From 84900bad0e7467fd77bf576ee1571c00b4995a63 Mon Sep 17 00:00:00 2001
From: Colin Megill <colinmegill@gmail.com>
Date: Thu, 7 Nov 2019 18:57:15 -0500
Subject: [PATCH 01/16] Warnings on anno textfields (#1023)

*  Warning for creating new label with an existing name

* category dup

* italics
---
 .../src/components/categorical/categorical.js | 73 ++++++++++++++-----
 client/src/components/categorical/category.js | 32 +++++++-
 client/src/reducers/annotations.js            |  4 +-
 3 files changed, 85 insertions(+), 24 deletions(-)

diff --git a/client/src/components/categorical/categorical.js b/client/src/components/categorical/categorical.js
index 98bb8785..660f3f51 100644
--- a/client/src/components/categorical/categorical.js
+++ b/client/src/components/categorical/categorical.js
@@ -7,7 +7,8 @@ import {
   InputGroup,
   Dialog,
   Classes,
-  MenuItem
+  MenuItem,
+  Colors
 } from "@blueprintjs/core";
 import { Select } from "@blueprintjs/select";
 import { connect } from "react-redux";
@@ -57,7 +58,11 @@ class Categories extends React.Component {
   };
 
   render() {
-    const { createAnnoModeActive, categoryToDuplicate } = this.state;
+    const {
+      createAnnoModeActive,
+      categoryToDuplicate,
+      newCategoryText
+    } = this.state;
     const {
       categoricalSelection,
       writableCategoriesEnabled,
@@ -76,26 +81,30 @@ class Categories extends React.Component {
       >
         {/* READ ONLY CATEGORICAL FIELDS */}
         {/* this is duplicative but flat, could be abstracted */}
-        {_.map(allCategoryNames, catName =>
-          !schema.annotations.obsByName[catName].writable ? (
-            <Category
-              key={catName}
-              metadataField={catName}
-              createAnnoModeActive={createAnnoModeActive}
-              isUserAnno={false}
-            />
-          ) : null
+        {_.map(
+          allCategoryNames,
+          catName =>
+            !schema.annotations.obsByName[catName].writable ? (
+              <Category
+                key={catName}
+                metadataField={catName}
+                createAnnoModeActive={createAnnoModeActive}
+                isUserAnno={false}
+              />
+            ) : null
         )}
         {/* WRITEABLE FIELDS */}
-        {_.map(allCategoryNames, catName =>
-          schema.annotations.obsByName[catName].writable ? (
-            <Category
-              key={catName}
-              metadataField={catName}
-              createAnnoModeActive={createAnnoModeActive}
-              isUserAnno
-            />
-          ) : null
+        {_.map(
+          allCategoryNames,
+          catName =>
+            schema.annotations.obsByName[catName].writable ? (
+              <Category
+                key={catName}
+                metadataField={catName}
+                createAnnoModeActive={createAnnoModeActive}
+                isUserAnno
+              />
+            ) : null
         )}
         {writableCategoriesEnabled ? (
           <div>
@@ -116,12 +125,33 @@ class Categories extends React.Component {
                     <p>New, unique category name:</p>
                     <InputGroup
                       autoFocus
+                      intent={
+                        allCategoryNames.indexOf(newCategoryText) !== -1
+                          ? "warning"
+                          : "none"
+                      }
                       onChange={e =>
                         this.setState({ newCategoryText: e.target.value })
                       }
                       leftIcon="tag"
                     />
+                    <p
+                      style={{
+                        marginTop: 7,
+                        visibility:
+                          allCategoryNames.indexOf(newCategoryText) !== -1
+                            ? "visible"
+                            : "hidden",
+                        color: Colors.ORANGE3
+                      }}
+                    >
+                      <span style={{ fontStyle: "italic" }}>
+                        {newCategoryText}
+                      </span>{" "}
+                      already exists
+                    </p>
                   </div>
+
                   <p>
                     Optionally duplicate all labels & cell assignments from
                     existing category into new category:
@@ -157,6 +187,9 @@ class Categories extends React.Component {
                     </Tooltip>
                     <Button
                       onClick={this.handleCreateUserAnno}
+                      disabled={
+                        allCategoryNames.indexOf(newCategoryText) !== -1
+                      }
                       intent="primary"
                       type="submit"
                     >
diff --git a/client/src/components/categorical/category.js b/client/src/components/categorical/category.js
index 24395911..84476ee0 100644
--- a/client/src/components/categorical/category.js
+++ b/client/src/components/categorical/category.js
@@ -2,7 +2,7 @@ import React from "react";
 import _ from "lodash";
 import { connect } from "react-redux";
 import { FaChevronRight, FaChevronDown } from "react-icons/fa";
-import { Flipper, Flipped, Spring } from "react-flip-toolkit";
+import { Flipper, Flipped } from "react-flip-toolkit";
 import {
   Button,
   Tooltip,
@@ -14,7 +14,8 @@ import {
   Classes,
   Icon,
   Position,
-  PopoverInteractionKind
+  PopoverInteractionKind,
+  Colors
 } from "@blueprintjs/core";
 
 import * as globals from "../../globals";
@@ -345,11 +346,38 @@ class Category extends React.Component {
                         <p>New, unique label name:</p>
                         <InputGroup
                           autoFocus
+                          intent={
+                            universe.schema.annotations.obsByName[
+                              metadataField
+                            ].categories.indexOf(newLabelText) !== -1
+                              ? "warning"
+                              : "none"
+                          }
                           onChange={e =>
                             this.setState({ newLabelText: e.target.value })
                           }
                           leftIcon="tag"
                         />
+                        <p
+                          style={{
+                            marginTop: 7,
+                            visibility:
+                              universe.schema.annotations.obsByName[
+                                metadataField
+                              ].categories.indexOf(newLabelText) !== -1
+                                ? "visible"
+                                : "hidden",
+                            color: Colors.ORANGE3
+                          }}
+                        >
+                          <span style={{ fontStyle: "italic" }}>
+                            {newLabelText}
+                          </span>{" "}
+                          already exists within{" "}
+                          <span style={{ fontStyle: "italic" }}>
+                            {metadataField}
+                          </span>
+                        </p>
                       </div>
                     </div>
                     <div className={Classes.DIALOG_FOOTER}>
diff --git a/client/src/reducers/annotations.js b/client/src/reducers/annotations.js
index a47a44b8..047b9abd 100644
--- a/client/src/reducers/annotations.js
+++ b/client/src/reducers/annotations.js
@@ -5,7 +5,7 @@ const Annotations = (
   state = {
     isEditingCategoryName: false,
     isEditingLabelName: false,
-    categoryBeingEdited: false,
+    categoryBeingEdited: null,
     categoryAddingNewLabel: null,
     labelEditable: { category: null, label: null }
   },
@@ -46,7 +46,7 @@ const Annotations = (
     case "annotation: category edited":
       return {
         ...state,
-        isEditingCategoryName: true,
+        isEditingCategoryName: false,
         categoryBeingEdited: null
       };
 

From cadf710bf84d585a2244944b4051cef07f918675 Mon Sep 17 00:00:00 2001
From: Colin Megill <colinmegill@gmail.com>
Date: Fri, 8 Nov 2019 11:18:29 -0500
Subject: [PATCH 02/16] remove duplicate handler (#1027)

---
 client/src/components/categorical/categorical.js | 1 -
 1 file changed, 1 deletion(-)

diff --git a/client/src/components/categorical/categorical.js b/client/src/components/categorical/categorical.js
index 660f3f51..9f9d2941 100644
--- a/client/src/components/categorical/categorical.js
+++ b/client/src/components/categorical/categorical.js
@@ -117,7 +117,6 @@ class Categories extends React.Component {
               <form
                 onSubmit={e => {
                   e.preventDefault();
-                  this.handleCreateUserAnno();
                 }}
               >
                 <div className={Classes.DIALOG_BODY}>

From 238b7420f731cb1fdb4ea9d1b70f8bb5414c3f2b Mon Sep 17 00:00:00 2001
From: Bruce Martin <bruce@chanzuckerberg.com>
Date: Fri, 8 Nov 2019 09:49:52 -0800
Subject: [PATCH 03/16] update deprecated Pandas API (#1021)

