Merge pull request #256 from ebi-webcomponents/master

Binding site tooltip and PTM changes
ebi-webcomponents · Jun 1, 2023 · 196e101 · 196e101
2 parents 5373882 + b8618d3
commit 196e101
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Showing 10 changed files with 100 additions and 31 deletions.
diff --git a/app/package.json b/app/package.json
@@ -1,6 +1,6 @@
 {
   "name": "nightingale-showcase-app",
-  "version": "3.8.10",
+  "version": "3.8.11",
   "private": true,
   "description": "A website to showcase all nightingale components",
   "files": [
@@ -21,7 +21,7 @@
     "interaction-viewer": "^3.8.4",
     "protvista-coloured-sequence": "^3.8.10",
     "protvista-datatable": "^3.8.10",
-    "protvista-feature-adapter": "^3.8.10",
+    "protvista-feature-adapter": "^3.8.11",
     "protvista-filter": "^3.8.4",
     "protvista-interpro-track": "^3.8.10",
     "protvista-links": "^3.8.10",
@@ -30,14 +30,14 @@
     "protvista-navigation": "^3.8.10",
     "protvista-saver": "^3.8.4",
     "protvista-sequence": "^3.8.10",
-    "protvista-structure": "^3.8.4",
+    "protvista-structure": "^3.8.11",
     "protvista-tooltip": "^3.8.4",
     "protvista-track": "^3.8.10",
     "protvista-uniprot": "^2.0.3",
     "protvista-variation": "^3.8.10",
-    "protvista-variation-adapter": "^3.8.10",
+    "protvista-variation-adapter": "^3.8.11",
     "protvista-variation-graph": "^3.8.10",
-    "protvista-vcf-adapter": "^3.8.10",
+    "protvista-vcf-adapter": "^3.8.11",
     "react": "^16.13.0",
     "react-dom": "^16.13.0",
     "react-router": "^5.0.1",

diff --git a/lerna.json b/lerna.json
@@ -2,5 +2,5 @@
   "packages": ["app", "packages/*"],
   "npmClient": "yarn",
   "useWorkspaces": true,
-  "version": "3.8.10"
+  "version": "3.8.11"
 }
diff --git a/packages/protvista-feature-adapter/package.json b/packages/protvista-feature-adapter/package.json
@@ -1,6 +1,6 @@
 {
   "name": "protvista-feature-adapter",
-  "version": "3.8.10",
+  "version": "3.8.11",
   "files": [
     "dist",
     "src"

diff --git a/packages/protvista-feature-adapter/src/BasicHelper.js b/packages/protvista-feature-adapter/src/BasicHelper.js
@@ -124,13 +124,25 @@ export const formatTooltip = (feature) => {
       dbReferences.map((ref) => ref.id)
     );
 
+  let { description } = feature;
+
+  if (feature.type === "BINDING" || feature.type === "Binding site") {
+    let bindingDescription = "";
+    if (feature.ligandPart) {
+      bindingDescription += `${feature.ligandPart.name} of `;
+    }
+    if (feature.ligand) {
+      bindingDescription += feature.ligand.name;
+    }
+    if (feature.description) {
+      bindingDescription += `; ${feature.description}`;
+    }
+    description = bindingDescription;
+  }
+
   try {
     return `
-      ${
-        feature.description
-          ? `<h5>Description</h5><p>${feature.description}</p>`
-          : ``
-      }
+      ${description ? `<h5>Description</h5><p>${description}</p>` : ``}
       ${
         feature.matchScore
           ? `<h5>Match score</h5><p>${feature.matchScore}%</p>`

diff --git a/packages/protvista-proteomics-adapter/package.json b/packages/protvista-proteomics-adapter/package.json
@@ -25,10 +25,10 @@
     "url": "https://github.com/ebi-webcomponents/nightingale/issues"
   },
   "homepage": "https://ebi-webcomponents.github.io/nightingale/",
-  "version": "3.8.10",
+  "version": "3.8.11",
   "gitHead": "726779864966d11f966f337f2dd84aa4f58d944a",
   "dependencies": {
-    "protvista-feature-adapter": "^3.8.10",
+    "protvista-feature-adapter": "^3.8.11",
     "uuid": "^8.3.1"
   }
 }
diff --git a/packages/protvista-proteomics-adapter/src/ProtvistaProteomicsAdapter.js b/packages/protvista-proteomics-adapter/src/ProtvistaProteomicsAdapter.js
@@ -1,20 +1,77 @@
 import ProtvistaFeatureAdapter, {
   renameProperties,
-  formatTooltip
+  formatTooltip,
 } from "protvista-feature-adapter";
 import { v1 } from "uuid";
 
