gramene-search 1.2.33 → 1.2.34

package/.parcel-cache/2b1c1cd7b577d2ca.txt

@@ -1,2 +1,2 @@
-85181864
-1653596527148200000
+112144132
+1654530679311291000

package/dist/index.js

@@ -302,12 +302,60 @@ $3ccb7bb553455c26$var$curatedGenes.reactCuratedGenes = $ByO3L$reduxbundler.creat
         actionCreator: 'doFetchCuratedGenes'
     };
 });
+var $3ccb7bb553455c26$var$grameneExpressionStudies = $ByO3L$reduxbundler.createAsyncResourceBundle({
+    name: 'grameneExpressionStudies',
+    actionBaseType: 'GRAMENE_EXPRESSION_STUDIES',
+    persist: true,
+    getPromise: function getPromise(_ref6) {
+        var store = _ref6.store;
+        return fetch("".concat(store.selectGrameneAPI(), "/experiments?rows=-1")).then(function(res) {
+            return res.json();
+        }).then(function(res) {
+            return $3ccb7bb553455c26$var$_lodash["default"].keyBy(res, '_id');
+        });
+    }
+});
+$3ccb7bb553455c26$var$grameneExpressionStudies.reactGrameneExpressionStudies = $ByO3L$reduxbundler.createSelector('selectGrameneExpressionStudiesShouldUpdate', function(shouldUpdate) {
+    if (shouldUpdate) return {
+        actionCreator: 'doFetchGrameneExpressionStudies'
+    };
+});
+var $3ccb7bb553455c26$var$grameneExpressionAssays = $ByO3L$reduxbundler.createAsyncResourceBundle({
+    name: 'grameneExpressionAssays',
+    actionBaseType: 'GRAMENE_EXPRESSION_ASSAYS',
+    persist: true,
+    getPromise: function getPromise(_ref7) {
+        var store = _ref7.store;
+        return fetch("".concat(store.selectGrameneAPI(), "/assays?rows=-1")).then(function(res) {
+            return res.json();
+        }).then(function(res) {
+            var expr = {
+            };
+            res.forEach(function(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(var tid in expr)for(var exp in expr[tid])expr[tid][exp].sort(function(a, b) {
+                return a.order - b.order;
+            });
+            return expr;
+        });
+    }
+});
+$3ccb7bb553455c26$var$grameneExpressionAssays.reactGrameneExpressionAssays = $ByO3L$reduxbundler.createSelector('selectGrameneExpressionAssaysShouldUpdate', function(shouldUpdate) {
+    if (shouldUpdate) return {
+        actionCreator: 'doFetchGrameneExpressionAssays'
+    };
+});
 var $3ccb7bb553455c26$var$grameneSearch = $ByO3L$reduxbundler.createAsyncResourceBundle({
     name: 'grameneSearch',
     actionBaseType: 'GRAMENE_SEARCH',
     persist: false,
-    getPromise: function getPromise(_ref6) {
-        var store = _ref6.store;
+    getPromise: function getPromise(_ref8) {
+        var store = _ref8.store;
         var offset = store.selectGrameneSearchOffset();
         var rows = store.selectGrameneSearchRows();
         var g = store.selectGrameneGenomes();
@@ -365,7 +413,7 @@ var $3ccb7bb553455c26$var$grameneTaxDist = {
         };
         return function() {
             var state = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : initialState;
-            var _ref7 = arguments.length > 1 ? arguments[1] : undefined, type = _ref7.type, payload = _ref7.payload;
+            var _ref9 = arguments.length > 1 ? arguments[1] : undefined, type = _ref9.type, payload = _ref9.payload;
             return state;
         };
     },
@@ -394,7 +442,7 @@ var $3ccb7bb553455c26$var$grameneOrthologs = {
         };
         return function() {
             var state = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : initialState;
-            var _ref8 = arguments.length > 1 ? arguments[1] : undefined, type = _ref8.type, payload = _ref8.payload;
+            var _ref10 = arguments.length > 1 ? arguments[1] : undefined, type = _ref10.type, payload = _ref10.payload;
             var newState;
             switch(type){
                 case 'GRAMENE_ORTHOLOGS_REQUESTED':
@@ -413,8 +461,8 @@ var $3ccb7bb553455c26$var$grameneOrthologs = {
         };
     },
     doRequestOrthologs: function doRequestOrthologs(geneId) {
-        return function(_ref9) {
-            var dispatch = _ref9.dispatch, store = _ref9.store;
+        return function(_ref11) {
+            var dispatch = _ref11.dispatch, store = _ref11.store;
             var orthologs = store.selectGrameneOrthologs();
             if (!orthologs.hasOwnProperty(geneId)) {
                 dispatch({
@@ -503,7 +551,7 @@ var $3ccb7bb553455c26$var$_default = [
     $3ccb7bb553455c26$var$grameneTaxDist,
     $3ccb7bb553455c26$var$grameneOrthologs,
     $3ccb7bb553455c26$var$curatedGenes
-];
+]; //, grameneExpressionStudies, grameneExpressionAssays];
 module.exports["default"] = $3ccb7bb553455c26$var$_default;
 
