gramene-search 1.2.77 → 1.2.79

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "gramene-search",
-  "version": "1.2.77",
+  "version": "1.2.79",
   "description": "search wrapper for gramene",
   "source": "src/index.js",
   "main": "dist/index.js",

package/src/bundles/api.js

@@ -76,6 +76,26 @@ grameneSuggestions.doFocusFirstGrameneSuggestion = arg => ({dispatch, getState})
   console.log('inside doFocusFirstGrameneSuggestion');
 };
 
+function compressLongTaxonName(node) {
+  const fullName = node.name;
+  const removedExtraineousWords = fullName.replace(/( Group$| subsp\.| ssp\.| var\.| strain)/, '');
+  let finalVersion;
+  if (removedExtraineousWords.length > 20) {
+    let words = removedExtraineousWords.split(' ');
+    if (words.length === 2) {
+      // abrreviate first word.
+      finalVersion = removedExtraineousWords.replace(/^([A-Z])[a-z]+/, '$1.')
+    }
+    if (words.length > 2) {
+      finalVersion = removedExtraineousWords.replace(/^([A-Z])[a-z]+\s([a-z])[a-z]+/, '$1$2.')
+    }
+  }
+  else {
+    finalVersion = removedExtraineousWords;
+  }
+  node.short_name = finalVersion;
+}
+
 const grameneTaxonomy = createAsyncResourceBundle({
   name: 'grameneTaxonomy',
   actionBaseType: 'GRAMENE_TAXONOMY',
@@ -87,6 +107,7 @@ const grameneTaxonomy = createAsyncResourceBundle({
         let taxonomy = _.keyBy(taxNodes, '_id');
         taxNodes.forEach(t => {
           t._id = +t._id; // ensure taxonomy id is a number
+          compressLongTaxonName(t);
           if (t.hasOwnProperty("is_a")) {
             t.is_a.forEach(p_id => {
               const p = taxonomy[p_id];

package/src/components/results/GeneList.js

@@ -56,27 +56,32 @@ const PanLink = (props) => {
 
 const ClosestOrthologCmp = (props) =>
 {
-  let id, taxon_id, name, desc, species;
+  let id, taxon_id, name, desc, species, className;
   const gene = props.gene;
 
-  if (gene.model_rep_id) {
+  if (gene.closest_rep_id) {
+    name = gene.closest_rep_name || gene.closest_rep_id;
+    desc = gene.closest_rep_description;
+    species = gene.closest_rep_species_name;
+    id = gene.closest_rep_id;
+    taxon_id = gene.closest_rep_taxon_id;
+    className = "closest-ortholog";
+  }
+  else if (gene.model_rep_id) {
     name = gene.model_rep_name || gene.model_rep_id;
     desc = gene.model_rep_description;
     species = gene.model_rep_species_name;
     id = gene.model_rep_id;
     taxon_id = gene.model_rep_taxon_id;
+    className = "model-ortholog";
   }
-
-  else if (gene.closest_rep_id) {
-    name = gene.closest_rep_name || gene.closest_rep_id;
-    desc = gene.closest_rep_description;
-    species = gene.closest_rep_species_name;
-    id = gene.closest_rep_id;
-    taxon_id = gene.closest_rep_taxon_id;
+  var isZm = new RegExp(/^Zm00001e/);
+  if (isZm.test(desc)) {
+    desc='';
   }
 
   return (
-    <div className="closest-ortholog" onClick={() => {
+    <div className={className} onClick={() => {
       props.doEnsureGrameneGenome(taxon_id);
       props.doReplaceGrameneFilters(suggestionToFilters({
         category: 'Gene',
@@ -85,10 +90,8 @@ const ClosestOrthologCmp = (props) =>
         name: name
       }))
     }}>
-      <h4>
-        <span className="gene-id">{name}</span>
-        <small className="species-name"> {species}</small>
-      </h4>
+      <div className="gene-species">{species}</div>
+      <h3 className="gene-id">{name}</h3>
       <p>{desc}</p>
     </div>
   );
@@ -206,10 +209,10 @@ class Gene extends React.Component {
   renderMetadata() {
     let gene = this.props.searchResult;
     if (gene.model_rep_taxon_id) {
-      gene.model_rep_species_name = this.props.taxLut[gene.model_rep_taxon_id].name;
+      gene.model_rep_species_name = this.props.taxLut[gene.model_rep_taxon_id].short_name;
     }
     if (gene.closest_rep_taxon_id) {
-      gene.closest_rep_species_name = this.props.taxLut[gene.closest_rep_taxon_id].name;
+      gene.closest_rep_species_name = this.props.taxLut[gene.closest_rep_taxon_id].short_name;
     }
     return renderTairSummary(gene) || renderClosestOrtholog(gene);
   }

package/src/components/results/genes.css

@@ -123,7 +123,7 @@
     flex: 1 1 auto;
     width: 1036px;
 }
-.closest-ortholog, .gene-summary-tair {
+.model-ortholog, .closest-ortholog, .gene-summary-tair {
     cursor: pointer;
     flex: 1 1 auto;
     width: 500px;
@@ -134,12 +134,15 @@
     border: 1px solid darkorange;
 }
 
-.closest-ortholog {
+.model-ortholog {
     border: 1px dotted darkorange;
 }
+.closest-ortholog {
+    border: 1px dotted darkgreen;
+}
 
 .gene-summary-tair {
-    border: 1px dotted darkgreen;
+    border: 1px dotted darkblue;
 }
 .gene-summary-tair .rest {
     display: none;
@@ -160,6 +163,7 @@
 
 /* this is the "title" of the closest ortholog box */
 .closest-ortholog::before,
+.model-ortholog::before,
 .gene-summary-tair::before {
     position: relative;
     float: right;
@@ -170,15 +174,19 @@
     background: #fff;
 }
 
-.closest-ortholog::before {
+.model-ortholog::before {
     content: "Model Species Homolog";
     color: orange;
 }
+.closest-ortholog::before {
+    content: "Closest Annotated Homolog";
+    color: darkgreen;
+}
 
 /* this is the "title" of the closest ortholog box */
 .gene-summary-tair::before {
     content: "TAIR Curated Description";
-    color: darkgreen;
+    color: darkblue;
 }
 
 .gene-search-pic-sugg {

package/.parcel-cache/bbfc6fab41a92806.txt

@@ -1,2 +0,0 @@
-282689524
-1698084271782824000