gramene-search 1.2.92 → 1.2.94

package/dist/index.js

@@ -9,6 +9,7 @@ var $gXNCa$reactjsxruntime = require("react/jsx-runtime");
 var $gXNCa$reduxbundlerreact = require("redux-bundler-react");
 var $gXNCa$react = require("react");
 var $gXNCa$reactbootstrap = require("react-bootstrap");
+var $gXNCa$reactswitch = require("react-switch");
 var $gXNCa$reacticonsio5 = require("react-icons/io5");
 var $gXNCa$reacticonsbs = require("react-icons/bs");
 var $gXNCa$reacticonsgr = require("react-icons/gr");
@@ -31,6 +32,49 @@ function $parcel$export(e, n, v, s) {
 function $parcel$interopDefault(a) {
   return a && a.__esModule ? a.default : a;
 }
+var $parcel$global =
+typeof globalThis !== 'undefined'
+  ? globalThis
+  : typeof self !== 'undefined'
+  ? self
+  : typeof window !== 'undefined'
+  ? window
+  : typeof global !== 'undefined'
+  ? global
+  : {};
+var $parcel$modules = {};
+var $parcel$inits = {};
+
+var parcelRequire = $parcel$global["parcelRequire7a41"];
+if (parcelRequire == null) {
+  parcelRequire = function(id) {
+    if (id in $parcel$modules) {
+      return $parcel$modules[id].exports;
+    }
+    if (id in $parcel$inits) {
+      var init = $parcel$inits[id];
+      delete $parcel$inits[id];
+      var module = {id: id, exports: {}};
+      $parcel$modules[id] = module;
+      init.call(module.exports, module, module.exports);
+      return module.exports;
+    }
+    var err = new Error("Cannot find module '" + id + "'");
+    err.code = 'MODULE_NOT_FOUND';
+    throw err;
+  };
+
+  parcelRequire.register = function register(id, init) {
+    $parcel$inits[id] = init;
+  };
+
+  $parcel$global["parcelRequire7a41"] = parcelRequire;
+}
+parcelRequire.register("7u0Mi", function(module, exports) {
+module.exports = Promise.resolve(require("./Study.5f95cb67.js")).then(()=>parcelRequire("7zuJ6"));
+
+});
+
 
 $parcel$export(module.exports, "bundles", () => $5df6c55c1bef3469$export$2e2bcd8739ae039);
 $parcel$export(module.exports, "resultList", () => $2fec4872fbf7ebd2$export$2e2bcd8739ae039);
@@ -150,6 +194,40 @@ $9d9aeaf9299e61a1$var$grameneMaps.reactGrameneMaps = (0, $gXNCa$reduxbundler.cre
         actionCreator: "doFetchGrameneMaps"
     };
 });
+const $9d9aeaf9299e61a1$var$expressionStudies = (0, $gXNCa$reduxbundler.createAsyncResourceBundle)({
+    name: "expressionStudies",
+    actionBaseType: "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))).groupBy(res, "taxon_id"));
+    }
+});
+$9d9aeaf9299e61a1$var$expressionStudies.reactExpressionStudies = (0, $gXNCa$reduxbundler.createSelector)("selectExpressionStudiesShouldUpdate", (shouldUpdate)=>{
+    if (shouldUpdate) return {
+        actionCreator: "doFetchExpressionStudies"
+    };
+});
+const $9d9aeaf9299e61a1$var$expressionSamples = (0, $gXNCa$reduxbundler.createAsyncResourceBundle)({
+    name: "expressionSamples",
+    actionBaseType: "EXPRESSION_SAMPLES",
+    persist: true,
+    getPromise: ({ store: store  })=>{
+        return fetch(`${store.selectGrameneAPI()}/assays?rows=-1`).then((res)=>res.json()).then((samples)=>(0, ($parcel$interopDefault($gXNCa$lodash))).groupBy(samples, "experiment")).then((studies)=>{
+            Object.keys(studies).forEach((study)=>{
+                studies[study].forEach((sample)=>{
+                    sample.order = +sample.group.replace("g", "");
+                });
+                studies[study].sort((a, b)=>a.order - b.order);
+            });
+            return studies;
+        });
+    }
+});
+$9d9aeaf9299e61a1$var$expressionSamples.reactExpressionSamples = (0, $gXNCa$reduxbundler.createSelector)("selectExpressionSamplesShouldUpdate", (shouldUpdate)=>{
+    if (shouldUpdate) return {
+        actionCreator: "doFetchExpressionSamples"
+    };
+});
 const $9d9aeaf9299e61a1$var$curatedGenes = (0, $gXNCa$reduxbundler.createAsyncResourceBundle)({
     name: "curatedGenes",
     actionBaseType: "CURATED_GENES",
@@ -163,24 +241,6 @@ $9d9aeaf9299e61a1$var$curatedGenes.reactCuratedGenes = (0, $gXNCa$reduxbundler.c
         actionCreator: "doFetchCuratedGenes"
     };
 });
-// 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',
@@ -532,8 +592,7 @@ var // function selectFacetIDs(store, field) {
 //       .then(res => res.json())
 //       .then(docs => {return {taxonomy: docs, numFound: docs.length}})
 // });
-$9d9aeaf9299e61a1$export$2e2bcd8739ae039 //, grameneExpressionStudies, grameneExpressionAssays];
- = [
+$9d9aeaf9299e61a1$export$2e2bcd8739ae039 = [
     $9d9aeaf9299e61a1$var$grameneSuggestions,
     $9d9aeaf9299e61a1$var$grameneSearch,
     $9d9aeaf9299e61a1$var$grameneMaps,
@@ -541,7 +600,9 @@ $9d9aeaf9299e61a1$export$2e2bcd8739ae039 //, grameneExpressionStudies, grameneEx
     $9d9aeaf9299e61a1$var$grameneTaxDist,
     $9d9aeaf9299e61a1$var$grameneOrthologs,
     $9d9aeaf9299e61a1$var$curatedGenes,
-    $9d9aeaf9299e61a1$var$grameneGeneAttribs
+    $9d9aeaf9299e61a1$var$grameneGeneAttribs,
+    $9d9aeaf9299e61a1$var$expressionSamples,
+    $9d9aeaf9299e61a1$var$expressionStudies
 ];
 
