wip with fixing the config a bit for gnomad and added the css to make…

… that row be horizontal
uab-cgds-worthey · Dec 10, 2024 · 2215466 · 2215466
1 parent 3e23ed5
commit 2215466
Show file tree

Hide file tree

Showing 3 changed files with 13 additions and 7 deletions.
diff --git a/etc/fixtures/initial-seed/annotations-config.json b/etc/fixtures/initial-seed/annotations-config.json
@@ -27,7 +27,7 @@
     "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;refseq=1;vcf_string=1;",
-    "attribute": ".[] | .vcf_string",
+    "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",
@@ -233,9 +233,9 @@
     "data_source": "Rosalution",
     "genomic_unit_type": "gene",
     "annotation_source_type": "forge",
-    "base_string": "https://gnomad.broadinstitute.org/gene/{ensembl_vep_vcf_string}?dataset=gnomad_r4",
+    "base_string": "https://gnomad.broadinstitute.org/variant/{ensembl_vep_vcf_string}?dataset=gnomad_r4",
     "attribute": "{ \"gnomAD_variant_url\": .gnomAD_variant_url }",
-    "dependencies": ["Ensembl Gene Id"],
+    "dependencies": ["ensembl_vep_vcf_string"],
     "versioning_type": "rosalution"
   },
   {
@@ -606,7 +606,7 @@
     "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;CADD=1;refseq=1;vcf_string=1;",
-    "attribute": ".[] | .vcf_string | split(\"-\") | \"chrom=chr\" + .[0] + \"&pos=\" + .[1] + \"&ref_base=\" + .[2] + \"&alt_base=\" + .[3] ",
+    "attribute": ".[] | .vcf_string | split(\"-\") | \"chrom=chr\" + .[0] + \"&pos=\" + .[1] + \"&ref_base=\" + .[2] + \"&alt_base=\" + .[3] | {\"opencravat_search_variant_vcf_string\": . }",
     "versioning_type": "rest",
     "dependencies": ["hgvs_variant_without_transcript_version"],
     "version_url": "https://rest.ensembl.org/info/data/?content-type=application/json",

diff --git a/frontend/src/models/analyses.js b/frontend/src/models/analyses.js
@@ -378,7 +378,7 @@ const annotationRenderingTemporary = [
     }],
     'rows': [
       {
-        'class': '',
+        'class': 'fill-horizontal',
         'datasets': [
           {
             'dataset': 'CADD',
@@ -426,7 +426,7 @@ const annotationRenderingTemporary = [
             'dataset': 'AlphaMissense',
             'type': 'score-dataset',
             'props': {
-              'label': 'REVEL',
+              'label': 'AlphaMissense',
               'minimum': 0,
               'maximum': 1,
               'bounds': {

diff --git a/frontend/src/views/AnnotationView.vue b/frontend/src/views/AnnotationView.vue
@@ -32,7 +32,7 @@
             />
         </template>
         <template #default>
-          <div v-for="(row, index) in section.rows" :key="`row-${index}`">
+          <div v-for="(row, index) in section.rows" :key="`row-${index}`" :class="row.class">
             <component
                 v-for="(datasetConfig, index) in row.datasets"
                 :key="`${datasetConfig.dataset}-${index}`"
@@ -296,6 +296,12 @@ app-header {
   flex: 1
 }
 
+.fill-horizontal {
+  display: flex;
+  flex-direction: row;
+  justify-content: space-between;
+}
+
 .sidebar {
   position: sticky;
   height: 90vh;