gramene-search 1.4.0 → 1.4.2

package/.parcel-cache/snapshot-369948a06d23ec44.txt

@@ -1,2 +1,2 @@
-54381261
-1711721228724960000
+59112323
+1711893581240648000

package/dist/index.js

@@ -21,7 +21,6 @@ var $gXNCa$lodashget = require("lodash/get");
 var $gXNCa$lodashisEqual = require("lodash/isEqual");
 var $gXNCa$flattonested = require("flat-to-nested");
 var $gXNCa$reactsimpletreemenu = require("react-simple-tree-menu");
-require("console");
 var $gXNCa$aggridreact = require("ag-grid-react");
 require("ag-grid-community/styles/ag-grid.css");
 require("ag-grid-community/styles/ag-theme-quartz.css");
@@ -3222,7 +3221,6 @@ var $54c74a4689d5a778$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 
 
 
-
 const $283508ffcf8a47c4$var$metaRenderer = (params)=>{
     if (params.value.field === "germplasm") {
         if (params.value.germplasm_dbid) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("a", {
@@ -3261,9 +3259,10 @@ const $283508ffcf8a47c4$var$metaRenderer = (params)=>{
         currentURL.searchParams.set("fq_field", `VEP__merged__${$283508ffcf8a47c4$var$study_info[params.value.pop_id].type}__attr_ss`);
         currentURL.searchParams.set("fq_value", params.value.ens_id);
         currentURL.searchParams.set("name", params.value.ens_id);
-        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("a", {
+        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+            size: "sm",
             href: currentURL.toString(),
-            children: params.value.ens_id
+            children: "Search"
         });
     }
     return params.value.label;
@@ -3302,27 +3301,32 @@ const $283508ffcf8a47c4$var$Detail = (props)=>{
         let accessionTable = [];
         let tableFields = [
             {
-                field: "Study/Population",
+                field: "Order Germplasm",
                 cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
                 comparator: $283508ffcf8a47c4$var$sortByLabel
             },
             {
-                field: "VEP consequence",
+                field: "Synonyms",
                 cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
                 comparator: $283508ffcf8a47c4$var$sortByLabel
             },
             {
-                field: "Allele Status",
+                field: "Study/Population",
+                cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
+                comparator: $283508ffcf8a47c4$var$sortByLabel
+            },
+            {
+                field: "VEP consequence",
                 cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
                 comparator: $283508ffcf8a47c4$var$sortByLabel
             },
             {
-                field: "Germplasm",
+                field: "Allele Status",
                 cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
                 comparator: $283508ffcf8a47c4$var$sortByLabel
             },
             {
-                field: "Other Genes",
+                field: "All LOF Genes",
                 cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
                 comparator: $283508ffcf8a47c4$var$sortByLabel
             }
@@ -3342,16 +3346,19 @@ const $283508ffcf8a47c4$var$Detail = (props)=>{
                         "Allele Status": {
                             label: parts[2] === "het" ? "heterozygous" : "homozygous"
                         },
-                        "Germplasm": {
+                        "Order Germplasm": {
                             field: "germplasm",
                             gene_id: props.searchResult.id,
                             label: germplasm.pub_id,
                             ...germplasm
                         },
-                        "Other Genes": {
+                        "All LOF Genes": {
                             field: "search",
                             label: germplasm.ens_id,
                             ...germplasm
+                        },
+                        "Synonyms": {
+                            label: germplasm.ens_id
                         }
                     };
                     accessionTable.push(accInfo);
@@ -3365,16 +3372,34 @@ const $283508ffcf8a47c4$var$Detail = (props)=>{
                 filter: true
             };
         }, []);
-        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-            className: "ag-theme-quartz",
-            style: {
-                height: `${44 * (accessionTable.length + 2)}px`
-            },
-            children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$aggridreact.AgGridReact), {
-                rowData: accessionTable,
-                columnDefs: tableFields,
-                defaultColDef: defaultColDef
-            })
+        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+            children: [
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h5", {
+                    children: "Predicted loss-of-function alleles were detected in these germplasm."
+                }),
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                    children: [
+                        "Explore other variants within this gene in the ",
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("a", {
+                            target: "_blank",
+                            href: `${props.configuration.ensemblURL}/${gene.system_name}/Gene/Variation_Gene/Image?db=core;g=${props.searchResult.id}`,
+                            children: "Variant image"
+                        }),
+                        " page in the Ensembl genome browser."
+                    ]
+                }),
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                    className: "ag-theme-quartz",
+                    style: {
+                        height: `${44 * (accessionTable.length + 2)}px`
+                    },
+                    children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$aggridreact.AgGridReact), {
+                        rowData: accessionTable,
+                        columnDefs: tableFields,
+                        defaultColDef: defaultColDef
+                    })
+                })
+            ]
         });
     } else {
         props.doRequestVEP(gene._id);
@@ -4320,6 +4345,12 @@ class $6c5c4f90059875bf$var$Gene extends (0, ($parcel$interopDefault($gXNCa$reac
         super(props);
         this.state = {
             details: [
+                {
+                    id: "VEP",
+                    label: "Germplasm",
+                    popup: "Germplasm with protein truncating variants (PTVs)",
+                    available: false
+                },
                 {
                     id: "sequences",
                     label: "Sequences",
@@ -4356,12 +4387,6 @@ class $6c5c4f90059875bf$var$Gene extends (0, ($parcel$interopDefault($gXNCa$reac
                     popup: "Curated Publications",
                     available: false
                 },
-                {
-                    id: "VEP",
-                    label: "Germplasm",
-                    popup: "Germplasm with protein truncating variants (PTVs)",
-                    available: false
-                },
                 {
                     id: "xrefs",
                     label: "Xrefs",