gramene-search 1.2.90 → 1.2.92

package/.parcel-cache/2126881b633272fa.txt

@@ -1,2 +1,2 @@
-288251140
-1704985571838555000
+412097457
+1706728927930901000

package/dist/index.js

@@ -65,7 +65,7 @@ const $9d9aeaf9299e61a1$var$grameneSuggestions = (0, $gXNCa$reduxbundler.createA
                 group.doclist.docs.forEach((sugg)=>{
                     sugg.num_genes = 0;
                     sugg.taxon_id.forEach((id, idx)=>{
-                        if (g.active[id]) sugg.num_genes += sugg.taxon_freq[idx];
+                        if (g.active[id] && !g.active[id].hidden) sugg.num_genes += sugg.taxon_freq[idx];
                     });
                 });
             });
@@ -163,43 +163,62 @@ $9d9aeaf9299e61a1$var$curatedGenes.reactCuratedGenes = (0, $gXNCa$reduxbundler.c
         actionCreator: "doFetchCuratedGenes"
     };
 });
-const $9d9aeaf9299e61a1$var$grameneExpressionStudies = (0, $gXNCa$reduxbundler.createAsyncResourceBundle)({
-    name: "grameneExpressionStudies",
-    actionBaseType: "GRAMENE_EXPRESSION_STUDIES",
-    persist: true,
-    getPromise: ({ store: store  })=>{
-        return fetch(`${store.selectGrameneAPI()}/experiments?rows=-1`).then((res)=>res.json()).then((res)=>(0, ($parcel$interopDefault($gXNCa$lodash))).keyBy(res, "_id"));
-    }
-});
-$9d9aeaf9299e61a1$var$grameneExpressionStudies.reactGrameneExpressionStudies = (0, $gXNCa$reduxbundler.createSelector)("selectGrameneExpressionStudiesShouldUpdate", (shouldUpdate)=>{
-    if (shouldUpdate) return {
-        actionCreator: "doFetchGrameneExpressionStudies"
-    };
-});
-const $9d9aeaf9299e61a1$var$grameneExpressionAssays = (0, $gXNCa$reduxbundler.createAsyncResourceBundle)({
-    name: "grameneExpressionAssays",
-    actionBaseType: "GRAMENE_EXPRESSION_ASSAYS",
-    persist: true,
-    getPromise: ({ store: store  })=>{
-        return fetch(`${store.selectGrameneAPI()}/assays?rows=-1`).then((res)=>res.json()).then((res)=>{
-            let expr = {};
-            res.forEach((assay)=>{
-                if (!expr.hasOwnProperty(assay.taxon_id)) expr[assay.taxon_id] = {};
-                if (!expr[assay.taxon_id].hasOwnProperty(assay.experiment)) expr[assay.taxon_id][assay.experiment] = [];
-                assay.order = +assay.group.replace("g", "");
-                expr[assay.taxon_id][assay.experiment].push(assay);
-            });
-            // sort each experiment
-            for(const tid in expr)for(const exp in expr[tid])expr[tid][exp].sort((a, b)=>a.order - b.order);
-            return expr;
-        });
-    }
-});
-$9d9aeaf9299e61a1$var$grameneExpressionAssays.reactGrameneExpressionAssays = (0, $gXNCa$reduxbundler.createSelector)("selectGrameneExpressionAssaysShouldUpdate", (shouldUpdate)=>{
-    if (shouldUpdate) return {
-        actionCreator: "doFetchGrameneExpressionAssays"
-    };
-});
+// const grameneExpressionStudies = createAsyncResourceBundle( {
+//   name: 'grameneExpressionStudies',
+//   actionBaseType: 'GRAMENE_EXPRESSION_STUDIES',
+//   persist: true,
+//   getPromise: ({store}) => {
+//     return fetch(`${store.selectGrameneAPI()}/experiments?rows=-1`)
+//       .then(res => res.json())
+//       .then(res => _.keyBy(res, '_id'))
+//   }
+// });
+// grameneExpressionStudies.reactGrameneExpressionStudies = createSelector(
+//   'selectGrameneExpressionStudiesShouldUpdate',
+//   (shouldUpdate) => {
+//     if (shouldUpdate) {
+//       return { actionCreator: 'doFetchGrameneExpressionStudies' }
+//     }
+//   }
+// );
+//
+// const grameneExpressionAssays = createAsyncResourceBundle( {
+//   name: 'grameneExpressionAssays',
+//   actionBaseType: 'GRAMENE_EXPRESSION_ASSAYS',
+//   persist: true,
+//   getPromise: ({store}) => {
+//     return fetch(`${store.selectGrameneAPI()}/assays?rows=-1`)
+//       .then(res => res.json())
+//       .then(res => {
+//         let expr={};
+//         res.forEach(assay => {
+//           if (!expr.hasOwnProperty(assay.taxon_id)) {
+//             expr[assay.taxon_id] = {};
+//           }
+//           if (!expr[assay.taxon_id].hasOwnProperty(assay.experiment)) {
+//             expr[assay.taxon_id][assay.experiment] = [];
+//           }
+//           assay.order = +assay.group.replace('g','');
+//           expr[assay.taxon_id][assay.experiment].push(assay);
