gramene-search 1.6.4 → 1.6.6

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

@@ -1,2 +1,2 @@
-143882109
-1728587443985155000
+152020407
+1729029155640539000

package/.parcel-cache/snapshot-524f09471ce7017b.txt

@@ -1,2 +1,2 @@
-143881606
-1728587434625576000
+152019833
+1729029148314911000

package/dist/index.js

@@ -3287,12 +3287,31 @@ var $54c74a4689d5a778$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 
 
 
+
 const $283508ffcf8a47c4$var$ggURL = {
     IRRI: "https://gringlobal.irri.org/gringlobal/accessiondetail?id=",
     ARS: "https://npgsweb.ars-grin.gov/gringlobal/accessiondetail.aspx?id=",
+    ICRISAT: "https://genebank.icrisat.org/IND/PassportSummary?ID=",
     sorbmutdb: "https://www.depts.ttu.edu/igcast/sorbmutdb.php"
 };
 const $283508ffcf8a47c4$var$metaRenderer = (params)=>{
+    if (params.value.field === "accessions") {
+        const accs = params.value.accessions;
+        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion), {
+            children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Accordion).Item, {
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion).Header, {
+                        children: accs.length
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion).Body, {
+                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("p", {
+                            children: 'This is where the "table" goes'
+                        })
+                    })
+                ]
+            })
+        });
+    }
     if (params.value.field === "germplasm") {
         const genebank = params.value.stock_center;
         const url = $283508ffcf8a47c4$var$ggURL[genebank];
@@ -3376,6 +3395,14 @@ const $283508ffcf8a47c4$var$study_info = {
         "5": {
             label: "Boatwright SAP",
             type: "NAT"
+        },
+        "7": {
+            label: "Kumar BAP",
+            type: "NAT"
+        },
+        "8": {
+            label: "Lasky landraces",
+            type: "NAT"
         }
     },
     "oryza_sativa": {
@@ -3400,86 +3427,231 @@ const $283508ffcf8a47c4$var$study_info = {
     "oryza_sativamh63": $283508ffcf8a47c4$var$rice_studies,
     "oryza_sativazs97": $283508ffcf8a47c4$var$rice_studies
 };
-const $283508ffcf8a47c4$var$Detail = (props)=>{
-    const gene = props.geneDocs[props.searchResult.id];
-    if (props.grameneConsequences && props.grameneConsequences[gene._id] && props.grameneGermplasm) {
-        const germplasmLUT = props.grameneGermplasm;
-        const vep_obj = props.grameneConsequences[gene._id];
-        let accessionTable = [];
-        let tableFields = [
-            {
-                field: "Order Germplasm",
-                cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
-                comparator: $283508ffcf8a47c4$var$sortByLabel
-            },
-            {
-                field: "Synonyms",
-                cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
-                comparator: $283508ffcf8a47c4$var$sortByLabel
-            },
-            {
-                field: "Study/Population",
-                cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
-                comparator: $283508ffcf8a47c4$var$sortByLabel
-            },
-            {
-                field: "VEP consequence",
-                cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
-                comparator: $283508ffcf8a47c4$var$sortByLabel
-            },
-            {
-                field: "Allele Status",
-                cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
-                comparator: $283508ffcf8a47c4$var$sortByLabel
-            },
-            {
-                field: "All LOF Genes",
-                cellRenderer: $283508ffcf8a47c4$var$metaRenderer,
-                comparator: $283508ffcf8a47c4$var$sortByLabel
+const $283508ffcf8a47c4$var$AccessionLink = ({ germplasm: germplasm, gene_id: gene_id })=>{
+    if (germplasm.germplasm_dbid) {
+        const germ_id = germplasm.germplasm_dbid;
+        const genebank = germplasm.stock_center;
+        const url = $283508ffcf8a47c4$var$ggURL[genebank];
+        if (germ_id && url && germ_id !== "0") return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("a", {
+            target: "_blank",
+            href: `${url}${germ_id}`,
+            children: [
+                germplasm.pub_id,
+                " (",
+                genebank,
+                ")"
+            ]
+        });
+        if (genebank === "sorbmutdb") return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("form", {
+            id: germplasm.pub_id,
+            action: url,
+            method: "post",
+            target: "_blank",
+            children: [
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("input", {
+                    type: "hidden",
+                    name: "search",
+                    value: gene_id.replace("SORBI_3", "Sobic.")
+                }),
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("input", {
+                    type: "hidden",