* update use of deprecated API

* update pandas depencency
---
 server/app/util/fbs/matrix.py | 2 +-
 server/requirements.txt       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/server/app/util/fbs/matrix.py b/server/app/util/fbs/matrix.py
index 1a0770b4..b29f4eb4 100644
--- a/server/app/util/fbs/matrix.py
+++ b/server/app/util/fbs/matrix.py
@@ -95,7 +95,7 @@ def serialize_typed_array(builder, source_array, encoding_info):
         if MatrixProxy.ismatrixproxy(arr) or sparse.issparse(arr):
             arr = arr.toarray()
         elif isinstance(arr, pd.Series):
-            arr = arr.get_values()
+            arr = arr.to_numpy()
         if arr.dtype != as_type:
             arr = arr.astype(as_type)
 
diff --git a/server/requirements.txt b/server/requirements.txt
index d3e000b0..ec853936 100644
--- a/server/requirements.txt
+++ b/server/requirements.txt
@@ -8,7 +8,7 @@ Flask-RESTful>=0.3.6
 flatbuffers>=1.10.0
 fsspec>=0.4.4
 numpy>=1.15.2
-pandas>=0.23.1
+pandas>=0.24.2
 scipy>=1.3.0
 tables==3.5.1
 # TEMP workaround for https://github.com/theislab/scanpy/issues/832 aka h5py regression

From 04c83993d202f44cef080a3728374016634cdfd1 Mon Sep 17 00:00:00 2001
From: Bruce Martin <bruce@chanzuckerberg.com>
Date: Tue, 12 Nov 2019 15:31:06 -0800
Subject: [PATCH 04/16] clear color-by mode when current category is deleted
 (#1033)

---
 client/src/reducers/colors.js | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/client/src/reducers/colors.js b/client/src/reducers/colors.js
index 8c131600..723f299b 100644
--- a/client/src/reducers/colors.js
+++ b/client/src/reducers/colors.js
@@ -53,6 +53,18 @@ const ColorsReducer = (
       };
     }
 
+    case "annotation: delete category": {
+      const { colorAccessor } = state;
+      if (action.metadataField != colorAccessor) {
+        return state;
+      }
+      /* else reset */
+      return {
+        ...state,
+        ...ColorHelpers.resetColors(prevSharedState.world)
+      };
+    }
+
     case "reset colorscale": {
       return {
         ...state,

From a52e86a69b2835551ae3eee73d7d3a51eeed47c6 Mon Sep 17 00:00:00 2001
From: Bruce Martin <bruce@chanzuckerberg.com>
Date: Wed, 13 Nov 2019 09:40:37 -0800
Subject: [PATCH 05/16] improve category and label name validation (#1034)

---
 .../src/components/categorical/categorical.js | 103 ++++++++++++------
 client/src/components/categorical/category.js |  83 ++++++++++----
 .../util/stateManager/annotationsHelpers.js   |   5 +
 3 files changed, 136 insertions(+), 55 deletions(-)

diff --git a/client/src/components/categorical/categorical.js b/client/src/components/categorical/categorical.js
index 9f9d2941..d9948a5d 100644
--- a/client/src/components/categorical/categorical.js
+++ b/client/src/components/categorical/categorical.js
@@ -14,6 +14,7 @@ import { Select } from "@blueprintjs/select";
 import { connect } from "react-redux";
 import * as globals from "../../globals";
 import Category from "./category";
+import { AnnotationsHelpers } from "../../util/stateManager";
 
 @connect(state => ({
   categoricalSelection: state.categoricalSelection,
@@ -50,13 +51,57 @@ class Categories extends React.Component {
   };
 
   handleDisableAnnoMode = () => {
-    this.setState({ createAnnoModeActive: false });
+    this.setState({
+      createAnnoModeActive: false,
+      categoryToDuplicate: null,
+      newCategoryText: ""
+    });
   };
 
   handleModalDuplicateCategorySelection = d => {
     this.setState({ categoryToDuplicate: d });
   };
 
+  categoryNameError = name => {
+    /*
+    return false if this is a LEGAL/acceptable category name,
+    or return an error type.
+    */
+    const { categoricalSelection } = this.props;
+    const allCategoryNames = Object.keys(categoricalSelection);
+
+    if (allCategoryNames.indexOf(name) !== -1) {
+      return "duplicate";
+    }
+
+    if (!AnnotationsHelpers.isLegalAnnotationName(name)) {
+      return "characters";
+    }
+
+    return false;
+  };
+
+  categoryNameErrorMessage = name => {
+    const err = this.categoryNameError(name);
+    if (err == "duplicate") {
+      return (
+        <span>
+          <span style={{ fontStyle: "italic" }}>{name}</span> already exists -
+          no duplicates allowed
+        </span>
+      );
+    }
+    if (err == "characters") {
+      return (
+        <span>
+          <span style={{ fontStyle: "italic" }}>{name}</span> contains illegal
+          characters. Hint: use alpha-numeric and underscore
+        </span>
+      );
+    }
+    return err;
+  };
+
   render() {
     const {
       createAnnoModeActive,
@@ -81,30 +126,26 @@ class Categories extends React.Component {
       >
         {/* READ ONLY CATEGORICAL FIELDS */}
         {/* this is duplicative but flat, could be abstracted */}
-        {_.map(
-          allCategoryNames,
-          catName =>
-            !schema.annotations.obsByName[catName].writable ? (
-              <Category
-                key={catName}
-                metadataField={catName}
-                createAnnoModeActive={createAnnoModeActive}
-                isUserAnno={false}
-              />
-            ) : null
+        {_.map(allCategoryNames, catName =>
+          !schema.annotations.obsByName[catName].writable ? (
+            <Category
+              key={catName}
+              metadataField={catName}
+              createAnnoModeActive={createAnnoModeActive}
+              isUserAnno={false}
+            />
+          ) : null
         )}
         {/* WRITEABLE FIELDS */}
-        {_.map(
-          allCategoryNames,
-          catName =>
-            schema.annotations.obsByName[catName].writable ? (
-              <Category
-                key={catName}
-                metadataField={catName}
-                createAnnoModeActive={createAnnoModeActive}
-                isUserAnno
-              />
-            ) : null
+        {_.map(allCategoryNames, catName =>
+          schema.annotations.obsByName[catName].writable ? (
+            <Category
+              key={catName}
+              metadataField={catName}
+              createAnnoModeActive={createAnnoModeActive}
+              isUserAnno
+            />
+          ) : null
         )}
         {writableCategoriesEnabled ? (
           <div>
@@ -124,8 +165,10 @@ class Categories extends React.Component {
                     <p>New, unique category name:</p>
                     <InputGroup
                       autoFocus
+                      value={newCategoryText}
                       intent={
-                        allCategoryNames.indexOf(newCategoryText) !== -1
+                        newCategoryText &&
+                        this.categoryNameError(newCategoryText)
                           ? "warning"
                           : "none"
                       }
@@ -138,16 +181,14 @@ class Categories extends React.Component {
                       style={{
                         marginTop: 7,
                         visibility:
-                          allCategoryNames.indexOf(newCategoryText) !== -1
+                          newCategoryText &&
+                          this.categoryNameError(newCategoryText)
                             ? "visible"
                             : "hidden",
                         color: Colors.ORANGE3
                       }}
                     >
-                      <span style={{ fontStyle: "italic" }}>
-                        {newCategoryText}
-                      </span>{" "}
-                      already exists
+                      {this.categoryNameErrorMessage(newCategoryText)}
                     </p>
                   </div>
 
@@ -186,9 +227,7 @@ class Categories extends React.Component {
                     </Tooltip>
                     <Button
                       onClick={this.handleCreateUserAnno}
-                      disabled={
-                        allCategoryNames.indexOf(newCategoryText) !== -1
-                      }
+                      disabled={this.categoryNameError(newCategoryText)}
                       intent="primary"
                       type="submit"
                     >
diff --git a/client/src/components/categorical/category.js b/client/src/components/categorical/category.js
index 84476ee0..078fc384 100644
--- a/client/src/components/categorical/category.js
+++ b/client/src/components/categorical/category.js
@@ -21,6 +21,7 @@ import {
 import * as globals from "../../globals";
 import Value from "./value";
 import sortedCategoryValues from "./util";
+import { AnnotationsHelpers } from "../../util/stateManager";
 
 @connect(state => ({
   colorAccessor: state.colors.colorAccessor,
@@ -82,18 +83,14 @@ class Category extends React.Component {
     dispatch({
       type: "annotation: disable add new label mode"
     });
+    this.setState({
+      newLabelText: ""
+    });
   };
 
   handleAddNewLabelToCategory = () => {
     const { dispatch, metadataField } = this.props;
     const { newLabelText } = this.state;
-    /*
-    XXX TODO - temporary code generates random label string. Remove
-    when the label creation UI is implemented.
-
-    const { newLabelText } = this.state;
-    */
-    // const newLabelText = `label${Math.random()}`;
     dispatch({
       type: "annotation: add new label to category",
       metadataField,
@@ -146,6 +143,48 @@ class Category extends React.Component {
     });
   };
 