+//         });
+//         // sort each experiment
+//         for (const tid in expr) {
+//           for (const exp in expr[tid]) {
+//             expr[tid][exp].sort((a,b) => a.order - b.order);
+//           }
+//         }
+//         return expr;
+//       })
+//   }
+// });
+// grameneExpressionAssays.reactGrameneExpressionAssays = createSelector(
+//   'selectGrameneExpressionAssaysShouldUpdate',
+//   (shouldUpdate) => {
+//     if (shouldUpdate) {
+//       return { actionCreator: 'doFetchGrameneExpressionAssays' }
+//     }
+//   }
+// );
 const $9d9aeaf9299e61a1$var$attribFacetFields = [
     "{!facet.limit='10' facet.mincount='1' key='age'}panset_age_attr_s",
     "{!facet.limit='100' facet.mincount='1' key='taxa'}panset_ntaxa_attr_i",
@@ -350,7 +369,7 @@ const $9d9aeaf9299e61a1$var$grameneSearch = (0, $gXNCa$reduxbundler.createAsyncR
         const offset = store.selectGrameneSearchOffset();
         const rows = store.selectGrameneSearchRows();
         const g = store.selectGrameneGenomes();
-        const taxa = Object.keys(g.active);
+        const taxa = Object.keys(g.active).filter((tid)=>!g.active[tid].hidden);
         let fq = "";
         if (taxa.length) {
             console.log("search add a fq for ", taxa);
@@ -367,8 +386,8 @@ const $9d9aeaf9299e61a1$var$grameneSearch = (0, $gXNCa$reduxbundler.createAsyncR
         });
     }
 });
-$9d9aeaf9299e61a1$var$grameneSearch.reactGrameneSearch = (0, $gXNCa$reduxbundler.createSelector)("selectGrameneSearchShouldUpdate", "selectGrameneFiltersStatus", (shouldUpdate, status)=>{
-    if (shouldUpdate && status === "search") return {
+$9d9aeaf9299e61a1$var$grameneSearch.reactGrameneSearch = (0, $gXNCa$reduxbundler.createSelector)("selectGrameneSearchShouldUpdate", "selectGrameneFiltersStatus", "selectGrameneGenomes", "selectGrameneMaps", (shouldUpdate, status, genomes, maps)=>{
+    if (shouldUpdate && status === "search" && genomes && maps) return {
         actionCreator: "doFetchGrameneSearch"
     };
 });
@@ -1172,6 +1191,11 @@ const $24971af0a229e0e3$var$grameneViews = {
                     id: "attribs",
                     name: "Gene attributes",
                     show: "off"
+                },
+                {
+                    id: "expression",
+                    name: "Gene expression",
+                    show: "off"
                 }
             ]
         };
@@ -1254,15 +1278,15 @@ const $671312b287158a8a$var$grameneDocs = {
                     newState.studies = Object.assign({}, state.studies, payload);
                     return newState;
                 case "ATLAS_SAMPLES_REQUESTED":
-                    if (!state.studies[payload].hasOwnProperty("samples")) {
+                    if (!state.studies.byID[payload].hasOwnProperty("samples")) {
                         newState = Object.assign({}, state);
-                        newState.studies[payload].samples = [];
+                        newState.studies.byID[payload].samples = [];
                         return newState;
                     }
                     break;
                 case "ATLAS_SAMPLES_RECEIVED":
                     newState = Object.assign({}, state);
-                    newState.studies[payload.id].samples = payload.samples;
+                    newState.studies.byID[payload.id].samples = payload.samples;
                     return newState;
                 case "GENE_SEQUENCE_REQUESTED":
                     if (!state.sequences.hasOwnProperty(payload)) {
@@ -1386,11 +1410,14 @@ const $671312b287158a8a$var$grameneDocs = {
         },
     doRequestExpressionStudies: (id)=>({ dispatch: dispatch , store: store  })=>{
             fetch(`${store.selectGrameneAPI()}/experiments?rows=-1`).then((res)=>res.json()).then((res)=>{
-                let studies = {};
+                let studies = {
+                    byID: {},
+                    byTaxon: {}
+                };
                 res.forEach((s)=>{
-                    studies[s._id] = s;
-                    if (!studies.hasOwnProperty("taxon_id")) studies[s.taxon_id] = [];
-                    studies[s.taxon_id].push(s._id);
+                    studies.byID[s._id] = s;
+                    if (!studies.byTaxon.hasOwnProperty(s.taxon_id)) studies.byTaxon[s.taxon_id] = [];