+                    name: "submit",
+                    value: "Search"
+                }),
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("button", {
+                    type: "submit",
+                    className: "button-like-link",
+                    children: "SorbMutDB"
+                })
+            ]
+        });
+    }
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+        children: germplasm.pub_id
+    });
+};
+function $283508ffcf8a47c4$var$group_germplasm(gene, germplasmLUT, vep_obj) {
+    let accessionTable = [];
+    Object.entries(vep_obj).forEach(([key, accessions])=>{
+        const parts = key.split("__");
+        if (parts[0] === "VEP") {
+            if (parts[1] !== "merged") accessions.forEach((ens_id)=>{
+                const germplasm = germplasmLUT[ens_id][0];
+                const pop = $283508ffcf8a47c4$var$study_info[parts[3]][parts[4]];
+                const conseq = parts[1].replaceAll("_", " ");
+                const status = parts[2] === "het" ? "heterozygous" : "homozygous";
+                const accInfo = {
+                    key: [
+                        pop.label,
+                        conseq,
+                        status
+                    ].join("%%%"),
+                    germplasm: germplasm,
+                    pop: pop
+                };
+                accessionTable.push(accInfo);
+            });
+        }
+    });
+    // group accessionTable by key field
+    const groups = (0, ($parcel$interopDefault($gXNCa$lodash))).groupBy(accessionTable, "key");
+    let grouped = [];
+    let id = 0;
+    Object.keys(groups).sort().forEach((group)=>{
+        const [pop, conseq, status] = group.split("%%%");
+        id++;
+        const tally = groups[group].length;
+        grouped.push({
+            id: id,
+            group: group,
+            summary: true,
+            pop: pop,
+            conseq: conseq,
+            status: status,
+            tally: tally
+        });
+        groups[group].forEach((acc)=>{
+            id++;
+            grouped.push({
+                id: id,
+                group: group,
+                summary: false,
+                pop: pop,
+                conseq: conseq,
+                status: status,
+                accession: acc,
+                tally: tally
+            });
+        });
+    });
+    return grouped;
+}
+const $283508ffcf8a47c4$var$THRESHOLD = 5;
+const $283508ffcf8a47c4$var$GridWithGroups = ({ groups: groups, gene_id: gene_id })=>{
+    const [rowData, setRowData] = (0, $gXNCa$react.useState)(groups);
+    const initialExpanded = {};
+    rowData.forEach((row)=>{
+        if (row.summary) initialExpanded[row.group] = row.tally < $283508ffcf8a47c4$var$THRESHOLD;
+    });
+    const [expandedGroups, setExpandedGroups] = (0, $gXNCa$react.useState)(initialExpanded);
+    // const gridRef = useRef();
+    // Toggle group visibility
+    const toggleGroup = (group)=>{
+        setExpandedGroups((prevExpandedGroups)=>({
+                ...prevExpandedGroups,
+                [group]: !prevExpandedGroups[group]
+            }));
+    };
+    // Filter the data to show/hide rows based on the expanded group state
+    const getVisibleRowData = ()=>{
+        const visibleRows = [];
+        rowData.forEach((row)=>{
+            if (row.summary) {
+                if (row.tally > 1) visibleRows.push(row);
+            } else if (expandedGroups[row.group]) visibleRows.push(row); // Show non-summary rows if the group is expanded
+        });
+        return visibleRows;
+    };
+    // Define columns with a custom renderer for the summary rows
+    const columnDefs = [
+        {
+            field: "pop",
+            headerName: "Study",
+            cellRenderer: (params)=>{
+                if (params.data.summary || params.data.tally === 1) return params.value;
+                return null;
             }
-        ];
-        Object.entries(vep_obj).forEach(([key, accessions])=>{
-            const parts = key.split("__");
-            if (parts[0] === "VEP") {
-                if (parts[1] !== "merged") accessions.forEach((ens_id)=>{
-                    const germplasm = germplasmLUT[ens_id][0];
-                    const accInfo = {
-                        "Study/Population": {
-                            label: $283508ffcf8a47c4$var$study_info[parts[3]][parts[4]].label
-                        },
-                        "VEP consequence": {
-                            label: parts[1].replaceAll("_", " ")
-                        },
-                        "Allele Status": {
-                            label: parts[2] === "het" ? "heterozygous" : "homozygous"
-                        },
-                        "Order Germplasm": {
-                            field: "germplasm",
-                            gene_id: props.searchResult.id,
-                            label: germplasm.pub_id,
-                            ...germplasm
-                        },
-                        "All LOF Genes": {