+  labelNameError = name => {
+    /*
+    return false if this is a LEGAL/acceptable category name,
+    or return an error type.
+    */
+    const { metadataField, universe } = this.props;
+    const obsByName = universe.schema.annotations.obsByName;
+
+    if (obsByName[metadataField].categories.indexOf(name) !== -1) {
+      return "duplicate";
+    }
+
+    if (!AnnotationsHelpers.isLegalAnnotationName(name)) {
+      return "characters";
+    }
+
+    return false;
+  };
+
+  labelNameErrorMessage = name => {
+    const { metadataField } = this.props;
+    const err = this.labelNameError(name);
+    if (err == "duplicate") {
+      return (
+        <span>
+          <span style={{ fontStyle: "italic" }}>{name}</span> already exists
+          already exists within{" "}
+          <span style={{ fontStyle: "italic" }}>{metadataField}</span>{" "}
+        </span>
+      );
+    }
+    if (err == "characters") {
+      return (
+        <span>
+          <span style={{ fontStyle: "italic" }}>{name}</span> contains illegal
+          characters. Hint: use alpha-numeric and underscore
+        </span>
+      );
+    }
+    return err;
+  };
+
   toggleAll() {
     const { dispatch, metadataField } = this.props;
     dispatch({
@@ -346,10 +385,12 @@ class Category extends React.Component {
                         <p>New, unique label name:</p>
                         <InputGroup
                           autoFocus
+                          value={newLabelText}
                           intent={
-                            universe.schema.annotations.obsByName[
-                              metadataField
-                            ].categories.indexOf(newLabelText) !== -1
+                            // universe.schema.annotations.obsByName[
+                            //   metadataField
+                            // ].categories.indexOf(newLabelText) !== -1
+                            newLabelText && this.labelNameError(newLabelText)
                               ? "warning"
                               : "none"
                           }
@@ -362,21 +403,16 @@ class Category extends React.Component {
                           style={{
                             marginTop: 7,
                             visibility:
-                              universe.schema.annotations.obsByName[
-                                metadataField
-                              ].categories.indexOf(newLabelText) !== -1
+                              // universe.schema.annotations.obsByName[
+                              //   metadataField
+                              // ].categories.indexOf(newLabelText) !== -1
+                              newLabelText && this.labelNameError(newLabelText)
                                 ? "visible"
                                 : "hidden",
                             color: Colors.ORANGE3
                           }}
                         >
-                          <span style={{ fontStyle: "italic" }}>
-                            {newLabelText}
-                          </span>{" "}
-                          already exists within{" "}
-                          <span style={{ fontStyle: "italic" }}>
-                            {metadataField}
-                          </span>
+                          {this.labelNameErrorMessage(newLabelText)}
                         </p>
                       </div>
                     </div>
@@ -390,9 +426,10 @@ class Category extends React.Component {
                         <Button
                           disabled={
                             newLabelText.length === 0 ||
-                            universe.schema.annotations.obsByName[
-                              metadataField
-                            ].categories.indexOf(newLabelText) !== -1
+                            // universe.schema.annotations.obsByName[
+                            //   metadataField
+                            // ].categories.indexOf(newLabelText) !== -1
+                            this.labelNameError(newLabelText)
                           }
                           onClick={this.handleAddNewLabelToCategory}
                           intent="primary"
diff --git a/client/src/util/stateManager/annotationsHelpers.js b/client/src/util/stateManager/annotationsHelpers.js
index 53b2c796..4310781c 100644
--- a/client/src/util/stateManager/annotationsHelpers.js
+++ b/client/src/util/stateManager/annotationsHelpers.js
@@ -182,3 +182,8 @@ export function createWritableAnnotationDimensions(world, crossfilter) {
 	}, crossfilter);
 	return crossfilter;
 }
+
+const legalNames = /^\w+$/;
+export function isLegalAnnotationName(name) {
+	return legalNames.test(name);
+}

From 68ad4b12283b327812860caa0da8f8faf1d5c37e Mon Sep 17 00:00:00 2001
From: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
Date: Wed, 13 Nov 2019 11:56:48 -0800
Subject: [PATCH 06/16] bump @blueprintjs dependencies (#1038)

---
 client/package-lock.json | 39 ++++++++++++++++++++-------------------
 client/package.json      |  6 +++---
 2 files changed, 23 insertions(+), 22 deletions(-)

diff --git a/client/package-lock.json b/client/package-lock.json
index 0fc7b466..aedc7bf4 100644
--- a/client/package-lock.json
+++ b/client/package-lock.json
@@ -1655,16 +1655,17 @@
       }
     },
     "@blueprintjs/core": {
-      "version": "3.18.1",
-      "resolved": "https://registry.npmjs.org/@blueprintjs/core/-/core-3.18.1.tgz",
-      "integrity": "sha512-G+IhJsN006Mb32NLOrne5TLScxyyd3Id9g2MvfYFq9zuyBcBA5+V/uQy3pTO9vkmuKEz0GLLy8ZbrQ7Us/+zTw==",
+      "version": "3.20.0",
+      "resolved": "https://registry.npmjs.org/@blueprintjs/core/-/core-3.20.0.tgz",
+      "integrity": "sha512-0ndz/lLMbSgWu1Z5hdpScfMbkQIOFESejsSW7Jjpin7Hmsjr8fRDU1efoVyG1uHBPmA4B6aYh+uShZHcZGJtig==",
       "requires": {
-        "@blueprintjs/icons": "^3.10.0",
+        "@blueprintjs/icons": "^3.12.0",
         "@types/dom4": "^2.0.1",
         "classnames": "^2.2",
         "dom4": "^2.1.5",
         "normalize.css": "^8.0.1",
         "popper.js": "^1.15.0",
+        "react-lifecycles-compat": "^3.0.4",
         "react-popper": "^1.3.3",
         "react-transition-group": "^2.9.0",
         "resize-observer-polyfill": "^1.5.1",
@@ -1672,20 +1673,20 @@
       }
     },
     "@blueprintjs/icons": {
-      "version": "3.10.0",
-      "resolved": "https://registry.npmjs.org/@blueprintjs/icons/-/icons-3.10.0.tgz",
-      "integrity": "sha512-lyAUpkr3qEStPcJpMnxRKuVAPvaRNSce1ySPbkE58zPmD4WBya2gNrWex41xoqRYM0GsiBSwH9CnpY8t6fZKUA==",
+      "version": "3.12.0",
+      "resolved": "https://registry.npmjs.org/@blueprintjs/icons/-/icons-3.12.0.tgz",
+      "integrity": "sha512-ERIODstzjBzRIHNqAqyXu4gVsdLyvxAZ0Cp7Dr4+d5BdgDbZYzMYf9ll05daQPOBWaFjLh3lhCRhbfk6MXdD7A==",
       "requires": {
         "classnames": "^2.2",
         "tslib": "~1.9.0"
       }
     },
     "@blueprintjs/select": {
-      "version": "3.10.0",
-      "resolved": "https://registry.npmjs.org/@blueprintjs/select/-/select-3.10.0.tgz",
-      "integrity": "sha512-Akm/L5tndrOUuf05od9IJ0WSQgHdbJ4/i2RRoLLH5ZiI8s1OZiCbKJYDSCbCOTviCdZSuL0qkJsBcYhOI/Czeg==",
+      "version": "3.11.2",
+      "resolved": "https://registry.npmjs.org/@blueprintjs/select/-/select-3.11.2.tgz",
+      "integrity": "sha512-fU0Km6QI/ayWhzYeu9N1gTj0+L0XUO4KB3u2LfJXgj648UGY8F4HX2ETdJ+XPdtsu6TesrIL7ghMQhtLcvafBg==",
       "requires": {
-        "@blueprintjs/core": "^3.18.0",
+        "@blueprintjs/core": "^3.20.0",
         "classnames": "^2.2",
         "tslib": "~1.9.0"
       }
@@ -7406,7 +7407,7 @@
         },
         "readable-stream": {
           "version": "1.0.34",
-          "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-1.0.34.tgz",
+          "resolved": "http://registry.npmjs.org/readable-stream/-/readable-stream-1.0.34.tgz",
           "integrity": "sha1-Elgg40vIQtLyqq+v5MKRbuMsFXw=",
           "dev": true,
           "requires": {
@@ -10286,9 +10287,9 @@
       "dev": true
     },
     "popper.js": {
-      "version": "1.15.0",
-      "resolved": "https://registry.npmjs.org/popper.js/-/popper.js-1.15.0.tgz",
-      "integrity": "sha512-w010cY1oCUmI+9KwwlWki+r5jxKfTFDVoadl7MSrIujHU5MJ5OR6HTDj6Xo8aoR/QsA56x8jKjA59qGH4ELtrA=="
+      "version": "1.16.0",
+      "resolved": "https://registry.npmjs.org/popper.js/-/popper.js-1.16.0.tgz",
+      "integrity": "sha512-+G+EkOPoE5S/zChTpmBSSDYmhXJ5PsW8eMhH8cP/CQHMFPBG/kC9Y5IIw6qNYgdJ+/COf0ddY2li28iHaZRSjw=="
     },
     "posix-character-classes": {
       "version": "0.1.1",
@@ -10705,7 +10706,7 @@
       "dependencies": {
         "minimist": {
           "version": "1.2.0",
-          "resolved": "https://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
+          "resolved": "http://registry.npmjs.org/minimist/-/minimist-1.2.0.tgz",
           "integrity": "sha1-o1AIsg9BOD7sH7kU9M1d95omQoQ=",
           "dev": true
         }
@@ -10791,9 +10792,9 @@
       "integrity": "sha512-fBASbA6LnOU9dOU2eW7aQ8xmYBSXUIWr+UmF9b1efZBazGNO+rcXT/icdKnYm2pTwcRylVUYwW7H1PHfLekVzA=="
     },
     "react-popper": {
-      "version": "1.3.4",
-      "resolved": "https://registry.npmjs.org/react-popper/-/react-popper-1.3.4.tgz",
-      "integrity": "sha512-9AcQB29V+WrBKk6X7p0eojd1f25/oJajVdMZkywIoAV6Ag7hzE1Mhyeup2Q1QnvFRtGQFQvtqfhlEoDAPfKAVA==",
+      "version": "1.3.6",
+      "resolved": "https://registry.npmjs.org/react-popper/-/react-popper-1.3.6.tgz",
+      "integrity": "sha512-kLTfa9z8n+0jJvRVal9+vIuirg41rObg4Bbrvv/ZfsGPQDN9reyVVSxqnHF1ZNgXgV7x11PeUfd5ItF8DZnqhg==",
       "requires": {
         "@babel/runtime": "^7.1.2",
         "create-react-context": "^0.3.0",
diff --git a/client/package.json b/client/package.json
index 94213959..d7f980e3 100644
--- a/client/package.json
+++ b/client/package.json
@@ -32,9 +32,9 @@
     "eslint-scope": "3.7.1"
   },
   "dependencies": {
-    "@blueprintjs/core": "^3.18.1",
-    "@blueprintjs/icons": "^3.10.0",
-    "@blueprintjs/select": "^3.10.0",
+    "@blueprintjs/core": "^3.20.0",
+    "@blueprintjs/icons": "^3.12.0",
+    "@blueprintjs/select": "^3.11.2",
     "d3": "^4.10.0",
     "d3-scale-chromatic": "^1.5.0",
     "flatbuffers": "^1.11.0",

