Merge remote-tracking branch 'origin/master' into v3

app/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nightingale-showcase-app",
-  "version": "3.8.11",
+  "version": "3.8.22",
   "private": true,
   "description": "A website to showcase all nightingale components",
   "files": [
@@ -18,26 +18,26 @@
   "dependencies": {
     "@babel/polyfill": "^7.11.5",
     "highlight.js": "10.2.1",
-    "interaction-viewer": "^3.8.4",
-    "protvista-coloured-sequence": "^3.8.10",
-    "protvista-datatable": "^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",
-    "protvista-manager": "^3.8.4",
-    "protvista-msa": "^3.8.10",
-    "protvista-navigation": "^3.8.10",
-    "protvista-saver": "^3.8.4",
-    "protvista-sequence": "^3.8.10",
-    "protvista-structure": "^3.8.11",
-    "protvista-tooltip": "^3.8.4",
-    "protvista-track": "^3.8.10",
+    "interaction-viewer": "^3.8.22",
+    "protvista-coloured-sequence": "^3.8.22",
+    "protvista-datatable": "^3.8.22",
+    "protvista-feature-adapter": "^3.8.22",
+    "protvista-filter": "^3.8.22",
+    "protvista-interpro-track": "^3.8.22",
+    "protvista-links": "^3.8.22",
+    "protvista-manager": "^3.8.22",
+    "protvista-msa": "^3.8.22",
+    "protvista-navigation": "^3.8.22",
+    "protvista-saver": "^3.8.22",
+    "protvista-sequence": "^3.8.22",
+    "protvista-structure": "^3.8.22",
+    "protvista-tooltip": "^3.8.22",
+    "protvista-track": "^3.8.22",
     "protvista-uniprot": "^2.0.3",
-    "protvista-variation": "^3.8.10",
-    "protvista-variation-adapter": "^3.8.11",
-    "protvista-variation-graph": "^3.8.10",
-    "protvista-vcf-adapter": "^3.8.11",
+    "protvista-variation": "^3.8.22",
+    "protvista-variation-adapter": "^3.8.22",
+    "protvista-variation-graph": "^3.8.22",
+    "protvista-vcf-adapter": "^3.8.22",
     "react": "^16.13.0",
     "react-dom": "^16.13.0",
     "react-router": "^5.0.1",
@@ -50,7 +50,7 @@
     "babel-plugin-syntax-dynamic-import": "^6.18.0",
     "clean-webpack-plugin": "^3.0.0",
     "css-loader": "^4.3.0",
-    "data-loader": "^3.8.4",
+    "data-loader": "^3.8.22",
     "eslint": "^7.10.0",
     "eslint-config-airbnb-base": "^14.0.0",
     "eslint-config-prettier": "^6.12.0",

lerna.json

@@ -2,5 +2,5 @@
   "packages": ["app", "packages/*"],
   "npmClient": "yarn",
   "useWorkspaces": true,
-  "version": "3.8.11"
+  "version": "3.8.22"
 }

packages/data-loader/package.json

@@ -1,6 +1,6 @@
 {
   "name": "data-loader",
-  "version": "3.8.4",
+  "version": "3.8.22",
   "description": "data-loader Custom Element to load data declaratively",
   "files": [
     "dist",
@@ -32,7 +32,7 @@
     "protvista"
   ],
   "homepage": "https://ebi-webcomponents.github.io/nightingale/",
-  "gitHead": "5a756316482fa31d085602d46438861fb45e5178",
+  "gitHead": "d5953d40c908b47eacce04bdc585af8a71eeebc9",
   "dependencies": {
     "@types/lodash-es": "4.17.3",
     "lodash-es": "^4.17.11"

packages/interaction-viewer/package.json

@@ -1,6 +1,6 @@
 {
   "name": "interaction-viewer",
-  "version": "3.8.4",
+  "version": "3.8.22",
   "description": "Display interaction information for different proteins and overlay information about diseases and subcellular location.",
   "main": "dist/interaction-viewer.js",
   "module": "dist/es/index.js",
@@ -34,12 +34,12 @@
   "author": "Xavier Watkins <xwatkins@ebi.ac.uk>",
   "license": "Apache-2.0",
   "dependencies": {
-    "data-loader": "^3.8.4",
+    "data-loader": "^3.8.22",
     "lit": "^2.1.1",
     "lodash-es": "^4.17.11",
-    "protvista-tooltip": "^3.8.4"
+    "protvista-tooltip": "^3.8.22"
   },
-  "gitHead": "337d88a3df2e52243aed81a123740d82917779db",
+  "gitHead": "d5953d40c908b47eacce04bdc585af8a71eeebc9",
   "devDependencies": {
     "d3": "^5.7.0"
   },