+                    studies.byTaxon[s.taxon_id].push(s._id);
                 });
                 dispatch({
                     type: "ATLAS_STUDIES_RECEIVED",
@@ -1400,7 +1427,7 @@ const $671312b287158a8a$var$grameneDocs = {
         },
     doRequestStudyMetadata: (id)=>({ dispatch: dispatch , store: store  })=>{
             const studies = store.selectAtlasStudies();
-            if (!studies[id].hasOwnProperty("samples")) {
+            if (!studies.byID[id].hasOwnProperty("samples")) {
                 dispatch({
                     type: "ATLAS_SAMPLES_REQUESTED",
                     payload: id
@@ -1559,6 +1586,9 @@ const $0d54502f6cafe273$var$grameneGenomes = {
                     newState = Object.assign({}, state);
                     newState.active = payload;
                     return newState;
+                case "GRAMENE_MAPS_FETCH_FINISHED":
+                    newState = Object.assign({}, state);
+                    newState.active = payload;
                 default:
                     return state;
             }
@@ -1569,6 +1599,20 @@ const $0d54502f6cafe273$var$grameneGenomes = {
                 type: "GRAMENE_GENOMES_TOGGLED"
             });
         },
+    doInitializeGrameneGenomes: (genomes)=>({ dispatch: dispatch , getState: getState  })=>{
+            dispatch({
+                type: "BATCH_ACTIONS",
+                actions: [
+                    {
+                        type: "GRAMENE_SEARCH_CLEARED"
+                    },
+                    {
+                        type: "GRAMENE_GENOMES_UPDATED",
+                        payload: genomes
+                    }
+                ]
+            });
+        },
     doUpdateGrameneGenomes: (genomes)=>({ dispatch: dispatch , getState: getState  })=>{
             dispatch({
                 type: "BATCH_ACTIONS",
@@ -4551,20 +4595,26 @@ class $76e15aea9236bd47$var$TaxonomyModal extends (0, ($parcel$interopDefault($g
             genomes: Object.values(props.grameneMaps).sort((a, b)=>a.left_index - b.left_index)
         };
         if (Object.keys(props.grameneGenomes.active).length === 0) this.state.genomes.forEach((g)=>{
-            g.selected = true;
+            g.selected = !g.hidden;
         });
         else this.state.genomes.forEach((g)=>{
-            g.selected = props.grameneGenomes.active[g.taxon_id];
+            g.selected = !g.hidden && props.grameneGenomes.active[g.taxon_id];
         });
     }
     getSelectedGenomes() {
         let selected = {};
-        let notAll = false;
+        let notHidden = {};
+        let somethingWasSelected = false;
         this.state.genomes.forEach((g)=>{
-            if (g.selected) selected[g.taxon_id] = true;
-            else notAll = true;
+            if (!g.hidden) {
+                notHidden[g.taxon_id] = true;
+                if (g.selected) {
+                    selected[g.taxon_id] = true;
+                    somethingWasSelected = true;
+                }
+            }
         });
-        return notAll ? selected : {};
+        return somethingWasSelected ? selected : notHidden;
     }
     handleChange(e) {
         const idx = +e.target.value;
@@ -4597,6 +4647,7 @@ class $76e15aea9236bd47$var$TaxonomyModal extends (0, ($parcel$interopDefault($g
         return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
             children: [
                 this.state.genomes.map((m, idx)=>{
+                    if (m.hidden) return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactjsxruntime.Fragment), {});
                     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
                         children: [
                             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("input", {
@@ -4654,11 +4705,94 @@ var $76e15aea9236bd47$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 
 
 
+
+const $261baeb81c4d4d8a$var$StudyCmp = (props)=>{
+    const study = props.atlasStudies.byID[props.sid];
+    if (!study.samples) {
+        props.doRequestStudyMetadata(props.sid);
+        return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("p", {
+            children: "loading"
+        });
+    } else return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+        children: "got eem!"
