From 876ceb4d8b9449947c9a7608a1616de4d9ca1818 Mon Sep 17 00:00:00 2001
From: Colin Megill <colinmegill@gmail.com>
Date: Wed, 21 Apr 2021 16:50:29 -0700
Subject: [PATCH] Create / edit geneset description (#2139)

* geneset description add

* edit geneset description

* default state for desc

* remove log

* naming, todo

* check for both dup name and desc

* fixes

* do not store gene set modal state in history stack

* Update createGenesetDialogue.js

* Update editGenesetNameDialogue.js

Co-authored-by: bkmartinjr <bruce@chanzuckerberg.com>
---
 client/__tests__/reducers/genesets.test.js    |   2 +-
 client/src/components/annoDialog.js           |   2 +
 .../src/components/geneExpression/geneSet.js  |  20 ++-
 client/src/components/geneExpression/index.js |   1 +
 .../menus/createGenesetDialogue.js            | 148 ++++++++++++------
 .../menus/editGenesetNameDialogue.js          |  48 ++++--
 .../geneExpression/menus/genesetMenus.js      |   2 +-
 client/src/reducers/genesets.js               |  15 +-
 client/src/reducers/index.js                  |   1 -
 9 files changed, 170 insertions(+), 69 deletions(-)

diff --git a/client/__tests__/reducers/genesets.test.js b/client/__tests__/reducers/genesets.test.js
index 7df76c6c..ad377f6c 100644
--- a/client/__tests__/reducers/genesets.test.js
+++ b/client/__tests__/reducers/genesets.test.js
@@ -276,7 +276,7 @@ describe("geneset: update", () => {
           },
         }
       );
-    }).toThrow("update specified existing name");
+    }).toThrow("update specified existing name and description");
   });
 });
 
diff --git a/client/src/components/annoDialog.js b/client/src/components/annoDialog.js
index e3842611..8064b146 100644
--- a/client/src/components/annoDialog.js
+++ b/client/src/components/annoDialog.js
@@ -48,6 +48,7 @@ class AnnoDialog extends React.PureComponent {
               >
                 {errorMessage}
               </p>
+              {/* we might rename, secondary button and secondary input are not related */}
               {secondaryInstructions && (
                 <p style={{ marginTop: secondaryInstructions ? 20 : 0 }}>
                   {secondaryInstructions}
@@ -62,6 +63,7 @@ class AnnoDialog extends React.PureComponent {
               <Tooltip content={cancelTooltipContent}>
                 <Button onClick={handleCancel}>Cancel</Button>
               </Tooltip>
+              {/* we might rename, secondary button and secondary input are not related */}
               {handleSecondaryButtonSubmit && secondaryButtonText ? (
                 <Button
                   onClick={handleSecondaryButtonSubmit}
diff --git a/client/src/components/geneExpression/geneSet.js b/client/src/components/geneExpression/geneSet.js
index aeb359ca..39ab5ef8 100644
--- a/client/src/components/geneExpression/geneSet.js
+++ b/client/src/components/geneExpression/geneSet.js
@@ -1,6 +1,7 @@
 import React from "react";
 import { connect } from "react-redux";
-import { Tooltip, Position, Switch } from "@blueprintjs/core";
+import { Position, Switch } from "@blueprintjs/core";
+import { Tooltip2 } from "@blueprintjs/popover2";
 import { FaChevronRight, FaChevronDown } from "react-icons/fa";
 import actions from "../../actions";
 import Gene from "./gene";
@@ -128,7 +129,7 @@ class GeneSet extends React.Component {
   }
 
   render() {
-    const { setName, setGenes } = this.props;
+    const { setName, setGenes, genesetDescription } = this.props;
     const { isOpen, toggleSummaryHisto } = this.state;
     const genesetNameLengthVisible = 120; /* this magic number determines how much of a long geneset name we see */
     const genesetIsEmpty = setGenes.length === 0;
@@ -156,7 +157,11 @@ class GeneSet extends React.Component {
             }}
             onClick={this.onGenesetMenuClick}
           >
-            <Truncate>
+            <Truncate
+              tooltipAddendum={
+                genesetDescription ? `: ${genesetDescription}` : ""
+              }
+            >
               <span
                 style={{
                   maxWidth: globals.leftSidebarWidth - genesetNameLengthVisible,
@@ -185,7 +190,7 @@ class GeneSet extends React.Component {
 
         <div style={{ marginLeft: 15, marginTop: 5, marginRight: 0 }}>
           {isOpen && !genesetIsEmpty && (
-            <Tooltip
+            <Tooltip2
               content="Aggregate all genes in this geneset, and allow coloring by and selecting on the entire set."
               position={Position.BOTTOM_RIGHT}
               usePortal
@@ -204,7 +209,7 @@ class GeneSet extends React.Component {
                 innerLabelChecked="on"
                 onChange={this.toggleSummaryHisto}
               />
-            </Tooltip>
+            </Tooltip2>
           )}
 