packages/nightingale-heatmap/package.json

@@ -7,7 +7,7 @@
   ],
   "main": "dist/nightingale-heatmap.js",
   "module": "src/nightingale-heatmap.js",
-  "version": "3.8.4",
+  "version": "3.8.22",
   "keywords": [
     "nightingale",
     "webcomponents",
@@ -28,5 +28,6 @@
   },
   "peerDependencies": {
     "d3": "5.X"
-  }
+  },
+  "gitHead": "d5953d40c908b47eacce04bdc585af8a71eeebc9"
 }

packages/nightingale-linegraph-track/package.json

@@ -7,7 +7,7 @@
   ],
   "main": "dist/nightingale-linegraph-track.js",
   "module": "src/nightingale-linegraph-track.js",
-  "version": "3.8.10",
+  "version": "3.8.22",
   "keywords": [
     "nightingale",
     "webcomponents",
@@ -24,13 +24,13 @@
   },
   "homepage": "https://ebi-webcomponents.github.io/nightingale/",
   "dependencies": {
-    "protvista-track": "^3.8.10"
+    "protvista-track": "^3.8.22"
   },
   "devDependencies": {
     "d3": "^5.7.0"
   },
   "peerDependencies": {
     "d3": "5.X"
   },
-  "gitHead": "563f7872ea6e92d7dc343cadcc7c4ed887c39d80"
+  "gitHead": "d5953d40c908b47eacce04bdc585af8a71eeebc9"
 }

packages/nightingale-sunburst/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nightingale-sunburst",
-  "version": "3.8.4",
+  "version": "3.8.22",
   "files": [
     "dist",
     "src"
@@ -28,5 +28,6 @@
     "d3": "^5.7.0",
     "lit-element": "^2.4.0",
     "lodash-es": "^4.17.11"
-  }
+  },
+  "gitHead": "d5953d40c908b47eacce04bdc585af8a71eeebc9"
 }

packages/protvista-coloured-sequence/package.json

@@ -1,6 +1,6 @@
 {
   "name": "protvista-coloured-sequence",
-  "version": "3.8.10",
+  "version": "3.8.22",
   "description": "Track that colors each base by a given function. The default function is hydrophobicity",
   "files": [
     "dist",
@@ -11,8 +11,8 @@
   "author": "Gustavo Salazar <gsalazar@ebi.ac.uk>",
   "license": "ISC",
   "dependencies": {
-    "protvista-sequence": "^3.8.10",
-    "protvista-utils": "^3.8.10"
+    "protvista-sequence": "^3.8.22",
+    "protvista-utils": "^3.8.22"
   },
   "repository": {
     "type": "git",
@@ -33,5 +33,5 @@
   "peerDependencies": {
     "d3": "5.X"
   },
-  "gitHead": "563f7872ea6e92d7dc343cadcc7c4ed887c39d80"
+  "gitHead": "d5953d40c908b47eacce04bdc585af8a71eeebc9"
 }

packages/protvista-datatable/package.json

@@ -1,6 +1,6 @@
 {
   "name": "protvista-datatable",
-  "version": "3.8.10",
+  "version": "3.8.22",
   "files": [
     "dist",
     "src",
@@ -32,11 +32,11 @@
   "dependencies": {
     "lit-element": "^2.4.0",
     "lit-html": "^1.3.0",
-    "protvista-utils": "^3.8.10",
+    "protvista-utils": "^3.8.22",
     "type-fest": "^1.2.1",
     "uuid": "^8.3.1"
   },
-  "gitHead": "726779864966d11f966f337f2dd84aa4f58d944a",
+  "gitHead": "d5953d40c908b47eacce04bdc585af8a71eeebc9",
   "devDependencies": {
     "@testing-library/dom": "^8.1.0",
     "@testing-library/jest-dom": "^5.14.1"

packages/protvista-feature-adapter/package.json

@@ -1,6 +1,6 @@
 {
   "name": "protvista-feature-adapter",
-  "version": "3.8.11",
+  "version": "3.8.22",
   "files": [
     "dist",
     "src"
@@ -22,8 +22,8 @@
   },
   "homepage": "https://ebi-webcomponents.github.io/nightingale/",
   "dependencies": {
-    "protvista-track": "^3.8.10",
+    "protvista-track": "^3.8.22",
     "uuid": "^8.3.1"
   },
-  "gitHead": "726779864966d11f966f337f2dd84aa4f58d944a"
+  "gitHead": "d5953d40c908b47eacce04bdc585af8a71eeebc9"
 }

packages/protvista-feature-adapter/src/BasicHelper.js

@@ -14,11 +14,18 @@ export const renameProperties = (features) => {
 };
 