+    });
+};
+const $261baeb81c4d4d8a$var$Study = (0, $gXNCa$reduxbundlerreact.connect)("selectGrameneSearch", "selectAtlasStudies", "doRequestStudyMetadata", $261baeb81c4d4d8a$var$StudyCmp);
+const $261baeb81c4d4d8a$var$Expression = (props)=>{
+    const [taxon, setTaxon] = (0, $gXNCa$react.useState)(0);
+    const [study, setStudy] = (0, $gXNCa$react.useState)(0);
+    let searchTaxa = {};
+    let availableTaxa = [];
+    if (props.grameneSearch) {
+        const taxon_id_facet = props.grameneSearch.facet_counts.facet_fields.taxon_id;
+        taxon_id_facet.filter((tid, idx)=>idx % 2 === 0).forEach((tid)=>searchTaxa[tid] = true);
+    }
+    if (!props.atlasStudies.byTaxon) props.doRequestExpressionStudies();
+    else availableTaxa = Object.keys(props.atlasStudies.byTaxon).filter((tid)=>searchTaxa[tid] || searchTaxa[tid + "001"]);
+    return availableTaxa && props.grameneTaxonomy && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+        children: [
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("label", {
+                htmlFor: "taxonomySelect",
+                children: "Select Genome:"
+            }),
+            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("select", {
+                id: "taxonomySelect",
+                value: taxon,
+                onChange: (e)=>{
+                    setTaxon(e.target.value);
+                    setStudy(0);
+                },
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("option", {
+                        value: "",
+                        children: "Select..."
+                    }),
+                    availableTaxa.map((tid, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("option", {
+                            value: tid,
+                            children: props.grameneTaxonomy[tid].name
+                        }, idx))
+                ]
+            }),
+            taxon > 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("label", {
+                        htmlFor: "studySelect",
+                        children: "Select Study:"
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("select", {
+                        id: "studySelect",
+                        value: study,
+                        onChange: (e)=>setStudy(e.target.value),
+                        children: [
+                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("option", {
+                                value: "",
+                                children: "Select..."
+                            }),
+                            props.atlasStudies.byTaxon[taxon].map((sid, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("option", {
+                                    value: sid,
+                                    children: props.atlasStudies.byID[sid].description
+                                }, idx))
+                        ]
+                    })
+                ]
+            }),
+            study !== 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($261baeb81c4d4d8a$var$Study, {
+                sid: study
+            })
+        ]
+    });
+};
+var $261baeb81c4d4d8a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)("selectConfiguration", "selectGrameneSearch", "selectGrameneTaxonomy", "selectAtlasStudies", "doRequestExpressionStudies", "doRequestStudyMetadata", $261baeb81c4d4d8a$var$Expression);
+
+
+
+
 const $693dd8c7a5607c3a$var$inventory = {
     help: (0, $b36244140732570a$export$2e2bcd8739ae039),
     list: (0, $6c5c4f90059875bf$export$2e2bcd8739ae039),
     taxonomy: (0, $a67cad486021eb32$export$2e2bcd8739ae039),
-    attribs: (0, $67bf5a43401bffdc$export$2e2bcd8739ae039)
+    attribs: (0, $67bf5a43401bffdc$export$2e2bcd8739ae039),
+    expression: (0, $261baeb81c4d4d8a$export$2e2bcd8739ae039)
 };
 const $693dd8c7a5607c3a$var$StatusCmp = (props)=>{
     let content = props.grameneFiltersStatus;