-                            field: "search",
-                            label: germplasm.ens_id,
-                            pop_type: $283508ffcf8a47c4$var$study_info[parts[3]][parts[4]].type,
-                            ...germplasm
-                        },
-                        "Synonyms": {
-                            label: germplasm.ens_id
-                        }
-                    };
-                    accessionTable.push(accInfo);
+        },
+        {
+            field: "conseq",
+            headerName: "VEP consequence",
+            cellRenderer: (params)=>{
+                if (params.data.summary || params.data.tally === 1) return params.value;
+                return null;
+            }
+        },
+        {
+            field: "status",
+            headerName: "Allele status",
+            cellRenderer: (params)=>{
+                if (params.data.summary || params.data.tally === 1) return params.value;
+                return null;
+            }
+        },
+        {
+            field: "accession",
+            headerName: "Order Germplasm",
+            cellRenderer: (params)=>{
+                if (params.value) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($283508ffcf8a47c4$var$AccessionLink, {
+                    germplasm: params.value.germplasm,
+                    gene_id: gene_id
+                });
+                if (params.data.summary) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("span", {
+                    onClick: ()=>toggleGroup(params.data.group),
+                    children: [
+                        params.data.tally,
+                        " Accessions ",
+                        expandedGroups[params.data.group] ? "\u25BC" : "\u25B6"
+                    ]
                 });
+                return null;
             }
-        });
-        // const [rowData, setRowData] = useState(accessionTable);
-        // const [colDefs, setColDefs] = useState(tableFields);
-        const defaultColDef = (0, $gXNCa$react.useMemo)(()=>{
-            return {
-                filter: true
+        },
+        {
+            field: "search",
+            headerName: "All LOF Genes",
+            cellRenderer: (params)=>{
+                if (params.data.accession) {
+                    const currentURL = new URL(window.location.href);
+                    const accession = params.data.accession;
+                    currentURL.search = "";
+                    currentURL.searchParams.set("category", "Germplasm");
+                    currentURL.searchParams.set("fq_field", `VEP__merged__${accession.pop.type}__attr_ss`);
+                    currentURL.searchParams.set("fq_value", accession.germplasm.ens_id);
+                    currentURL.searchParams.set("name", accession.germplasm.ens_id);
+                    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Button), {
+                        size: "sm",
+                        href: currentURL.toString(),
+                        children: "Search"
+                    });
+                }
+                return null;
+            }
+        }
+    ];
+    const defaultColDef = {
+        sortable: false,
+        cellStyle: (params)=>{
+            // if (!params.data.summary) {
+            //   return {paddingLeft: '30px'};
+            // }
+            if (params.data.summary) return {
+                cursor: "pointer"
             };
-        }, []);
+            return null;
+        }
+    };
+    const nVisible = getVisibleRowData().length;
+    const tableHeight = 50 + Math.min(nVisible, 10) * 42;
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        className: "ag-theme-quartz",
+        style: {
+            height: tableHeight,
+            width: "100%"
+        },
+        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$aggridreact.AgGridReact), {
+            rowData: getVisibleRowData(),
+            columnDefs: columnDefs,
+            getRowNodeId: (data)=>data.id,
+            animateRows: true,
+            defaultColDef: defaultColDef
+        })
+    });
+};
+const $283508ffcf8a47c4$var$Detail = (props)=>{
+    const gene = props.geneDocs[props.searchResult.id];
+    if (props.grameneConsequences && props.grameneConsequences[gene._id] && props.grameneGermplasm) {
+        const groups = $283508ffcf8a47c4$var$group_germplasm(gene, props.grameneGermplasm, props.grameneConsequences[gene._id]);
         return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
             children: [
                 /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("h5", {
@@ -3496,16 +3668,9 @@ const $283508ffcf8a47c4$var$Detail = (props)=>{
                         " 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
-                    })
+                /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($283508ffcf8a47c4$var$GridWithGroups, {
+                    groups: groups,
+                    gene_id: gene._id
                 })
             ]
         });