 
@@ -1175,27 +1236,32 @@ const $24971af0a229e0e3$var$grameneViews = {
                 {
                     id: "help",
                     name: "Help / Demo",
-                    show: "off"
+                    show: "disabled",
+                    shouldScroll: false
                 },
                 {
                     id: "taxonomy",
                     name: "Taxonomic distribution",
-                    show: "on"
+                    show: "on",
+                    shouldScroll: false
                 },
                 {
                     id: "list",
                     name: "Gene list",
-                    show: "on"
-                },
-                {
-                    id: "attribs",
-                    name: "Gene attributes",
-                    show: "off"
+                    show: "on",
+                    shouldScroll: false
                 },
                 {
                     id: "expression",
                     name: "Gene expression",
-                    show: "off"
+                    show: "off",
+                    shouldScroll: false
+                },
+                {
+                    id: "attribs",
+                    name: "Gene attributes",
+                    show: "disabled",
+                    shouldScroll: false
                 }
             ]
         };
@@ -1204,7 +1270,23 @@ const $24971af0a229e0e3$var$grameneViews = {
             switch(type){
                 case "GRAMENE_VIEW_TOGGLED":
                     newState = Object.assign({}, state);
-                    newState.options[payload].show = newState.options[payload].show === "on" ? "off" : "on";
+                    newState.options.forEach((view)=>{
+                        view.shouldScroll = false;
+                        if (view.id === payload) {
+                            view.show = view.show === "on" ? "off" : "on";
+                            view.shouldScroll = view.show === "on";
+                        }
+                    });
+                    return newState;
+                case "GRAMENE_VIEW_CLICKED":
+                    newState = Object.assign({}, state);
+                    newState.options.forEach((view)=>{
+                        view.shouldScroll = false;
+                        if (view.id === payload) {
+                            view.show = view.show === "on" ? "on" : "on";
+                            view.shouldScroll = view.show === "on";
+                        }
+                    });
                     return newState;
                 default:
                     return state;
@@ -1217,6 +1299,12 @@ const $24971af0a229e0e3$var$grameneViews = {
                 payload: idx
             });
         },
+    dontToggleGrameneView: (idx)=>({ dispatch: dispatch , getState: getState  })=>{
+            dispatch({
+                type: "GRAMENE_VIEW_CLICKED",
+                payload: idx
+            });
+        },
     selectGrameneViews: (state)=>state.grameneViews
 };
 var $24971af0a229e0e3$export$2e2bcd8739ae039 = $24971af0a229e0e3$var$grameneViews;
@@ -2015,6 +2103,7 @@ var $541b8b0d8c5501d2$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.conn
 