From 89d748b007863175b38e4080dda5ae36b92cd948 Mon Sep 17 00:00:00 2001
From: Colin Megill <colinmegill@gmail.com>
Date: Wed, 13 Nov 2019 15:13:15 -0500
Subject: [PATCH 07/16] state (#1032)


From 5ea9ac8a9ebe95037d90a3c4768a07f2ec8c7070 Mon Sep 17 00:00:00 2001
From: Bruce Martin <bruce@chanzuckerberg.com>
Date: Thu, 14 Nov 2019 12:33:48 -0800
Subject: [PATCH 08/16] Add provenance header to labels CSV file (#1041)

* add last mod time lookup to data locator

* store data locator in Driver

* save metadata header in labels csv

* lint

* fix tests

* change datetime format to second precision
---
 server/app/driver/driver.py                 | 14 ++++++++------
 server/app/scanpy_engine/labels.py          |  9 ++++++---
 server/app/scanpy_engine/scanpy_engine.py   | 18 +++++++++++++-----
 server/app/util/data_locator.py             |  9 +++++++++
 server/test/test_scanpy_engine_data_load.py |  4 ++--
 server/test/test_writable_annotation.py     |  4 ++--
 6 files changed, 40 insertions(+), 18 deletions(-)

diff --git a/server/app/driver/driver.py b/server/app/driver/driver.py
index c8052323..0b970ab0 100644
--- a/server/app/driver/driver.py
+++ b/server/app/driver/driver.py
@@ -11,18 +11,20 @@ Sort order for methods
 
 
 class CXGDriver(metaclass=ABCMeta):
-    def __init__(self, data=None, args={}):
+    def __init__(self, data_locator=None, args={}):
         self.config = self._get_default_config()
         self.config.update(args)
-        if data:
-            self._load_data(data)
+        if data_locator:
+            self._load_data(data_locator)
+            self.data_locator = data_locator
         else:
             self.data = None
 
-    def update(self, data=None, args={}):
+    def update(self, data_locator=None, args={}):
         self.config.update(args)
-        if data:
-            self._load_data(data)
+        if data_locator:
+            self._load_data(data_locator)
+            self.data_locator = data_locator
 
     @staticmethod
     def _get_default_config():
diff --git a/server/app/scanpy_engine/labels.py b/server/app/scanpy_engine/labels.py
index 32a74dc3..f06aeb40 100644
--- a/server/app/scanpy_engine/labels.py
+++ b/server/app/scanpy_engine/labels.py
@@ -8,15 +8,18 @@ import pandas as pd
 
 def read_labels(fname):
     if exists(fname) and getsize(fname) > 0:
-        return pd.read_csv(fname, dtype='category', index_col=0)
+        return pd.read_csv(fname, dtype='category', index_col=0, header=0, comment='#')
     else:
         return pd.DataFrame()
 
 
-def write_labels(fname, df):
+def write_labels(fname, df, header=None):
     rotate_fname(fname)
     if not df.empty:
-        df.to_csv(fname)
+        f = open(fname, 'a', newline="")
+        if header is not None:
+            f.write(header)
+        df.to_csv(f)
     else:
         open(fname, 'a').close()
 
diff --git a/server/app/scanpy_engine/scanpy_engine.py b/server/app/scanpy_engine/scanpy_engine.py
index addcbf69..0392a9cb 100644
--- a/server/app/scanpy_engine/scanpy_engine.py
+++ b/server/app/scanpy_engine/scanpy_engine.py
@@ -1,6 +1,7 @@
 import warnings
 import copy
 import threading
+from datetime import datetime
 
 import numpy as np
 import pandas
@@ -8,6 +9,7 @@ from pandas.core.dtypes.dtypes import CategoricalDtype
 import anndata
 from scipy import sparse
 
+from server import __version__ as cellxgene_version
 from server.app.driver.driver import CXGDriver
 from server.app.util.constants import Axis, DEFAULT_TOP_N, MAX_LAYOUTS
 from server.app.util.errors import (
@@ -32,15 +34,15 @@ def has_method(o, name):
 
 
 class ScanpyEngine(CXGDriver):
-    def __init__(self, data=None, args={}):
-        super().__init__(data, args)
+    def __init__(self, data_locator=None, args={}):
+        super().__init__(data_locator, args)
         # lock used to protect label file write ops
         self.label_lock = threading.Lock()
         if self.data:
             self._validate_and_initialize()
 
-    def update(self, data=None, args={}):
-        super().__init__(data, args)
+    def update(self, data_locator=None, args={}):
+        super().__init__(data_locator, args)
         if self.data:
             self._validate_and_initialize()
 
@@ -484,7 +486,13 @@ class ScanpyEngine(CXGDriver):
         # so treat this as a critical section.
         with self.label_lock:
             self.labels = new_label_df
-            write_labels(fname, self.labels)
+            lastmod = self.data_locator.lastmodtime()
+            lastmodstr = "'unknown'" if lastmod is None else lastmod.isoformat(timespec="seconds")
+            header = f"# Annotations generated on {datetime.now().isoformat(timespec='seconds')} " \
+                     f"using cellxgene version {cellxgene_version}\n" \
+                     f"# Input data file was {self.data_locator.uri_or_path}, " \
+                     f"which was last modified on {lastmodstr}\n"
+            write_labels(fname, self.labels, header)
 
         return jsonify_scanpy({"status": "OK"})
 
diff --git a/server/app/util/data_locator.py b/server/app/util/data_locator.py
index b2402047..e4d1af5d 100644
--- a/server/app/util/data_locator.py
+++ b/server/app/util/data_locator.py
@@ -1,6 +1,7 @@
 import os
 import tempfile
 import fsspec
+from datetime import datetime
 
 
 class DataLocator():
@@ -48,6 +49,14 @@ class DataLocator():
     def size(self):
         return self.fs.size(self.cname)
 