-export const transformData = data => {
+const proteomicsTrackProperties = (feature) => {
+  return {
+    category: "PROTEOMICS",
+    type: feature.unique ? "unique" : "non_unique",
+    tooltipContent: formatTooltip(feature),
+    protvistaFeatureId: v1(),
+  };
+};
+
+export const transformData = (data) => {
   let adaptedData = [];
+
   if (data && data.length !== 0) {
-    adaptedData = data.features.map(feature => {
-      return Object.assign(feature, {
-        category: "PROTEOMICS",
-        type: feature.unique ? "unique" : "non_unique",
-        tooltipContent: formatTooltip(feature),
-        protvistaFeatureId: v1()
-      });
+    /* Important: The PTM map is a temporary patch until multiple modifications are shown in the peptide. At this point, only 'phospho' sites are of interest. 
+    Once they are available in the data, there is no need for the below merging */
+
+    // To merge PTM data present in same residue in a same length peptide, have a map [key: start-end-phospho site 1-... phosphosite n, value: corresponding feature elements]
+    const ptmMap = {};
+    data.features.forEach((feature) => {
+      let ft = `${feature.begin}-${feature.end}`;
+      if (feature.ptms) {
+        feature.ptms.forEach((ptm) => {
+          ft += `-${ptm.position}`;
+        });
+        ptmMap[ft] = ft in ptmMap ? [...ptmMap[ft], feature] : [feature];
+      }
     });
+
+    // The else part alone is enough if the PTM information need not be merged.
+    if (Object.keys(ptmMap).length) {
+      adaptedData = Object.values(ptmMap).map((features) => {
+        // Only the dbReferences have to be merged as the rest is all the same
+        const mergedDbReferences = [];
+        features.forEach((feature) => {
+          feature.ptms.forEach((ptm) => {
+            ptm.dbReferences.forEach((dbReference) => {
+              mergedDbReferences.push(dbReference);
+            });
+          });
+        });
+
+        const mergedFeatures = {
+          type: features[0].type,
+          begin: features[0].begin,
+          end: features[0].end,
+          xrefs: features[0].xrefs,
+          evidences: features[0].evidences,
+          peptide: features[0].peptide,
+          unique: features[0].unique,
+          ptms: features[0].ptms.map((ptm) => ({
+            name: ptm.name,
+            position: ptm.position,
+            sources: ptm.sources,
+            dbReferences: mergedDbReferences,
+          })),
+        };
+
+        return Object.assign(
+          mergedFeatures,
+          proteomicsTrackProperties(mergedFeatures)
+        );
+      }, []);
+    } else {
+      adaptedData = data.features.map((feature) => {
+        return Object.assign(feature, proteomicsTrackProperties(feature));
+      });
+    }
+
     adaptedData = renameProperties(adaptedData);
   }
   return adaptedData;

diff --git a/packages/protvista-structure-adapter/package.json b/packages/protvista-structure-adapter/package.json
@@ -1,6 +1,6 @@
 {
   "name": "protvista-structure-adapter",
-  "version": "3.8.10",
+  "version": "3.8.11",
   "description": "A dataloader and parser (ProtVista compliant) for 3D structures",
   "main": "dist/protvista-structure-adapter.js",
   "module": "src/ProtVistaStructureAdapter.js",
@@ -33,7 +33,7 @@
   "license": "Apache-2.0",
   "gitHead": "726779864966d11f966f337f2dd84aa4f58d944a",
   "dependencies": {
-    "protvista-feature-adapter": "^3.8.10",
+    "protvista-feature-adapter": "^3.8.11",
     "uuid": "^8.3.1"
   }
 }
diff --git a/packages/protvista-structure/package.json b/packages/protvista-structure/package.json
@@ -1,6 +1,6 @@
 {
   "name": "protvista-structure",
-  "version": "3.8.4",
+  "version": "3.8.11",
   "description": "A custom element wrapper for Mol*",
   "main": "dist/protvista-structure.js",
   "module": "dist/es/protvista-structure.js",

diff --git a/packages/protvista-variation-adapter/package.json b/packages/protvista-variation-adapter/package.json
@@ -1,6 +1,6 @@
 {
   "name": "protvista-variation-adapter",
-  "version": "3.8.10",
+  "version": "3.8.11",
   "description": "Data adapter for variation data",
   "files": [
     "dist",
@@ -34,7 +34,7 @@
     "d3-scale": "^3.2.3",
     "data-loader": "^3.8.4",
     "lodash-es": "^4.17.11",
-    "protvista-feature-adapter": "^3.8.10",
+    "protvista-feature-adapter": "^3.8.11",
     "protvista-variation": "^3.8.10",
     "uuid": "^8.3.1"
   },

diff --git a/packages/protvista-vcf-adapter/package.json b/packages/protvista-vcf-adapter/package.json
@@ -1,6 +1,6 @@
 {
   "name": "protvista-vcf-adapter",
-  "version": "3.8.10",
+  "version": "3.8.11",
   "files": [
     "dist",
     "types",
@@ -28,9 +28,9 @@
   "dependencies": {
     "data-loader": "^3.8.4",
     "lit-html": "^1.3.0",
-    "protvista-feature-adapter": "^3.8.10",
+    "protvista-feature-adapter": "^3.8.11",
     "protvista-variation": "^3.8.10",
-    "protvista-variation-adapter": "^3.8.10",
+    "protvista-variation-adapter": "^3.8.11",
     "vcftojson": "^1.1.0"
   },
   "gitHead": "726779864966d11f966f337f2dd84aa4f58d944a"