           {isOpen && genesetIsEmpty && (
@@ -223,7 +228,10 @@ class GeneSet extends React.Component {
                   setGenes={setGenes}
                 />
               ))}
-        <EditGenesetNameDialogue parentGeneset={setName} />
+        <EditGenesetNameDialogue
+          parentGeneset={setName}
+          parentGenesetDescription={genesetDescription}
+        />
       </div>
     );
   }
diff --git a/client/src/components/geneExpression/index.js b/client/src/components/geneExpression/index.js
index 59d7f400..666d32ad 100644
--- a/client/src/components/geneExpression/index.js
+++ b/client/src/components/geneExpression/index.js
@@ -23,6 +23,7 @@ class GeneExpression extends React.Component {
           setGenes={Array.from(geneset.genes.keys())}
           setGenesWithDescriptions={geneset.genes}
           setName={name}
+          genesetDescription={geneset.genesetDescription}
         />
       );
     }
diff --git a/client/src/components/geneExpression/menus/createGenesetDialogue.js b/client/src/components/geneExpression/menus/createGenesetDialogue.js
index beda0fba..5d7b6fca 100644
--- a/client/src/components/geneExpression/menus/createGenesetDialogue.js
+++ b/client/src/components/geneExpression/menus/createGenesetDialogue.js
@@ -2,7 +2,8 @@ import pull from "lodash.pull";
 import uniq from "lodash.uniq";
 import React from "react";
 import { connect } from "react-redux";
-import AnnoDialog from "../../annoDialog";
+import { Button, Dialog, Classes, Colors } from "@blueprintjs/core";
+import { Tooltip2 } from "@blueprintjs/popover2";
 import LabelInput from "../../labelInput";
 import actions from "../../../actions";
 
@@ -20,6 +21,7 @@ class CreateGenesetDialogue extends React.PureComponent {
     this.state = {
       genesetName: "",
       genesToPopulateGeneset: "",
+      genesetDescription: "",
     };
   }
 
@@ -28,6 +30,7 @@ class CreateGenesetDialogue extends React.PureComponent {
     this.setState({
       genesetName: "",
       genesToPopulateGeneset: "",
+      genesetDescription: "",
     });
     dispatch({
       type: "geneset: disable create geneset mode",
@@ -37,12 +40,16 @@ class CreateGenesetDialogue extends React.PureComponent {
 
   createGeneset = (e) => {
     const { dispatch } = this.props;
-    const { genesetName, genesToPopulateGeneset } = this.state;
+    const {
+      genesetName,
+      genesToPopulateGeneset,
+      genesetDescription,
+    } = this.state;
 
     dispatch({
       type: "geneset: create",
       genesetName,
-      genesetDescription: "",
+      genesetDescription,
     });
     if (genesToPopulateGeneset) {
       const genesTmpHardcodedFormat = [];
@@ -82,10 +89,14 @@ class CreateGenesetDialogue extends React.PureComponent {
     this.setState({ genesToPopulateGeneset: e });
   };
 
+  handleDescriptionInputChange = (e) => {
+    this.setState({ genesetDescription: e });
+  };
+
   instruction = (genesetName, genesets) => {
     return genesets.has(genesetName)
-      ? "Geneset name must be unique."
-      : "New, unique geneset name";
+      ? "Gene set name must be unique."
+      : "New, unique gene set name";
   };
 
   validate = (genesetName, genesets) => {
@@ -98,47 +109,94 @@ class CreateGenesetDialogue extends React.PureComponent {
 
