gramene-search 1.2.38 → 1.2.39

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gramene-search",
-  "version": "1.2.38",
+  "version": "1.2.39",
   "description": "search wrapper for gramene",
   "main": "dist/index.js",
   "scripts": {
@@ -25,7 +25,7 @@
     "flat-to-nested": "^1.1.1",
     "formik": "^3.0.0-next.8",
     "gramene-bins-client": "^2.3.3",
-    "gramene-dbxrefs": "^3.0.4",
+    "gramene-dbxrefs": "^3.0.11",
     "gramene-genetree-vis": "^4.1.13",
     "gramene-mdview": "^1.1.8",
     "gramene-search-vis": "^4.1.10",
@@ -37,16 +37,16 @@
     "numeral": "^2.0.6",
     "querystringify": "^2.2.0",
     "react": "^17.0.2",
-    "react-bootstrap": "^1.6.3",
-    "react-debounce-input": "^3.2.3",
+    "react-bootstrap": "^2.5.0",
+    "react-debounce-input": "^3.2.5",
     "react-dom": "17.0.2",
     "react-ga": "^3.3.0",
-    "react-icons": "^4.1.0",
+    "react-icons": "^4.3.1",
     "react-markdown": "^5.0.3",
-    "react-router-dom": "^5.2.0",
+    "react-router-dom": "^5.3.0",
     "react-tree-menu": "https://github.com/ajo2995/react-tree-menu",
     "redux-bundler": "21.0.0",
-    "redux-bundler-react": "1.0.1",
+    "redux-bundler-react": "^1.2.0",
     "yup": "^0.32.9"
   },
   "prettier": {
@@ -57,9 +57,15 @@
     "@babel/core": "latest",
     "@babel/preset-env": "latest",
     "@babel/preset-react": "latest",
-    "@parcel/transformer-image": "2.0.0",
-    "@parcel/transformer-less": "2.0.0",
-    "parcel": "2.0.0"
+    "@parcel/config-default": "^2.0.0-rc.0",
+    "@parcel/core": "^2.8.0",
+    "@parcel/transformer-image": "^2.8.0",
+    "@parcel/transformer-js": "^2.8.0",
+    "@parcel/transformer-less": "^2.8.0",
+    "buffer": "^5.7.1",
+    "http-proxy-middleware": "^2.0.6",
+    "parcel": "^2.8.0",
+    "process": "^0.11.10"
   },
   "repository": {
     "type": "git",

package/src/components/results/details/Xrefs.js

@@ -44,20 +44,13 @@ class Xref extends React.Component {
   }
 
   render() {
-    var members, vals, db;
-    db = this.props.displayName;
+    var db = this.props.xref.label;
+    var urlfcn = this.props.xref.url;
 
-    members = this.props.members;
+    var members = this.props.members.sort();
 
-    vals = _(members)
-      .map(function (m) {
-        return m.val;
-      })
-      .flatten(true)
-      .sort()
-      .uniq(true) // TODO figure out why there are duplicates.
-      .map(function (item, idx) {
-        var url = members[0].url(item),
+    var vals = members.map(function (item, idx) {
+        var url = urlfcn(item),
           liClass = idx < HOW_MANY_TO_SHOW_BY_DEFAULT ? "default" : "extra";
         let external = <small title="This link opens a page from an external site"> <i className="fa fa-external-link"/></small>;
         return (
@@ -72,16 +65,17 @@ class Xref extends React.Component {
           </li>
         )
       })
-      .value();
 
     vals = this.possiblyTruncateList(vals);
 
     return (
       <tr>
-        <td className="xref-name-col">{this.props.displayName}</td>
+        <td className="xref-name-col">{db}</td>
         <td className="xref-value-col">
           <ol className="xref-id-list">{vals}</ol>
         </td>
+        <td className="xref-name-col">{this.props.source}</td>
+        <td className="xref-value-col">{this.props.text}</td>
       </tr>
     );
   }
@@ -91,22 +85,39 @@ function formatXrefsForGene(gene) {
   if(!gene || !_.isArray(gene.xrefs)) {
     throw new Error("No xrefs for " + _.get(gene._id));
   }
-  return _(gene.xrefs)
-    .keyBy('db')
-    .pickBy(function(val, name) {
-      return dbxrefs.isKnown(name);
-    })
-    .map(function(val, name) {
-      var xref = dbxrefs.fetch(name);
-      return {url: xref.url, label: xref.label, val: val.ids};
+  return gene.xrefs
+    .filter(xr => dbxrefs.isKnown(xr.db))
+    .sort((a,b) => {
+      if (a.source) {
+        if (b.source) {
+          if (a.source < b.source) {
+            return -1;
+          }
+          if (a.source > b.source) {
+            return 1;
+          }
+        }
+        else {
+          return -1;
+        }
+      }
+      else if (b.source) {
+        return 1;
+      }
+      if (a.db < b.db) {
+        return -1;
+      }
+      if (a.db > b.db) {
+        return 1;
+      }
+      return 0;
     })
-    .groupBy('label')
-    .map(function(members, displayName) {
+    .map((xr,idx) => {
+      var xref = dbxrefs.fetch(xr.db);
       return (
-        <Xref key={displayName} displayName={displayName} members={members} />
+        <Xref key={idx} xref={xref} members={xr.ids} source={xr.source} text={xr.text} />
       )
     })
-    .value();
 }
 
 const Xrefs = ({searchResult, geneDocs}) => (
@@ -117,8 +128,10 @@ const Xrefs = ({searchResult, geneDocs}) => (
       <table className="xrefs table">
         <thead>
         <tr>
-          <th className="xref-name-col">Database</th>
-          <th className="xref-value-col">IDs and links</th>
+          <th className="xref-10-col">Database</th>
+          <th className="xref-10-col">IDs and links</th>
+          <th className="xref-10-col">Source</th>
+          <th className="xref-70-col">Text</th>
         </tr>
         </thead>
         <tbody>

package/src/components/results/genes.css

@@ -24,6 +24,12 @@
 .xref-value-col {
     width: 80%;
 }
+.xref-70-col {
+    width: 70%;
+}
+.xref-10-col {
+    width: 10%;
+}
 .xref-id-list {
     padding-left: 0;
     list-style: none;

package/src/demo.js

@@ -44,7 +44,7 @@ const panSites = [
     ensemblURL: 'https://ensembl.gramene.org',
     ensemblSite: 'https://ensembl.gramene.org',
     ensemblRest: 'https://data.gramene.org/ensembl',
-    grameneData: 'https://data.gramene.org/v64',
+    grameneData: 'https://data.gramene.org/v66',
     targetTaxonId: 3702,
     alertText: 'Main site'
   },

package/src/index.html

@@ -5,7 +5,7 @@
     <title>Gramene Search</title>
     <script>
       window.gramene = {};
-      gramene.defaultServer = 'https://data.gramene.org/v65/swagger';
+      gramene.defaultServer = 'https://data.gramene.org/v66/swagger';
     </script>
     <script async src="./static/gramene-dalliance/dalliance-all.js"></script>
     <script async src="https://plantreactome.gramene.org/DiagramJs/diagram/diagram.nocache.js"></script>

package/.parcel-cache/2b1c1cd7b577d2ca.txt

@@ -1,2 +0,0 @@
-43337522
-1663863196280298000