 
 
+
 const $9e29a4f60318db7a$var$Detail = (props)=>{
     const gene = props.geneDocs[props.searchResult.id];
     let paralogs_url;
@@ -4706,83 +4795,71 @@ 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$LazyStudy = /*#__PURE__*/ (0, ($parcel$interopDefault($gXNCa$react))).lazy(()=>(parcelRequire("7u0Mi")));
+const $261baeb81c4d4d8a$var$StudyList = (props)=>{
+    return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion), {
+        alwaysOpen: true,
+        defaultActiveKey: props.studies.length === 1 ? "study_0" : undefined,
+        children: props.studies.map((study, idx)=>{
+            return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Accordion).Item, {
+                eventKey: "study_" + idx,
+                children: [
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion).Header, {
+                        children: study.description
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion).Body, {
+                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$react.Suspense), {
+                            fallback: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                                children: "Loading..."
+                            }),
+                            children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($261baeb81c4d4d8a$var$LazyStudy, {
+                                id: study._id
+                            })
+                        })
+                    })
+                ]
+            }, idx);
+        })
     });
 };
-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", {
+    const availableTaxa = Object.keys(props.expressionStudies).filter((tid)=>searchTaxa[tid] || searchTaxa[tid + "001"]).sort((a, b)=>props.grameneMaps[a + "001"].left_index - props.grameneMaps[b + "001"].left_index);
+    return availableTaxa && props.grameneTaxonomy && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion), {
+        alwaysOpen: true,
+        defaultActiveKey: availableTaxa.length === 1 ? "tax_0" : undefined,
+        children: availableTaxa.map((tid, idx)=>{
+            const n = props.expressionStudies[tid].length;
+            return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Accordion).Item, {
+                eventKey: "tax_" + idx,
                 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),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)((0, $gXNCa$reactbootstrap.Accordion).Header, {
                         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))
+                            props.grameneTaxonomy[tid].name,
+                            " - ",
+                            n,
+                            " ",
+                            n === 1 ? "study" : "studies"
                         ]
+                    }),
+                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, $gXNCa$reactbootstrap.Accordion).Body, {
+                        children: /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($261baeb81c4d4d8a$var$StudyList, {
+                            studies: props.expressionStudies[tid]
+                        })
                     })
                 ]
-            }),
-            study !== 0 && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)($261baeb81c4d4d8a$var$Study, {
-                sid: study
-            })
-        ]
+            }, idx);
+        })
     });
 };
-var $261baeb81c4d4d8a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)("selectConfiguration", "selectGrameneSearch", "selectGrameneTaxonomy", "selectAtlasStudies", "doRequestExpressionStudies", "doRequestStudyMetadata", $261baeb81c4d4d8a$var$Expression);
+var $261baeb81c4d4d8a$export$2e2bcd8739ae039 = (0, $gXNCa$reduxbundlerreact.connect)("selectConfiguration", "selectGrameneSearch", "selectGrameneTaxonomy", "selectGrameneMaps", "selectExpressionStudies", $261baeb81c4d4d8a$var$Expression);
 
 
 