     return (
       <>
-        <AnnoDialog
-          isActive={genesetsUI.createGenesetModeActive}
-          inputProps={{
-            "data-testid": `${metadataField}:create-geneset-dialog`,
-          }}
-          primaryButtonProps={{
-            "data-testid": `${metadataField}:submit-geneset`,
-          }}
+        <Dialog
+          icon="tag"
           title="Create gene set"
-          instruction={this.instruction(genesetName, genesets)}
-          cancelTooltipContent="Close this dialog without creating a new gene set."
-          primaryButtonText="Create gene set"
-          text={genesetName}
-          validationError={this.validate(genesetName, genesets)}
-          annoInput={
-            <LabelInput
-              onChange={this.handleChange}
-              inputProps={{
-                "data-testid": "create-geneset-modal",
-                leftIcon: "manually-entered-data",
-                intent: "none",
-                autoFocus: true,
-              }}
-              newLabelMessage="Create gene set"
-            />
-          }
-          secondaryInstructions="Optionally add a list of comma separated genes to populate the gene set"
-          secondaryInput={
-            <LabelInput
-              onChange={this.handleGenesetInputChange}
-              inputProps={{
-                "data-testid": "add-genes",
-                intent: "none",
-                autoFocus: false,
-              }}
-              newLabelMessage="populate geneset with genes"
-            />
-          }
-          handleSubmit={this.createGeneset}
-          handleCancel={this.disableCreateGenesetMode}
-        />
+          isOpen={genesetsUI.createGenesetModeActive}
+          onClose={this.disableCreateGenesetMode}
+        >
+          <form
+            onSubmit={(e) => {
+              e.preventDefault();
+            }}
+          >
+            <div className={Classes.DIALOG_BODY}>
+              <div style={{ marginBottom: 20 }}>
+                <p>{this.instruction(genesetName, genesets)}</p>
+                <LabelInput
+                  onChange={this.handleChange}
+                  inputProps={{
+                    "data-testid": "create-geneset-modal",
+                    leftIcon: "manually-entered-data",
+                    intent: "none",
+                    autoFocus: true,
+                  }}
+                  newLabelMessage="Create gene set"
+                />
+                <p
+                  style={{
+                    marginTop: 7,
+                    visibility: this.validate(genesetName, genesets)
+                      ? "visible"
+                      : "hidden",
+                    color: Colors.ORANGE3,
+                  }}
+                >
+                  {this.genesetNameError()}
+                </p>
+                <p style={{ marginTop: 20 }}>
+                  Optionally add a{" "}
+                  <span style={{ fontWeight: 700 }}>description</span> for this
+                  gene set
+                </p>
+                <LabelInput
+                  onChange={this.handleDescriptionInputChange}
+                  inputProps={{
+                    "data-testid": "add-geneset-description",
+                    intent: "none",
+                    autoFocus: false,
+                  }}
+                  newLabelMessage="Add geneset description"
+                />
+
+                <p style={{ marginTop: 20 }}>
+                  Optionally add a list of comma separated{" "}
+                  <span style={{ fontWeight: 700 }}>genes</span> to populate the
+                  gene set
+                </p>
+                <LabelInput
+                  onChange={this.handleGenesetInputChange}
+                  inputProps={{
+                    "data-testid": "add-genes",
+                    intent: "none",
+                    autoFocus: false,
+                  }}
+                  newLabelMessage="populate geneset with genes"
+                />
+              </div>
+            </div>
+            <div className={Classes.DIALOG_FOOTER}>
+              <div className={Classes.DIALOG_FOOTER_ACTIONS}>
+                <Tooltip2 content="Close this dialog without creating a new gene set.">
+                  <Button onClick={this.disableCreateGenesetMode}>
+                    Cancel
+                  </Button>
+                </Tooltip2>
+                <Button
+                  data-testid={`${metadataField}:submit-geneset`}
+                  onClick={this.createGeneset}
+                  disabled={
+                    !genesetName || this.validate(genesetName, genesets)
+                  }
+                  intent="primary"
+                  type="submit"
+                >
+                  Create gene set
+                </Button>
+              </div>
+            </div>
+          </form>
+        </Dialog>
       </>
     );
   }
diff --git a/client/src/components/geneExpression/menus/editGenesetNameDialogue.js b/client/src/components/geneExpression/menus/editGenesetNameDialogue.js
index c4dc321d..276492d4 100644
--- a/client/src/components/geneExpression/menus/editGenesetNameDialogue.js
+++ b/client/src/components/geneExpression/menus/editGenesetNameDialogue.js
@@ -14,14 +14,16 @@ class RenameGeneset extends React.PureComponent {
   constructor(props) {
     super(props);
     this.state = {
-      genesetName: props.parentGeneset,
+      newGenesetName: props.parentGeneset,
+      newGenesetDescription: props.parentGenesetDescription,
     };
   }
 
   disableEditGenesetNameMode = (e) => {
     const { dispatch } = this.props;
     this.setState({
-      genesetName: "",
+      newGenesetName: "",
+      newGenesetDescription: "",
     });
     dispatch({
       type: "geneset: disable rename geneset mode",
@@ -31,12 +33,15 @@ class RenameGeneset extends React.PureComponent {
 
   renameGeneset = (e) => {
     const { dispatch, genesetsUI } = this.props;
-    const { genesetName } = this.state;
+    const { newGenesetName, newGenesetDescription } = this.state;
 
     dispatch({
       type: "geneset: update",
       genesetName: genesetsUI.isEditingGenesetName,
-      update: { genesetName },
+      update: {
+        genesetName: newGenesetName,
+        genesetDescription: newGenesetDescription,
+      },
     });
     dispatch({
       type: "geneset: disable rename geneset mode",
@@ -49,12 +54,16 @@ class RenameGeneset extends React.PureComponent {
   };
 