+    def lastmodtime(self):
+        """ return datetime object representing last modification time, or None if unavailable """
+        info = self.fs.info(self.cname)
+        if self.islocal() and info is not None:
+            return datetime.fromtimestamp(info['mtime'])
+        else:
+            return getattr(info, 'LastModified', None)
+
     def isfile(self):
         return self.fs.isfile(self.cname)
 
diff --git a/server/test/test_scanpy_engine_data_load.py b/server/test/test_scanpy_engine_data_load.py
index cba82dc1..3379a5dc 100644
--- a/server/test/test_scanpy_engine_data_load.py
+++ b/server/test/test_scanpy_engine_data_load.py
@@ -37,7 +37,7 @@ class DataLoadEngineTest(unittest.TestCase):
             self.data._create_schema()
 
     def test_delayed_load_data(self):
-        self.data.update(data=self.data_file)
+        self.data.update(data_locator=self.data_file)
         self.data._create_schema()
         self.assertEqual(self.data.cell_count, 2638)
         self.assertEqual(self.data.gene_count, 1838)
@@ -45,7 +45,7 @@ class DataLoadEngineTest(unittest.TestCase):
         self.assertTrue(self.data.data.X[0, 0] - -0.171_469_51 < epsilon)
 
     def test_diffexp_topN(self):
-        self.data.update(data=self.data_file)
+        self.data.update(data_locator=self.data_file)
         f1 = {"filter": {"obs": {"index": [[0, 500]]}}}
         f2 = {"filter": {"obs": {"index": [[500, 1000]]}}}
         result = json.loads(self.data.diffexp_topN(f1["filter"], f2["filter"]))
diff --git a/server/test/test_writable_annotation.py b/server/test/test_writable_annotation.py
index bf260053..4e817566 100644
--- a/server/test/test_writable_annotation.py
+++ b/server/test/test_writable_annotation.py
@@ -60,7 +60,7 @@ class WritableAnnotationTest(unittest.TestCase):
         res = self.data.annotation_put_fbs("obs", fbs)
         self.assertEqual(res, json.dumps({"status": "OK"}))
         self.assertTrue(path.exists(self.label_file))
-        df = pd.read_csv(self.label_file, index_col=0)
+        df = pd.read_csv(self.label_file, index_col=0, header=0, comment='#')
         self.assertEqual(df.shape, (n_rows, 2))
         self.assertEqual(set(df.columns), set(['cat_A', 'cat_B']))
         self.assertTrue(self.data.original_obs_index.equals(df.index))
@@ -75,7 +75,7 @@ class WritableAnnotationTest(unittest.TestCase):
         res = self.data.annotation_put_fbs("obs", fbs)
         self.assertEqual(res, json.dumps({"status": "OK"}))
         self.assertTrue(path.exists(self.label_file))
-        df = pd.read_csv(self.label_file, index_col=0)
+        df = pd.read_csv(self.label_file, index_col=0, header=0, comment='#')
         self.assertEqual(set(df.columns), set(['cat_A', 'cat_C']))
         self.assertTrue(np.all(df['cat_A'] == ['label_A1' for l in range(0, n_rows)]))
         self.assertTrue(np.all(df['cat_C'] == ['label_C' for l in range(0, n_rows)]))

From b284e6f820567e6936a29bcc67bb0c664d95a906 Mon Sep 17 00:00:00 2001
From: Bruce Martin <bruce@chanzuckerberg.com>
Date: Thu, 14 Nov 2019 13:02:40 -0800
Subject: [PATCH 09/16] Improve CLI help (#1025)

* launch option changes

* more CLI help improvements

* change plot help

* additional changes requested

* change metavars for options and subcommand
---
 server/cli/cli.py     |  13 +++++-
 server/cli/launch.py  | 104 ++++++++++++++++++++++++++++--------------
 server/cli/prepare.py |  53 +++++++++++++--------
 server/utils/utils.py |   9 ++++
 4 files changed, 123 insertions(+), 56 deletions(-)

diff --git a/server/cli/cli.py b/server/cli/cli.py
index 969ec83c..e7f644ec 100644
--- a/server/cli/cli.py
+++ b/server/cli/cli.py
@@ -4,8 +4,17 @@ from .launch import launch
 from .prepare import prepare
 
 
-@click.group(name="cellxgene", context_settings=dict(max_content_width=85))
-@click.version_option(version="0.12.0", prog_name="cellxgene", message="[%(prog)s] Version %(version)s")
+@click.group(name="cellxgene",
+             subcommand_metavar="COMMAND <args>",
+             options_metavar="<options>",
+             context_settings=dict(max_content_width=85,
+                                   help_option_names=['-h', '--help']))
+@click.help_option("--help", "-h", help="Show this message and exit.")
+@click.version_option(
+    version="0.12.0",
+    prog_name="cellxgene",
+    message="[%(prog)s] Version %(version)s",
+    help="Show the software version and exit.")
 def cli():
     pass
 
diff --git a/server/cli/launch.py b/server/cli/launch.py
index f5b13d9f..1d9b5691 100644
--- a/server/cli/launch.py
+++ b/server/cli/launch.py
@@ -13,7 +13,7 @@ import click
 from server.app.app import Server
 from server.app.util.errors import ScanpyFileError
 from server.app.util.utils import custom_format_warning
-from server.utils.utils import find_available_port, is_port_available
+from server.utils.utils import find_available_port, is_port_available, sort_options
 from server.app.util.data_locator import DataLocator
 
 # anything bigger than this will generate a special message
@@ -25,55 +25,70 @@ def common_args(func):
     Decorator to contain CLI args that will be common to both CLI and GUI: title and engine args.
     """
 
-    @click.option("--title", "-t", help="Title to display (if omitted will use file name).")
-    @click.option("--about",
-                  help="A URL to more information about the dataset."
-                       "(This must be an absolute URL including HTTP(S) protocol)")
+    @click.option(
+        "--title",
+        "-t",
+        metavar="<text>",
+        help="Title to display. If omitted will use file name.")
+    @click.option(
+        "--about",
+        metavar="<URL>",
+        help="URL providing more information about the dataset "
+             "(hint: must be a fully specified absolute URL).")
     @click.option(
         "--embedding",
         "-e",
         default=[],
         multiple=True,
         show_default=False,
+        metavar="<text>",
         help="Embedding name, eg, 'umap'. Repeat option for multiple embeddings. Defaults to all."
     )
-    @click.option("--obs-names", default=None, metavar="", help="Name of annotation field to use for observations.")
-    @click.option("--var-names", default=None, metavar="", help="Name of annotation to use for variables.")
+    @click.option(
+        "--obs-names",
+        "-obs",
+        default=None,
+        metavar="<text>",
+        help="Name of annotation field to use for observations. If not specified cellxgene will use the the obs index.")
+    @click.option(
+        "--var-names",
+        "-var",
+        default=None,
+        metavar="<text>",
+        help="Name of annotation to use for variables. If not specified cellxgene will use the the var index.")
     @click.option(
         "--max-category-items",
         default=1000,
-        metavar="",
+        metavar="<integer>",
         show_default=True,
-        help="Categories with more distinct values than this will not be displayed.",
-    )
+        help="Will not display categories with more distinct values than specified.",)
     @click.option(
         "--diffexp-lfc-cutoff",
+        "-de",
         default=0.01,
         show_default=True,
-        help="Relative expression cutoff used when selecting top N differentially expressed genes",
-    )
+        metavar="<float>",
+        help="Minimum log fold change threshold for differential expression.",)
     @click.option(
         "--experimental-label-file",
         default=None,
         show_default=True,
         multiple=False,
-        metavar="<user labels CSV file>",
-        help="CSV file containing user annotations; will be overwritten.  Created if does not exist.",
-    )
+        metavar="<path>",
+        help="CSV file containing user annotations; will be overwritten.  Created if does not exist.",)
     @click.option(
         "--backed",
+        "-b",
         is_flag=True,
         default=False,
         show_default=False,
-        help="Load data in file-backed mode, which may save memory, but result in slower overall performance."
-    )
+        help="Load data in file-backed mode. This may save memory, but may result in slower overall performance.")
     @click.option(
         "--disable-diffexp",
         is_flag=True,
         default=False,
         show_default=False,
-        help="Disable on-demand differential expression."
-    )
+        help="Disable on-demand differential expression.")
     @functools.wraps(func)
     def wrapper(*args, **kwargs):
         return func(*args, **kwargs)
@@ -96,17 +111,26 @@ def parse_engine_args(embedding, obs_names, var_names, max_category_items,
     }
 
