feat(geneset): save diff exp result as geneset (#2216)

* update package lock

* allow falsey vals

* remove old diff exp handling

* save diff exp results as geneset

* delete test

* check for undefined or null

* use global geneset description for diffexp

* remove diffexp special code, no longer showing adjpval + logfoldchange

* remove differential map to state

* remove clear from FSM, since we no longer support those actions

* restore controlHelpers test with todo

client/src/reducers/colors.js

@@ -7,9 +7,7 @@ const ColorsReducer = (
     colorMode: null /* by continuous, by expression */,
     colorAccessor: null /* tissue, Apod */,
   },
-  action,
-  nextSharedState,
-  prevSharedState
+  action
 ) => {
   switch (action.type) {
     case "universe: user color load success": {
@@ -20,19 +18,6 @@ const ColorsReducer = (
       };
     }
 
-    case "clear differential expression":
-    case "set clip quantiles":
-    case "subset to selection": {
-      const { controls: prevControls } = prevSharedState;
-      if (prevControls.diffexpGenes.includes(state.colorAccessor)) {
-        return {
-          colorMode: null,
-          colorAccessor: null,
-        };
-      }
-      return state;
-    }
-
     case "annotation: category edited": {
       const { colorAccessor } = state;
       if (action.metadataField !== colorAccessor) {

client/src/reducers/controls.js

@@ -1,6 +1,5 @@
 import uniq from "lodash.uniq";
 import filter from "lodash.filter";
-import { subsetAndResetGeneLists } from "../util/stateManager/controlsHelpers";
 
 const Controls = (
   state = {
@@ -11,7 +10,6 @@ const Controls = (
     // all of the data + selection state
     userDefinedGenes: [],
     userDefinedGenesLoading: false,
-    diffexpGenes: [],
 
     resettingInterface: false,
     graphInteractionMode: "select",
@@ -45,26 +43,16 @@ const Controls = (
       };
     }
     case "reset subset": {
-      const [newUserDefinedGenes, newDiffExpGenes] = subsetAndResetGeneLists(
-        state
-      );
       return {
         ...state,
         resettingInterface: false,
-        userDefinedGenes: newUserDefinedGenes,
-        diffexpGenes: newDiffExpGenes,
       };
     }
     case "subset to selection": {
-      const [newUserDefinedGenes, newDiffExpGenes] = subsetAndResetGeneLists(
-        state
-      );
       return {
         ...state,
         loading: false,
         error: null,
-        userDefinedGenes: newUserDefinedGenes,
-        diffexpGenes: newDiffExpGenes,
       };
     }
     case "request user defined gene started": {
@@ -90,19 +78,6 @@ const Controls = (
         userDefinedGenesLoading: false,
       };
     }
-    case "request differential expression success": {
-      const diffexpGenes = action.data.map((v) => v[0]);
-      return {
-        ...state,
-        diffexpGenes,
-      };
-    }
-    case "clear differential expression": {
-      return {
-        ...state,
-        diffexpGenes: [],
-      };
-    }
     case "clear user defined gene": {
       const { userDefinedGenes } = state;
       const newUserDefinedGenes = filter(

client/src/reducers/differential.js

@@ -1,6 +1,5 @@
 const Differential = (
   state = {
-    diffExp: null,
     loading: null,
     error: null,
     celllist1: null,
@@ -20,7 +19,6 @@ const Differential = (
         ...state,
         error: null,
         loading: false,
-        diffExp: action.data,
       };
     case "request differential expression error":
       return {
@@ -38,18 +36,10 @@ const Differential = (
         ...state,
         celllist2: action.data,
       };
-    case "clear differential expression":
-      return {
-        ...state,
-        diffExp: null,
-        celllist1: null,
-        celllist2: null,
-      };
     case "reset subset":
     case "subset to selection":
       return {
         ...state,
-        diffExp: null,
         celllist1: null,
         celllist2: null,
       };

client/src/reducers/genesets.js

@@ -69,6 +69,7 @@ const GeneSets = (
       }
 
       return {
+        ...state,
         initialized: true,
         lastTid,
         genesets,
@@ -353,6 +354,33 @@ const GeneSets = (
       };
     }
 
+    case "request differential expression success": {
+      const { data } = action;
+
+      const genes = new Map(
+        data.map((diffExpGene) => [
+          diffExpGene[0],
+          {
+            geneSymbol: diffExpGene[0],
+          },
+        ])
+      );
+
+      const genesetName = `DiffExp Set (${new Date().toLocaleString()})`;
+
+      const genesets = new Map(state.genesets); // clone
+      genesets.set(genesetName, {
+        genesetName,
+        genesetDescription: "",
+        genes,
+      });
+
+      return {
+        ...state,
+        genesets,
+      };
+    }
+
     default:
       return state;
   }

client/src/reducers/undoableFsm.js

@@ -185,20 +185,6 @@ const createFsmTransitions = (
       action: applyPending,
     },
 
-    /* Clear Differential Expression button user action */
-    {
-      event: "clear differential expression",
-      from: "init",
-      to: "CDE Button in progress",
-      action: stashPending,
-    },
-    {
-      event: "clear scatterplot",
-      from: "CDE Button in progress",
-      to: "done",
-      action: applyPending,
-    },
-
     /* clear scatter plot button (eg, on scatterplot view) */
     {
       event: "clear scatterplot",