@@ -4856,7 +4933,6 @@ const $693dd8c7a5607c3a$var$StatusCmp = (props)=>{
     return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
         style: {
             padding: "5px",
-            backgroundColor: "dimgray",
             color: "cornsilk",
             fontSize: "small"
         },
@@ -5055,20 +5131,39 @@ const $693dd8c7a5607c3a$var$FiltersCmp = (props)=>{
 };
 const $693dd8c7a5607c3a$export$92a576f896a9bf72 = (0, $gXNCa$reduxbundlerreact.connect)("selectGrameneFilters", "doNegateGrameneFilter", "doDeleteGrameneFilter", "doChangeGrameneFilterOperation", "doMoveOrCopyGrameneFilter", "doMarkGrameneFilterTargets", "doUnmarkGrameneFilterTargets", "doToggleGrameneFilterMenu", "doClearGrameneFilters", $693dd8c7a5607c3a$var$FiltersCmp);
 const $693dd8c7a5607c3a$var$ResultsCmp = (props)=>{
-    let activeViews = props.grameneViews.options.filter((v, idx)=>{
-        v.idx = idx;
-        return v.show === "on";
-    });
+    let activeViews = props.grameneViews.options;
     return props.grameneFilters.rightIdx > 0 ? /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
         style: {
             padding: "10px"
         },
-        children: activeViews.map((v)=>{
+        children: activeViews.map((v, idx)=>{
             let p = Object.assign({}, props);
-            p.key = v.idx;
-            return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
-                children: /*#__PURE__*/ (0, ($parcel$interopDefault($gXNCa$react))).createElement($693dd8c7a5607c3a$var$inventory[v.id], p)
-            }, v.idx);
+            const divRef = (0, $gXNCa$react.useRef)(null);
+            (0, $gXNCa$react.useEffect)(()=>{
+                if (v.shouldScroll) {
+                    const navBarHeight = 106;
+                    const scrollPosition = divRef.current.offsetTop - navBarHeight;
+                    window.scrollTo({
+                        top: scrollPosition,
+                        behavior: "smooth"
+                    });
+                }
+            }, [
+                v.shouldScroll
+            ]);
+            return /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                ref: divRef,
+                children: [
+                    v.show === "on" && /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("div", {
+                        style: {
+                            borderTopWidth: "medium"
+                        },
+                        className: "gramene-view-header",
+                        children: v.name
+                    }),
+                    v.show === "on" && /*#__PURE__*/ (0, ($parcel$interopDefault($gXNCa$react))).createElement($693dd8c7a5607c3a$var$inventory[v.id], p)
+                ]
+            }, idx);
         })
     }) : null;
 };
@@ -5079,41 +5174,32 @@ const $693dd8c7a5607c3a$var$ViewsCmp = (props)=>/*#__PURE__*/ (0, $gXNCa$reactjs
             /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("b", {
                 children: "Views"
             }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("ul", {
-                className: "gramene-view",
-                children: props.grameneViews.options.map((view, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("li", {
-                        className: `gramene-view-${view.show}`,
-                        onClick: (e)=>{
-                            if (view.show !== "disabled") props.doToggleGrameneView(idx);
-                        },
-                        children: view.name
-                    }, idx))
-            }),
-            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
-                children: [
-                    "\xa0Key:",
-                    /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("ul", {
-                        className: "gramene-view",
-                        children: [
-                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("li", {
-                                className: "gramene-view-on",
-                                children: "On"
-                            }),
-                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("li", {
-                                className: "gramene-view-off",
-                                children: "Off"
-                            }),
-                            /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("li", {
-                                className: "gramene-view-disabled",
-                                children: "Disabled"
-                            })
-                        ]
-                    })
-                ]
-            })
+            props.grameneViews.options.filter((view)=>view.show !== "disabled").map((view, idx)=>/*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsxs)("div", {
+                    style: {
+                        textWrap: "nowrap"
+                    },
+                    children: [
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)((0, ($parcel$interopDefault($gXNCa$reactswitch))), {
+                            onChange: ()=>props.doToggleGrameneView(view.id),
+                            checked: view.show === "on",
+                            height: 18,
+                            width: 30,
+                            handleDiameter: 16,
+                            checkedIcon: false,
+                            uncheckedIcon: false
+                        }),
+                        /*#__PURE__*/ (0, $gXNCa$reactjsxruntime.jsx)("span", {
+                            className: `gramene-view-span-${view.show}`,
+                            onClick: (e)=>{
+                                props.dontToggleGrameneView(view.id);
+                            },
+                            children: view.name
+                        })
+                    ]
+                }, idx))
         ]
     });
-const $693dd8c7a5607c3a$export$5cb791131c501f6a = (0, $gXNCa$reduxbundlerreact.connect)("selectGrameneViews", "doToggleGrameneView", $693dd8c7a5607c3a$var$ViewsCmp);
+const $693dd8c7a5607c3a$export$5cb791131c501f6a = (0, $gXNCa$reduxbundlerreact.connect)("selectGrameneViews", "doToggleGrameneView", "dontToggleGrameneView", $693dd8c7a5607c3a$var$ViewsCmp);