protvista-uniprot 2.13.2 → 3.0.0

package/src/config.json

@@ -12,7 +12,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -25,7 +25,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -38,7 +38,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -51,7 +51,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -65,7 +65,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -78,7 +78,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -98,7 +98,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -111,7 +111,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -124,7 +124,7 @@
           "label": "Non-adjacent residues",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -137,7 +137,7 @@
           "label": "Non-terminal residue",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -150,7 +150,7 @@
           "label": "Sequence uncertainty",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -163,7 +163,7 @@
           "label": "Non-standard residue",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -183,7 +183,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -196,7 +196,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -209,7 +209,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -229,7 +229,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -241,7 +241,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-interpro-adapter",
+              "adapter": "interpro-adapter",
               "url": "https://www.ebi.ac.uk/interpro/api/entry/all/protein/uniprot/{accession}?type=domain&page_size=100"
             }
           ],
@@ -254,7 +254,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -267,7 +267,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -280,7 +280,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -293,7 +293,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -313,7 +313,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -326,7 +326,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -339,7 +339,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -352,7 +352,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -365,7 +365,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -378,7 +378,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -391,7 +391,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -411,7 +411,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -424,7 +424,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-proteomics-ptm-adapter",
+              "adapter": "proteomics-ptm-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
             }
           ],
@@ -437,7 +437,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -450,7 +450,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -463,7 +463,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -476,7 +476,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -495,7 +495,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/epitope/{accession}"
             }
           ],
@@ -514,7 +514,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/antigen/{accession}"
             }
           ],
@@ -534,7 +534,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -546,7 +546,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/mutagenesis/{accession}"
             }
           ],
@@ -565,7 +565,7 @@
           "trackType": "nightingale-linegraph-track",
           "data": [
             {
-              "adapter": "protvista-variation-graph-adapter",
+              "adapter": "variation-graph-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/variation/{accession}"
             }
           ],
@@ -573,11 +573,11 @@
         },
         {
           "name": "variation",
-          "filterComponent": "protvista-filter",
+          "filterComponent": "nightingale-filter",
           "trackType": "nightingale-variation",
           "data": [
             {
-              "adapter": "protvista-variation-adapter",
+              "adapter": "variation-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/variation/{accession}"
             }
           ],
@@ -589,7 +589,7 @@
       "name": "PROTEOMICS",
       "label": "Proteomics",
       "trackType": "nightingale-track",
-      "adapter": "protvista-proteomics-adapter",
+      "adapter": "proteomics-adapter",
       "urls": [
         "https://www.ebi.ac.uk/proteins/api/proteomics/{accession}",
         "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
@@ -602,7 +602,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-proteomics-adapter",
+              "adapter": "proteomics-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/proteomics/{accession}"
             }
           ],
@@ -615,7 +615,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-proteomics-adapter",
+              "adapter": "proteomics-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/proteomics/{accession}"
             }
           ],
@@ -627,7 +627,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-proteomics-adapter",
+              "adapter": "proteomics-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/hpp/{accession}"
             }
           ],
@@ -639,7 +639,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-proteomics-adapter",
+              "adapter": "proteomics-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}"
             }
           ],
@@ -659,7 +659,7 @@
           "tooltip": "PDBe 3D structure coverage",
           "data": [
             {
-              "adapter": "protvista-structure-adapter",
+              "adapter": "structure-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
             }
           ]
@@ -680,7 +680,7 @@
           "trackType": "nightingale-colored-sequence",
           "data": [
             {
-              "adapter": "protvista-alphafold-confidence-adapter",
+              "adapter": "alphafold-confidence-adapter",
               "url": [
                 "https://alphafold.ebi.ac.uk/api/prediction/{accession}",
                 "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
@@ -704,7 +704,7 @@
           "trackType": "nightingale-colored-sequence",
           "data": [
             {
-              "adapter": "protvista-alphamissense-pathogenicity-adapter",
+              "adapter": "alphamissense-pathogenicity-adapter",
               "url": [
                 "https://alphafold.ebi.ac.uk/api/prediction/{accession}",
                 "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
@@ -720,7 +720,7 @@
           "trackType": "nightingale-sequence-heatmap",
           "data": [
             {
-              "adapter": "protvista-alphamissense-heatmap-adapter",
+              "adapter": "alphamissense-heatmap-adapter",
               "url": [
                 "https://alphafold.ebi.ac.uk/api/prediction/{accession}",
                 "https://www.ebi.ac.uk/proteins/api/proteins/{accession}"
@@ -743,7 +743,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -756,7 +756,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -769,7 +769,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],
@@ -782,7 +782,7 @@
           "trackType": "nightingale-track",
           "data": [
             {
-              "adapter": "protvista-feature-adapter",
+              "adapter": "feature-adapter",
               "url": "https://www.ebi.ac.uk/proteins/api/features/{accession}"
             }
           ],