 
-@click.command()
-@click.argument("data", nargs=1, metavar="<data file>", required=True)
+@sort_options
+@click.command(short_help="Launch the cellxgene data viewer. "
+                          "Run `cellxgene launch --help` for more information.",
+               options_metavar="<options>",)
+@click.argument("data", nargs=1, metavar="<path to data file>", required=True)
 @click.option(
     "--verbose",
     "-v",
     is_flag=True,
     default=False,
     show_default=True,
-    help="Provide verbose output, including warnings and all server requests.",
-)
-@click.option("--debug", is_flag=True, default=False, show_default=True, help="Run in debug mode.")
+    help="Provide verbose output, including warnings and all server requests.",)
+@click.option(
+    "--debug",
+    "-d",
+    is_flag=True,
+    default=False,
+    show_default=True,
+    help="Run in debug mode. This is helpful for cellxgene developers, "
+         "or when you want more information about an error condition.",)
 @click.option(
     "--open",
     "-o",
@@ -114,18 +138,29 @@ def parse_engine_args(embedding, obs_names, var_names, max_category_items,
     is_flag=True,
     default=False,
     show_default=True,
-    help="Open the web browser after launch.",
-)
-@click.option("--port", "-p", help="Port to run server on, if not specified cellxgene will find an available port.",
-              metavar="", show_default=True)
-@click.option("--host", default="127.0.0.1", help="Host IP address")
+    help="Open web browser after launch.",)
+@click.option(
+    "--port",
+    "-p",
+    metavar="<port>",
+    show_default=True,
+    help="Port to run server on. If not specified cellxgene will find an available port.",)
+@click.option(
+    "--host",
+    metavar="<IP address>",
+    default="127.0.0.1",
+    show_default=False,
+    help="Host IP address. By default cellxgene will use localhost (e.g. 127.0.0.1).")
 @click.option(
     "--scripts",
+    "-s",
     default=[],
     multiple=True,
-    help="Additional script files to include in html page",
-    show_default=True,
-)
+    metavar="<text>",
+    help="Additional script files to include in HTML page. If not specified, "
+         "no additional script files will be included.",
+    show_default=False,)
+@click.help_option("--help", "-h", help="Show this message and exit.")
 @common_args
 def launch(
         data,
@@ -148,8 +183,9 @@ def launch(
 ):
     """Launch the cellxgene data viewer.
     This web app lets you explore single-cell expression data.
-    Data must be in a format that cellxgene expects, read the
-    "getting started" guide.
+    Data must be in a format that cellxgene expects.
+    Read the "getting started" guide to learn more:
+    https://chanzuckerberg.github.io/cellxgene/getting-started.html
 
     Examples:
 
diff --git a/server/cli/prepare.py b/server/cli/prepare.py
index 730e4f86..224fa17c 100644
--- a/server/cli/prepare.py
+++ b/server/cli/prepare.py
@@ -4,16 +4,21 @@ import click
 from numpy import ndarray, unique
 from scipy.sparse.csc import csc_matrix
 
+from server.utils.utils import sort_options
 
-@click.command()
-@click.argument("data", nargs=1, metavar="<dataset: file or path to data>", required=True)
+
+@sort_options
+@click.command(short_help="Preprocess data for use with cellxgene. "
+                          "Run `cellxgene prepare --help` for more information.",
+               options_metavar="<options>",)
+@click.argument("data", nargs=1, metavar="<path to data file>", required=True)
 @click.option(
     "--embedding",
     "-e",
     default=["umap", "tsne"],
     multiple=True,
     type=click.Choice(["umap", "tsne"]),
-    help="Embedding algorithm",
+    help="Embedding algorithm(s). Repeat option for multiple embeddings.",
     show_default=True,
 )
 @click.option(
@@ -25,21 +30,29 @@ from scipy.sparse.csc import csc_matrix
     show_default=True,
 )
 @click.option("--output", "-o", default="", help="Save a new file to filename.", metavar="<filename>")
-@click.option("--plotting", "-p", default=False, is_flag=True, help="Whether to generate plots.", show_default=True)
-@click.option("--sparse", default=False, is_flag=True, help="Whether to force sparsity.", show_default=True)
+@click.option("--plotting", "-p", default=False, is_flag=True, help="Generate plots.", show_default=True)
+@click.option("--sparse", default=False, is_flag=True, help="Force sparsity.", show_default=True)
 @click.option("--overwrite", default=False, is_flag=True, help="Allow file overwriting.", show_default=True)
 @click.option("--set-obs-names", default="", help="Named field to set as index for obs.", metavar="<name>")
 @click.option("--set-var-names", default="", help="Named field to set as index for var.", metavar="<name>")
+@click.option("--skip-qc", default=False, is_flag=True,
+              help="Do not run quality control metrics. By default cellxgene runs them "
+                   "(saved to adata.obs and adata.var; see scanpy.pp.calculate_qc_metrics for details).")
 @click.option(
-    "--run-qc/--skip-qc", default=True, is_flag=True,
-    help="Whether to calculate QC metrics (saved to adata.obs and adata.var). \
-    See scanpy.pp.calculate_qc_metrics for details.", show_default=True)
-@click.option(
-    "--make-obs-names-unique", default=True, is_flag=True, help="Ensure obs index is unique.", show_default=True
+    "--make-obs-names-unique",
+    default=True,
+    is_flag=True,
+    help="Ensure obs index is unique.",
+    show_default=True
 )
 @click.option(
-    "--make-var-names-unique", default=True, is_flag=True, help="Ensure var index is unique.", show_default=True
+    "--make-var-names-unique",
+    default=True,
+    is_flag=True,
+    help="Ensure var index is unique.",
+    show_default=True
 )
+@click.help_option("--help", "-h", help="Show this message and exit.")
 def prepare(
         data,
         embedding,
@@ -50,18 +63,18 @@ def prepare(
         overwrite,
         set_obs_names,
         set_var_names,
-        run_qc,
+        skip_qc,
         make_obs_names_unique,
         make_var_names_unique,
 ):
-    """Preprocesses data for use with cellxgene.
-
-    This tool runs a series of scanpy routines for preparing a dataset
-    for use with cellxgene. It loads data from different formats
+    """
+    Preprocess data for use with cellxgene.
+    This tool runs a series of scanpy routines for preparing a dataset for use
+    with cellxgene. It loads data from different formats
     (h5ad, loom, or a 10x directory), runs dimensionality reduction,
     computes nearest neighbors, computes an embedding, performs clustering,
-    and saves the results. Includes additional options for naming
-    annotations, ensuring sparsity, and plotting results."""
+    and saves the results. Includes additional options for naming annotations,
+    ensuring sparsity, and plotting results."""
 