 const formatSource = (source) => {
-  return source.name?.toLowerCase() === "PubMed".toLowerCase()
-    ? `${source.id}&nbsp;(<a href='${source.url}' style="color:#FFF" target='_blank'>${source.name}</a>&nbsp;<a href='${source.alternativeUrl}' style="color:#FFF" target='_blank'>EuropePMC</a>)`
-    : `&nbsp;<a href='${source.url}' style="color:#FFF" target='_blank'>${
-        source.id
-      }</a>&nbsp;${source.name ? `(${source.name})` : ""}`;
+  if (source.name?.toLowerCase() === "PubMed".toLowerCase()) {
+    return `${source.id}&nbsp;(<a href='${source.url}' style="color:#FFF" target='_blank'>${source.name}</a>&nbsp;<a href='${source.alternativeUrl}' style="color:#FFF" target='_blank'>EuropePMC</a>)`;
+  }
+  const sourceLink = `&nbsp;<a href='${source.url}' style="color:#FFF" target='_blank'>${source.id}</a>`;
+  if (source.name) {
+    // Temporary until we get the expected value as 'PeptideAtlas' instead of 'HppPeptideAtlas'
+    if (source.name.startsWith("Hpp")) {
+      return `${sourceLink}&nbsp;(${source.name.slice(3)})`;
+    }
+    return `${sourceLink}&nbsp;(${source.name})`;
+  }
+  return sourceLink;
 };
 
 export const getEvidenceFromCodes = (evidenceList) => {
@@ -58,13 +65,13 @@ const getPTMEvidence = (ptms) => {
   );
   const uniqueIds = [...new Set(ids.flat())];
   // Urls in the payload are not relevant. For 'Glue project' dataset, Dataset ID and publication reference is hardcoded. Need to be checked in 2024 if it still exists in the payload
-  const prideArchive = "https://www.ebi.ac.uk/pride/archive/projects/";
+  const proteomexchange =
+    "https://proteomecentral.proteomexchange.org/dataset/";
   return `
   <ul>${uniqueIds
     .map((id) => {
       const datasetID = id === "Glue project" ? "PXD012174" : id;
-      return `<li title='${datasetID}' style="padding: .25rem 0">${datasetID}&nbsp;(<a href="${prideArchive}${datasetID}" style="color:#FFF" target="_blank">PRIDE</a>
-      ${
+      return `<li title='${datasetID}' style="padding: .25rem 0">${datasetID}&nbsp;(<a href="${proteomexchange}${datasetID}" style="color:#FFF" target="_blank">ProteomeXchange</a>${
         id === "Glue project"
           ? `)</li><li title="publication" style="padding: .25rem 0">Publication:&nbsp;31819260&nbsp;(<a href="https://pubmed.ncbi.nlm.nih.gov/31819260" style="color:#FFF" target="_blank">PubMed</a>)</li>`
           : `&nbsp;<a href="http://www.peptideatlas.org/builds/rice/phospho/" style="color:#FFF" target="_blank">PeptideAtlas</a>)</li>`
@@ -206,11 +213,11 @@ export const formatTooltip = (feature) => {
                         ref.properties["Universal Spectrum Id"]
                       }" style="color:#FFF" target="_blank">View on ProteomeXchange</a>
                       </li>
-                      <li style="text-indent: 2em">PSM Count: ${
-                        ref.properties["PSM Count"]
+                      <li style="text-indent: 2em">PSM Count (0.05 gFLR): ${
+                        ref.properties["PSM Count (0.05 gFLR)"]
                       }</li>
-                      <li style="text-indent: 2em">Site probability: ${
-                        ref.properties["Site probability"]
+                      <li style="text-indent: 2em">Final site probability: ${
+                        ref.properties["Final site probability"]
                       }</li>
                       `
                   )

packages/protvista-filter/package.json

@@ -1,6 +1,6 @@
 {
   "name": "protvista-filter",
-  "version": "3.8.4",
+  "version": "3.8.22",
   "description": "Filter component for variants",
   "files": [
     "dist",
@@ -30,5 +30,5 @@
     "url": "https://github.com/ebi-webcomponents/nightingale/issues"
   },
   "homepage": "https://ebi-webcomponents.github.io/nightingale/",
-  "gitHead": "337d88a3df2e52243aed81a123740d82917779db"
+  "gitHead": "d5953d40c908b47eacce04bdc585af8a71eeebc9"
 }

packages/protvista-interpro-adapter/package.json

@@ -1,6 +1,6 @@
 {
   "name": "protvista-interpro-adapter",
-  "version": "3.8.4",
+  "version": "3.8.22",
   "files": [
     "dist",
     "src"
@@ -19,5 +19,9 @@
   "bugs": {
     "url": "https://github.com/ebi-webcomponents/nightingale/issues"
   },
-  "homepage": "https://ebi-webcomponents.github.io/nightingale/"
+  "homepage": "https://ebi-webcomponents.github.io/nightingale/",
+  "dependencies": {
+    "color-hash": "2.0.2"
+  },
+  "gitHead": "d5953d40c908b47eacce04bdc585af8a71eeebc9"
 }