package/src/{filterConfig.ts → filter-config.ts}

@@ -1,4 +1,5 @@
-import { ClinicalSignificance } from 'protvista-variation-adapter/dist/es/variants';
+import { VariationDatum } from '@nightingale-elements/nightingale-variation';
+import { ClinicalSignificance } from '@nightingale-elements/nightingale-variation';
 
 const scaleColors = {
   UPDiseaseColor: '#990000',
@@ -19,9 +20,13 @@ const significanceMatches = (
     return values.some((rx) => rx.test(type));
   });
 
+export type VariantsForFilter = {
+  variants: VariationDatum[];
+}[];
+
 export const getFilteredVariants = (
-  variants: ProtvistaVariationData,
-  callbackFilter: (variantPos: ProtvistaVariant) => void
+  variants: VariantsForFilter,
+  callbackFilter: (variantPos: VariationDatum) => void
 ) =>
   variants.map((variant) => {
     const matchingVariants = variant.variants.filter((variantPos) =>
@@ -74,7 +79,7 @@ const filterConfig = [
       color: scaleColors.UPDiseaseColor,
     },
     filterPredicate: filterPredicates['disease'],
-    filterData: (variants: ProtvistaVariationData) =>
+    filterData: (variants: VariantsForFilter) =>
       getFilteredVariants(variants, filterPredicates['disease']),
   },
   {
@@ -88,7 +93,7 @@ const filterConfig = [
       color: scaleColors.predictedColor,
     },
     filterPredicate: filterPredicates['predicted'],
-    filterData: (variants: ProtvistaVariationData) =>
+    filterData: (variants: VariantsForFilter) =>
       getFilteredVariants(variants, filterPredicates['predicted']),
   },
   {
@@ -102,7 +107,7 @@ const filterConfig = [
       color: scaleColors.UPNonDiseaseColor,
     },
     filterPredicate: filterPredicates['nonDisease'],
-    filterData: (variants: ProtvistaVariationData) =>
+    filterData: (variants: VariantsForFilter) =>
       getFilteredVariants(variants, filterPredicates['nonDisease']),
   },
   {
@@ -116,7 +121,7 @@ const filterConfig = [
       color: scaleColors.othersColor,
     },
     filterPredicate: filterPredicates['uncertain'],
-    filterData: (variants: ProtvistaVariationData) =>
+    filterData: (variants: VariantsForFilter) =>
       getFilteredVariants(variants, filterPredicates['uncertain']),
   },
   {
@@ -130,7 +135,7 @@ const filterConfig = [
       color: '#9f9f9f',
     },
     filterPredicate: filterPredicates['UniProt'],
-    filterData: (variants: ProtvistaVariationData) =>
+    filterData: (variants: VariantsForFilter) =>
       getFilteredVariants(variants, filterPredicates['UniProt']),
   },
   {
@@ -144,7 +149,7 @@ const filterConfig = [
       color: '#9f9f9f',
     },
     filterPredicate: filterPredicates['ClinVar'],
-    filterData: (variants: ProtvistaVariationData) =>
+    filterData: (variants: VariantsForFilter) =>
       getFilteredVariants(variants, filterPredicates['ClinVar']),
   },
   {
@@ -158,16 +163,16 @@ const filterConfig = [
       color: '#9f9f9f',
     },
     filterPredicate: filterPredicates['LSS'],
-    filterData: (variants: ProtvistaVariationData) =>
+    filterData: (variants: VariantsForFilter) =>
       getFilteredVariants(variants, filterPredicates['LSS']),
   },
 ];
 