 });
@@ -1270,6 +1318,8 @@ var $13d6dde2feda3111$var$grameneDocs = {
             domains: {
             },
             pathways: {
+            },
+            expression: {
             }
         };
         return function() {
@@ -1321,6 +1371,21 @@ var $13d6dde2feda3111$var$grameneDocs = {
                     newState.pathways = Object.assign({
                     }, state.pathways, payload);
                     return newState;
+                case 'PARALOG_EXPRESSION_REQUESTED':
+                    if (!state.expression.hasOwnProperty(payload)) {
+                        newState = Object.assign({
+                        }, state);
+                        newState.expression[payload] = [];
+                        return newState;
+                    }
+                    break;
+                case 'PARALOG_EXPRESSION_RECEIVED':
+                    newState = Object.assign({
+                    }, state);
+                    newState.expression = Object.assign({
+                    }, state.expression);
+                    newState.expression[payload.id] = payload.paralogs;
+                    return newState;
             }
             return state;
         };
@@ -1414,6 +1479,58 @@ var $13d6dde2feda3111$var$grameneDocs = {
             }
         };
     },
+    doRequestParalogExpression: function doRequestParalogExpression(id) {
+        return function(_ref5) {
+            var dispatch = _ref5.dispatch, store = _ref5.store;
+            var expr = store.selectParalogExpression();
+            if (!expr.hasOwnProperty(id)) {
+                dispatch({
+                    type: 'PARALOG_EXPRESSION_REQUESTED',
+                    payload: id
+                });
+                fetch("".concat(store.selectGrameneAPI(), "/search?q=homology__within_species_paralog:").concat(id, "&fl=id,name,*__expr&rows=100")).then(function(res) {
+                    return res.json();
+                }).then(function(res) {
+                    var assay_re = /(.+)_tpms_g(\d+)/;
+                    var paralogs = res.response.docs.map(function(d) {
+                        var p = {
+                            id: d.id,
+                            name: d.name,
+                            experiments: {
+                            },
+                            min: 1000,
+                            max: 0
+                        };
+                        delete d.id;
+                        delete d.name;
+                        Object.entries(d).forEach(function(assay) {
+                            var parsed = assay[0].match(assay_re);
+                            var expr1 = parsed[1].replace('_', '-');
+                            if (!p.experiments.hasOwnProperty(expr1)) p.experiments[expr1] = [];
+                            var g = parsed[2] - 1;
+                            var e = d[assay[0]];
+                            if (e < p.min) p.min = e;
+                            if (e > p.max) p.max = e;
+                            p.experiments[expr1][g] = e;
+                        });
+                        return p;
+                    }).map(function(p) {
+                        for(var _expr in p.experiments)p.experiments[_expr] = p.experiments[_expr].filter(function(e) {
+                            return e >= 0;
+                        });
+                        return p;
+                    });
+                    dispatch({
+                        type: 'PARALOG_EXPRESSION_RECEIVED',
+                        payload: {
+                            id: id,
+                            paralogs: paralogs
+                        }
+                    });
+                });
+            }
+        };
+    },
     selectGrameneGenes: function selectGrameneGenes(state) {
         return state.grameneDocs.genes;
     },
@@ -1422,6 +1539,9 @@ var $13d6dde2feda3111$var$grameneDocs = {
     },
     selectGramenePathways: function selectGramenePathways(state) {
         return state.grameneDocs.pathways;
+    },
+    selectParalogExpression: function selectParalogExpression(state) {
+        return state.grameneDocs.expression;
     }
 };
 var $13d6dde2feda3111$var$_default = $13d6dde2feda3111$var$grameneDocs;
@@ -2197,24 +2317,41 @@ module.exports["default"] = void 0;
 