     # collect slow imports here to make CLI startup more responsive
     click.echo("[cellxgene] Starting CLI...")
@@ -129,7 +142,7 @@ def prepare(
         return adata
 
     def calculate_qc_metrics(adata):
-        if run_qc:
+        if not skip_qc:
             sc.pp.calculate_qc_metrics(adata, inplace=True)
         return adata
 
@@ -179,7 +192,7 @@ def prepare(
                 sc.pl.tsne(adata, color="louvain", palette=palette, save="_louvain")
 
     def show_step(item):
-        if run_qc:
+        if not skip_qc:
             qc_name = "Calculating QC metrics"
         else:
             qc_name = "Skipping QC"
diff --git a/server/utils/utils.py b/server/utils/utils.py
index 239f45bd..417aeb7b 100644
--- a/server/utils/utils.py
+++ b/server/utils/utils.py
@@ -24,3 +24,12 @@ def is_port_available(host, port):
         except socket.error:
             pass
     return is_available
+
+
+def sort_options(command):
+    """
+    Helper for the click options - will sort options in a command, and can
+    be used as a decorator.
+    """
+    command.params.sort(key=lambda p: p.name)
+    return command

From 2d0b64695644f3e5662e252ab1f8fcedf1dd4ced Mon Sep 17 00:00:00 2001
From: Bruce Martin <bruce@chanzuckerberg.com>
Date: Mon, 18 Nov 2019 11:22:13 -0800
Subject: [PATCH 10/16] js dependency update (#1045)

---
 client/package-lock.json | 2839 ++++++++++++++++++++++++++++----------
 client/package.json      |   52 +-
 2 files changed, 2110 insertions(+), 781 deletions(-)