 const countVariantsForFilter = (
   filterName: 'disease' | 'nonDisease' | 'uncertain' | 'predicted',
-  variant: ProtvistaVariant
+  variant: VariationDatum
 ) => {
-  const variantWrapper = [{ variants: [variant] }];
+  const variantWrapper: VariantsForFilter = [{ variants: [variant] }];
   const filter = filterConfig.find((filter) => filter.name === filterName);
   if (filter) {
     return filter.filterData(variantWrapper)[0].variants.length > 0;

package/src/index.ts

@@ -1,22 +1,18 @@
-import { loadComponent } from './loadComponents';
-
 import ProtvistaUniprot from './protvista-uniprot';
-import _ProtvistaUniprotStructure from './protvista-uniprot-structure';
-
-import { transformDataFeatureAdapter as _transformDataFeatureAdapter } from './protvista-uniprot';
-import { transformDataProteomicsAdapter as _transformDataProteomicsAdapter } from './protvista-uniprot';
-import { transformDataStructureAdapter as _transformDataStructureAdapter } from './protvista-uniprot';
-import { transformDataVariationAdapter as _transformDataVariationAdapter } from './protvista-uniprot';
-import { transformDataInterproAdapter as _transformDataInterproAdapter } from './protvista-uniprot';
+import ProtvistaUniprotStructure from './protvista-uniprot-structure';
 
-export const transformDataFeatureAdapter = _transformDataFeatureAdapter;
-export const transformDataProteomicsAdapter = _transformDataProteomicsAdapter;
-export const transformDataStructureAdapter = _transformDataStructureAdapter;
-export const transformDataVariationAdapter = _transformDataVariationAdapter;
-export const transformDataInterproAdapter = _transformDataInterproAdapter;
-export const ProtvistaUniprotStructure = _ProtvistaUniprotStructure;
+import filterConfig, { colorConfig } from './filter-config';
 
-loadComponent('protvista-uniprot', ProtvistaUniprot);
-loadComponent('protvista-uniprot-structure', _ProtvistaUniprotStructure);
+import getFeatureTooltip from './tooltips/featureTooltip';
+import getStructureTooltip from './tooltips/structureTooltip';
+import getVariationTooltip from './tooltips/variationTooltip';
 
-export default ProtvistaUniprot;
+export {
+  ProtvistaUniprot as default,
+  ProtvistaUniprotStructure,
+  filterConfig,
+  colorConfig,
+  getFeatureTooltip,
+  getStructureTooltip,
+  getVariationTooltip,
+};

package/src/protvista-uniprot-structure.ts

@@ -1,12 +1,13 @@
 import { LitElement, html, svg, TemplateResult, css } from 'lit';
+// eslint-disable-next-line @typescript-eslint/no-unused-vars
+import { customElement } from 'lit/decorators.js';
 import { unsafeHTML } from 'lit/directives/unsafe-html.js';
-import { load } from 'data-loader';
 import NightingaleStructure, {
   PredictionData,
   StructureData,
 } from '@nightingale-elements/nightingale-structure';
 import ProtvistaDatatable from 'protvista-datatable';
-import { loadComponent } from './loadComponents';
+import { fetchAll, loadComponent } from './utils';
 
 import loaderIcon from './icons/spinner.svg';
 import downloadIcon from './icons/download.svg';
@@ -140,6 +141,8 @@ const foldseekURL = (accession, sourceDB) => {
 };
 
 const styleId = 'protvista-styles';
+
+@customElement('protvista-uniprot-structure')
 class ProtvistaUniprotStructure extends LitElement {
   accession?: string;
   data?: ProcessedStructureData[];
@@ -175,18 +178,7 @@ class ProtvistaUniprotStructure extends LitElement {
     const pdbUrl = `https://www.ebi.ac.uk/proteins/api/proteins/${this.accession}`;
     const alphaFoldURl = `https://alphafold.ebi.ac.uk/api/prediction/${this.accession}`;
 
-    const rawData: { [key: string]: any } = [];
-
-    await Promise.all(
-      [pdbUrl, alphaFoldURl].map((url: string) =>
-        load(url).then(
-          (data) => (rawData[url] = data.payload),
-          // TODO handle this better based on error code
-          // Fail silently for now
-          (error) => console.warn(error)
-        )
-      )
-    );
+    const rawData = await fetchAll([pdbUrl, alphaFoldURl]);
 
     this.loading = false;
     // TODO: return if no data at all