 var $9552550dff566159$var$_react = $9552550dff566159$var$_interopRequireDefault($ByO3L$react);
 
+
 function $9552550dff566159$var$_interopRequireDefault(obj) {
     return obj && obj.__esModule ? obj : {
         "default": obj
     };
 }
-var $9552550dff566159$var$PREFIX = $parcel$global.location ? $parcel$global.location.origin + $parcel$global.location.pathname + '/' : '';
 var $9552550dff566159$var$Detail = function Detail(props) {
     var gene = props.geneDocs[props.searchResult.id];
-    var url = "/static/atlasWidget.html?".concat(gene.taxon_id === 112509 ? gene.synonyms[0] : gene._id);
-    var height = '500px';
-    return(/*#__PURE__*/ $9552550dff566159$var$_react["default"].createElement("iframe", {
-        src: url,
+    var paralogs_url;
+    var gene_url = "/static/atlasWidget.html?reference=0&genes=".concat(gene._id);
+    if (props.paralogExpression && props.paralogExpression[gene._id]) {
+        var paralogs = props.paralogExpression[gene._id].map(function(p) {
+            return p.id;
+        });
+        paralogs_url = "/static/atlasWidget.html?reference=1&genes=".concat(paralogs.join(' '));
+    } else props.doRequestParalogExpression(gene._id);
+    return(/*#__PURE__*/ $9552550dff566159$var$_react["default"].createElement($ByO3L$reactbootstrap.Tabs, null, /*#__PURE__*/ $9552550dff566159$var$_react["default"].createElement($ByO3L$reactbootstrap.Tab, {
+        eventKey: "gene",
+        title: "All Studies"
+    }, /*#__PURE__*/ $9552550dff566159$var$_react["default"].createElement("iframe", {
+        src: gene_url,
+        frameBorder: "0",
+        width: "100%",
+        height: "500px"
+    })), /*#__PURE__*/ $9552550dff566159$var$_react["default"].createElement($ByO3L$reactbootstrap.Tab, {
+        eventKey: "paralogs",
+        title: "Reference Study (all paralogs)"
+    }, paralogs_url && /*#__PURE__*/ $9552550dff566159$var$_react["default"].createElement("iframe", {
+        src: paralogs_url,
         frameBorder: "0",
         width: "100%",
-        height: height
-    }, /*#__PURE__*/ $9552550dff566159$var$_react["default"].createElement("p", null, "browser doesn't support iframes")));
+        height: "500px"
+    }))));
 };
-var $9552550dff566159$var$_default = $ByO3L$reduxbundlerreact.connect($9552550dff566159$var$Detail);
+var $9552550dff566159$var$_default = $ByO3L$reduxbundlerreact.connect('selectParalogExpression', 'doRequestParalogExpression', $9552550dff566159$var$Detail);
 module.exports["default"] = $9552550dff566159$var$_default;
 
 });