   handleChange = (e) => {
-    this.setState({ genesetName: e });
+    this.setState({ newGenesetName: e });
+  };
+
+  handleChangeDescription = (e) => {
+    this.setState({ newGenesetDescription: e });
   };
 
   render() {
-    const { genesetName } = this.state;
-    const { genesetsUI, parentGeneset } = this.props;
+    const { newGenesetName, newGenesetDescription } = this.state;
+    const { genesetsUI, parentGeneset, parentGenesetDescription } = this.props;
 
     return (
       <>
@@ -66,15 +75,19 @@ class RenameGeneset extends React.PureComponent {
           primaryButtonProps={{
             "data-testid": `${genesetsUI.isEditingGenesetName}:submit-geneset`,
           }}
-          title="Rename gene set"
+          title="Edit gene set name and description"
           instruction={`Rename ${genesetsUI.isEditingGenesetName}`}
           cancelTooltipContent="Close this dialog without renaming the gene set."
-          primaryButtonText="Rename gene set"
-          text={genesetName}
-          validationError={genesetsUI.isEditingGenesetName === genesetName}
+          primaryButtonText="Edit gene set name and description"
+          text={newGenesetName}
+          secondaryText={newGenesetDescription}
+          validationError={
+            genesetsUI.isEditingGenesetName === newGenesetName &&
+            parentGenesetDescription === newGenesetDescription
+          }
           annoInput={
             <LabelInput
-              label={genesetName}
+              label={newGenesetName}
               onChange={this.handleChange}
               inputProps={{
                 "data-testid": "rename-geneset-modal",
@@ -82,7 +95,16 @@ class RenameGeneset extends React.PureComponent {
                 intent: "none",
                 autoFocus: true,
               }}
-              newLabelMessage="Rename gene set"
+            />
+          }
+          secondaryInstructions="Edit description"
+          secondaryInput={
+            <LabelInput
+              label={newGenesetDescription}
+              onChange={this.handleChangeDescription}
+              inputProps={{ "data-testid": "change geneset description" }}
+              intent="none"
+              autoFocus={false}
             />
           }
           handleSubmit={this.renameGeneset}
diff --git a/client/src/components/geneExpression/menus/genesetMenus.js b/client/src/components/geneExpression/menus/genesetMenus.js
index 7f48948d..129098d6 100644
--- a/client/src/components/geneExpression/menus/genesetMenus.js
+++ b/client/src/components/geneExpression/menus/genesetMenus.js
@@ -82,7 +82,7 @@ class GenesetMenus extends React.PureComponent {
                     data-testclass="activateEditGenesetNameMode"
                     data-testid={`${geneset}:edit-genesetName-mode`}
                     onClick={this.activateEditGenesetNameMode}
-                    text="Edit gene set name"
+                    text="Edit gene set name and description"
                   />
                   <MenuItem
                     icon="trash"
diff --git a/client/src/reducers/genesets.js b/client/src/reducers/genesets.js
index 0944e84d..a0d66599 100644
--- a/client/src/reducers/genesets.js
+++ b/client/src/reducers/genesets.js
@@ -149,6 +149,7 @@ const GeneSets = (
      */
     case "geneset: update": {
       const { genesetName, update } = action;
+
       if (
         typeof genesetName !== "string" ||
         !genesetName ||
@@ -157,8 +158,18 @@ const GeneSets = (
         throw new Error(
           "geneset: update -- geneset name unspecified or does not exist."
         );
-      if (state.genesets.has(update.genesetName))
-        throw new Error("geneset: update -- update specified existing name.");
+
+      /* now that we've confirmed the gene set exists, check for duplicates */
+      const genesetNameIsDuplicate = state.genesets.has(update.genesetName);
+      const descriptionIsDuplicate =
+        state.genesets.get(update.genesetName) &&
+        state.genesets.get(update.genesetName).genesetDescription ===
+          update.genesetDescription;
+
+      if (genesetNameIsDuplicate && descriptionIsDuplicate)
+        throw new Error(
+          "geneset: update -- update specified existing name and description."
+        );
 
       const prevGs = state.genesets.get(genesetName);
       const newGs = {
diff --git a/client/src/reducers/index.js b/client/src/reducers/index.js
index 46812339..074072a0 100644
--- a/client/src/reducers/index.js
+++ b/client/src/reducers/index.js
@@ -60,7 +60,6 @@ const Reducer = undoable(
     "layoutChoice",
     "centroidLabels",
     "genesets",
-    "genesetsUI",
     "annotations",
   ],
   undoableConfig