src/core/annotation_unit.py b/backend/src/core/annotation_unit.py
@@ -103,7 +103,7 @@ def delay_count_exceeds(self):
         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/etc/fixtures/initial-seed/annotations-config.json b/etc/fixtures/initial-seed/annotations-config.json
@@ -231,13 +231,22 @@
   {
     "data_set": "gnomAD_variant_url",
     "data_source": "Rosalution",
-    "genomic_unit_type": "gene",
+    "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": "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",
@@ -474,7 +483,7 @@
      "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[]"
    },
    {
@@ -489,6 +498,42 @@
     "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[]"
+  },
   {
     "data_set": "Impact",
     "data_source": "Ensembl",

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": [
           {
@@ -480,7 +508,7 @@
           {
             "data_source": "Rosalution",
             "version": "rosalution-manifest-00",
-            "value": "https://gnomad.broadinstitute.org/gene/X-151404916-G-T?dataset=gnomad_r4"
+            "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
diff --git a/frontend/src/models/analyses.js b/frontend/src/models/analyses.js
@@ -317,6 +317,13 @@ const annotationRenderingTemporary = [
         'altText': 'National Center for Biotechnology Information Gene Linkout',
       },
     }, {
+      'dataset': 'COSMIC_gene_url',
+      'type': 'icon-linkout-dataset',
+      'props': {
+        'imageFilename': 'cosmic_logo.png',
+        'altText': 'Catalogue Of Somatic Mutations In Cancer, COSMIC',
+      },
+    },{
       'dataset': 'gnomAD_gene_url',
       'type': 'icon-linkout-dataset',
       'props': {
@@ -423,10 +430,10 @@ const annotationRenderingTemporary = [
             },
           },
           {
-            'dataset': 'AlphaMissense',
+            'dataset': 'alphamissense_pathogenicity',
             'type': 'score-dataset',
             'props': {
-              'label': 'AlphaMissense',
+              'label': 'AlphaMissense Score',
               'minimum': 0,
               'maximum': 1,
               'bounds': {
@@ -436,6 +443,18 @@ const annotationRenderingTemporary = [
               'cutoff': 1,
             },
           },
+          {
+            'dataset': 'alphamissense_classification',
+            'type': 'set-dataset',
+            'props': {
+              'label': 'AlphaMissense Pathogenicity',
+              'set': [
+                {'value': 'likely_benign', 'classification': 'Likely Benign', 'colour': 'Blue'},
+                {'value': 'ambiguous', 'classification': 'Ambiguous', 'colour': 'Yellow'},
+                {'value': 'likely_pathogenic', 'classification': 'Likely Pathogenic', 'colour': 'Red'}
+              ],
+            },
+          },
           // {
           //   'dataset': 'Phylop100',
           //   'type': 'score-dataset',

diff --git a/frontend/src/views/AnnotationView.vue b/frontend/src/views/AnnotationView.vue
@@ -70,6 +70,7 @@ import ClinvarDataset from '@/components/AnnotationView/ClinvarDataset.vue';
 import IconLinkoutDataset from '@/components/AnnotationView/IconLinkoutDataset.vue';
 import ImagesDataset from '@/components/AnnotationView/ImagesDataset.vue';
 import ScoreDataset from '@/components/AnnotationView/ScoreDataset.vue';
+import SetDataset from '@/components/AnnotationView/SetDataset.vue';
 import TextDataset from '@/components/AnnotationView/TextDataset.vue';
 import TranscriptDatasets from '@/components/AnnotationView/TranscriptDatasets.vue';
 import InputDialog from '@/components/Dialogs/InputDialog.vue';
@@ -94,6 +95,7 @@ export default {
     InputDialog,
     NotificationDialog,
     ScoreDataset,
+    SetDataset,
     TextDataset,
     TranscriptDatasets,
     TagDataset,
@@ -300,6 +302,7 @@ app-header {
   display: flex;
   flex-direction: row;
   justify-content: space-between;
+  flex-wrap: wrap;
 }
 
 .sidebar {