diff --git a/client/package-lock.json b/client/package-lock.json
index aedc7bf4..87a21c05 100644
--- a/client/package-lock.json
+++ b/client/package-lock.json
@@ -14,19 +14,19 @@
       }
     },
     "@babel/core": {
-      "version": "7.6.0",
-      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.6.0.tgz",
-      "integrity": "sha512-FuRhDRtsd6IptKpHXAa+4WPZYY2ZzgowkbLBecEDDSje1X/apG7jQM33or3NdOmjXBKWGOg4JmSiRfUfuTtHXw==",
+      "version": "7.7.2",
+      "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.7.2.tgz",
+      "integrity": "sha512-eeD7VEZKfhK1KUXGiyPFettgF3m513f8FoBSWiQ1xTvl1RAopLs42Wp9+Ze911I6H0N9lNqJMDgoZT7gHsipeQ==",
       "dev": true,
       "requires": {
         "@babel/code-frame": "^7.5.5",
-        "@babel/generator": "^7.6.0",
-        "@babel/helpers": "^7.6.0",
-        "@babel/parser": "^7.6.0",
-        "@babel/template": "^7.6.0",
-        "@babel/traverse": "^7.6.0",
-        "@babel/types": "^7.6.0",
-        "convert-source-map": "^1.1.0",
+        "@babel/generator": "^7.7.2",
+        "@babel/helpers": "^7.7.0",
+        "@babel/parser": "^7.7.2",
+        "@babel/template": "^7.7.0",
+        "@babel/traverse": "^7.7.2",
+        "@babel/types": "^7.7.2",
+        "convert-source-map": "^1.7.0",
         "debug": "^4.1.0",
         "json5": "^2.1.0",
         "lodash": "^4.17.13",
@@ -45,65 +45,84 @@
           }
         },
         "@babel/generator": {
-          "version": "7.6.0",
-          "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.6.0.tgz",
-          "integrity": "sha512-Ms8Mo7YBdMMn1BYuNtKuP/z0TgEIhbcyB8HVR6PPNYp4P61lMsABiS4A3VG1qznjXVCf3r+fVHhm4efTYVsySA==",
+          "version": "7.7.2",
+          "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.7.2.tgz",
+          "integrity": "sha512-WthSArvAjYLz4TcbKOi88me+KmDJdKSlfwwN8CnUYn9jBkzhq0ZEPuBfkAWIvjJ3AdEV1Cf/+eSQTnp3IDJKlQ==",
           "dev": true,
           "requires": {
-            "@babel/types": "^7.6.0",
+            "@babel/types": "^7.7.2",
             "jsesc": "^2.5.1",
             "lodash": "^4.17.13",
-            "source-map": "^0.5.0",
-            "trim-right": "^1.0.1"
+            "source-map": "^0.5.0"
+          }
+        },
+        "@babel/helper-function-name": {
+          "version": "7.7.0",
+          "resolved": "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.7.0.tgz",
+          "integrity": "sha512-tDsJgMUAP00Ugv8O2aGEua5I2apkaQO7lBGUq1ocwN3G23JE5Dcq0uh3GvFTChPa4b40AWiAsLvCZOA2rdnQ7Q==",
+          "dev": true,
+          "requires": {
+            "@babel/helper-get-function-arity": "^7.7.0",
+            "@babel/template": "^7.7.0",
+            "@babel/types": "^7.7.0"
+          }
+        },
+        "@babel/helper-get-function-arity": {
+          "version": "7.7.0",
+          "resolved": "https://registry.npmjs.org/@babel/helper-get-function-arity/-/helper-get-function-arity-7.7.0.tgz",
+          "integrity": "sha512-tLdojOTz4vWcEnHWHCuPN5P85JLZWbm5Fx5ZsMEMPhF3Uoe3O7awrbM2nQ04bDOUToH/2tH/ezKEOR8zEYzqyw==",
+          "dev": true,
+          "requires": {
+            "@babel/types": "^7.7.0"
           }
         },
         "@babel/helper-split-export-declaration": {
-          "version": "7.4.4",
-          "resolved": "https://registry.npmjs.org/@babel/helper-split-export-declaration/-/helper-split-export-declaration-7.4.4.tgz",
-          "integrity": "sha512-Ro/XkzLf3JFITkW6b+hNxzZ1n5OQ80NvIUdmHspih1XAhtN3vPTuUFT4eQnela+2MaZ5ulH+iyP513KJrxbN7Q==",
+          "version": "7.7.0",
+          "resolved": "https://registry.npmjs.org/@babel/helper-split-export-declaration/-/helper-split-export-declaration-7.7.0.tgz",
+          "integrity": "sha512-HgYSI8rH08neWlAH3CcdkFg9qX9YsZysZI5GD8LjhQib/mM0jGOZOVkoUiiV2Hu978fRtjtsGsW6w0pKHUWtqA==",
           "dev": true,
           "requires": {
-            "@babel/types": "^7.4.4"
+            "@babel/types": "^7.7.0"
           }
         },
         "@babel/parser": {
-          "version": "7.6.0",
-          "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.6.0.tgz",
-          "integrity": "sha512-+o2q111WEx4srBs7L9eJmcwi655eD8sXniLqMB93TBK9GrNzGrxDWSjiqz2hLU0Ha8MTXFIP0yd9fNdP+m43ZQ==",
+          "version": "7.7.3",
+          "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.7.3.tgz",
+          "integrity": "sha512-bqv+iCo9i+uLVbI0ILzKkvMorqxouI+GbV13ivcARXn9NNEabi2IEz912IgNpT/60BNXac5dgcfjb94NjsF33A==",
           "dev": true
         },
         "@babel/template": {
-          "version": "7.6.0",
-          "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.6.0.tgz",
-          "integrity": "sha512-5AEH2EXD8euCk446b7edmgFdub/qfH1SN6Nii3+fyXP807QRx9Q73A2N5hNwRRslC2H9sNzaFhsPubkS4L8oNQ==",
+          "version": "7.7.0",
+          "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.7.0.tgz",
+          "integrity": "sha512-OKcwSYOW1mhWbnTBgQY5lvg1Fxg+VyfQGjcBduZFljfc044J5iDlnDSfhQ867O17XHiSCxYHUxHg2b7ryitbUQ==",
           "dev": true,
           "requires": {
             "@babel/code-frame": "^7.0.0",
-            "@babel/parser": "^7.6.0",
-            "@babel/types": "^7.6.0"
+            "@babel/parser": "^7.7.0",
+            "@babel/types": "^7.7.0"
           }
         },
         "@babel/traverse": {
-          "version": "7.6.0",
-          "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.6.0.tgz",
-          "integrity": "sha512-93t52SaOBgml/xY74lsmt7xOR4ufYvhb5c5qiM6lu4J/dWGMAfAh6eKw4PjLes6DI6nQgearoxnFJk60YchpvQ==",
+          "version": "7.7.2",
+          "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.7.2.tgz",
+          "integrity": "sha512-TM01cXib2+rgIZrGJOLaHV/iZUAxf4A0dt5auY6KNZ+cm6aschuJGqKJM3ROTt3raPUdIDk9siAufIFEleRwtw==",
           "dev": true,
           "requires": {
             "@babel/code-frame": "^7.5.5",
-            "@babel/generator": "^7.6.0",
-            "@babel/helper-function-name": "^7.1.0",
-            "@babel/helper-split-export-declaration": "^7.4.4",
-            "@babel/parser": "^7.6.0",
-            "@babel/types": "^7.6.0",
+            "@babel/generator": "^7.7.2",
+            "@babel/helper-function-name": "^7.7.0",
+            "@babel/helper-split-export-declaration": "^7.7.0",
+            "@babel/parser": "^7.7.2",
+            "@babel/types": "^7.7.2",
             "debug": "^4.1.0",
             "globals": "^11.1.0",
             "lodash": "^4.17.13"
           }
         },
         "@babel/types": {
-          "version": "7.6.1",
-          "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.6.1.tgz",
-          "integrity": "sha512-X7gdiuaCmA0uRjCmRtYJNAVCc/q+5xSgsfKJHqMN4iNLILX39677fJE1O40arPMh0TTtS9ItH67yre6c7k6t0g==",
+          "version": "7.7.2",
+          "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.7.2.tgz",
+          "integrity": "sha512-YTf6PXoh3+eZgRCBzzP25Bugd2ngmpQVrk7kXX0i5N9BO7TFBtIgZYs7WtxtOGs8e6A4ZI7ECkbBCEHeXocvOA==",
           "dev": true,
           "requires": {
             "esutils": "^2.0.2",
@@ -111,6 +130,15 @@
             "to-fast-properties": "^2.0.0"
           }
         },
+        "convert-source-map": {
+          "version": "1.7.0",
+          "resolved": "https://registry.npmjs.org/convert-source-map/-/convert-source-map-1.7.0.tgz",
+          "integrity": "sha512-4FJkXzKXEDB1snCFZlLP4gpC3JILicCpGbzG9f9G7tGqGCzETQ2hWPrcinA9oU4wtf2biUaEH5065UnMeR33oA==",
+          "dev": true,
+          "requires": {
+            "safe-buffer": "~5.1.1"
+          }
+        },
         "debug": {
           "version": "4.1.1",
           "resolved": "https://registry.npmjs.org/debug/-/debug-4.1.1.tgz",
@@ -121,9 +149,9 @@
           }
         },
         "json5": {
-          "version": "2.1.0",
-          "resolved": "https://registry.npmjs.org/json5/-/json5-2.1.0.tgz",
-          "integrity": "sha512-8Mh9h6xViijj36g7Dxi+Y4S6hNGV96vcJZr/SrlHh1LR/pEn/8j/+qIBbs44YKl69Lrfctp4QD+AdWLTMqEZAQ==",
+          "version": "2.1.1",
+          "resolved": "https://registry.npmjs.org/json5/-/json5-2.1.1.tgz",
+          "integrity": "sha512-l+3HXD0GEI3huGq1njuqtzYK8OYJyXMkOLtQ53pjWh89tvWS2h6l+1zMkYWqlb57+SiQodKZyvMEFb2X+KrFhQ==",
           "dev": true,
           "requires": {
             "minimist": "^1.2.0"
@@ -160,34 +188,60 @@
       }
     },
     "@babel/helper-builder-binary-assignment-operator-visitor": {
-      "version": "7.1.0",
-      "resolved": "https://registry.npmjs.org/@babel/helper-builder-binary-assignment-operator-visitor/-/helper-builder-binary-assignment-operator-visitor-7.1.0.tgz",
-      "integrity": "sha512-qNSR4jrmJ8M1VMM9tibvyRAHXQs2PmaksQF7c1CGJNipfe3D8p+wgNwgso/P2A2r2mdgBWAXljNWR0QRZAMW8w==",
+      "version": "7.7.0",
+      "resolved": "https://registry.npmjs.org/@babel/helper-builder-binary-assignment-operator-visitor/-/helper-builder-binary-assignment-operator-visitor-7.7.0.tgz",
+      "integrity": "sha512-Cd8r8zs4RKDwMG/92lpZcnn5WPQ3LAMQbCw42oqUh4s7vsSN5ANUZjMel0OOnxDLq57hoDDbai+ryygYfCTOsw==",
       "dev": true,
       "requires": {
-        "@babel/helper-explode-assignable-expression": "^7.1.0",
-        "@babel/types": "^7.0.0"
+        "@babel/helper-explode-assignable-expression": "^7.7.0",
+        "@babel/types": "^7.7.0"
+      },
+      "dependencies": {
+        "@babel/types": {
+          "version": "7.7.2",
+          "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.7.2.tgz",
+          "integrity": "sha512-YTf6PXoh3+eZgRCBzzP25Bugd2ngmpQVrk7kXX0i5N9BO7TFBtIgZYs7WtxtOGs8e6A4ZI7ECkbBCEHeXocvOA==",
+          "dev": true,
+          "requires": {
+            "esutils": "^2.0.2",
+            "lodash": "^4.17.13",
+            "to-fast-properties": "^2.0.0"
+          }
+        }
       }
     },
     "@babel/helper-builder-react-jsx": {
-      "version": "7.0.0",
-      "resolved": "https://registry.npmjs.org/@babel/helper-builder-react-jsx/-/helper-builder-react-jsx-7.0.0.tgz",
-      "integrity": "sha512-ebJ2JM6NAKW0fQEqN8hOLxK84RbRz9OkUhGS/Xd5u56ejMfVbayJ4+LykERZCOUM6faa6Fp3SZNX3fcT16MKHw==",
+      "version": "7.7.0",
+      "resolved": "https://registry.npmjs.org/@babel/helper-builder-react-jsx/-/helper-builder-react-jsx-7.7.0.tgz",
+      "integrity": "sha512-LSln3cexwInTMYYoFeVLKnYPPMfWNJ8PubTBs3hkh7wCu9iBaqq1OOyW+xGmEdLxT1nhsl+9SJ+h2oUDYz0l2A==",
       "dev": true,
       "requires": {
-        "@babel/types": "^7.0.0",
+        "@babel/types": "^7.7.0",
         "esutils": "^2.0.0"
+      },
+      "dependencies": {
+        "@babel/types": {
+          "version": "7.7.2",
+          "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.7.2.tgz",
+          "integrity": "sha512-YTf6PXoh3+eZgRCBzzP25Bugd2ngmpQVrk7kXX0i5N9BO7TFBtIgZYs7WtxtOGs8e6A4ZI7ECkbBCEHeXocvOA==",
+          "dev": true,
+          "requires": {
+            "esutils": "^2.0.2",
+            "lodash": "^4.17.13",
+            "to-fast-properties": "^2.0.0"
+          }
+        }
       }
     },
     "@babel/helper-call-delegate": {
-      "version": "7.4.4",
-      "resolved": "https://registry.npmjs.org/@babel/helper-call-delegate/-/helper-call-delegate-7.4.4.tgz",
-      "integrity": "sha512-l79boDFJ8S1c5hvQvG+rc+wHw6IuH7YldmRKsYtpbawsxURu/paVy57FZMomGK22/JckepaikOkY0MoAmdyOlQ==",
+      "version": "7.7.0",
+      "resolved": "https://registry.npmjs.org/@babel/helper-call-delegate/-/helper-call-delegate-7.7.0.tgz",
+      "integrity": "sha512-Su0Mdq7uSSWGZayGMMQ+z6lnL00mMCnGAbO/R0ZO9odIdB/WNU/VfQKqMQU0fdIsxQYbRjDM4BixIa93SQIpvw==",
       "dev": true,
       "requires": {
-        "@babel/helper-hoist-variables": "^7.4.4",
-        "@babel/traverse": "^7.4.4",
-        "@babel/types": "^7.4.4"
+        "@babel/helper-hoist-variables": "^7.7.0",
+        "@babel/traverse": "^7.7.0",
+        "@babel/types": "^7.7.0"
       },
       "dependencies": {
         "@babel/code-frame": {
@@ -200,54 +254,84 @@
           }
         },
         "@babel/generator": {
-          "version": "7.6.0",
-          "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.6.0.tgz",
-          "integrity": "sha512-Ms8Mo7YBdMMn1BYuNtKuP/z0TgEIhbcyB8HVR6PPNYp4P61lMsABiS4A3VG1qznjXVCf3r+fVHhm4efTYVsySA==",
+          "version": "7.7.2",
+          "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.7.2.tgz",
+          "integrity": "sha512-WthSArvAjYLz4TcbKOi88me+KmDJdKSlfwwN8CnUYn9jBkzhq0ZEPuBfkAWIvjJ3AdEV1Cf/+eSQTnp3IDJKlQ==",
           "dev": true,
           "requires": {
-            "@babel/types": "^7.6.0",
+            "@babel/types": "^7.7.2",
             "jsesc": "^2.5.1",
             "lodash": "^4.17.13",
-            "source-map": "^0.5.0",
-            "trim-right": "^1.0.1"
+            "source-map": "^0.5.0"
+          }
+        },
+        "@babel/helper-function-name": {
+          "version": "7.7.0",
+          "resolved": "https://registry.npmjs.org/@babel/helper-function-name/-/helper-function-name-7.7.0.tgz",
+          "integrity": "sha512-tDsJgMUAP00Ugv8O2aGEua5I2apkaQO7lBGUq1ocwN3G23JE5Dcq0uh3GvFTChPa4b40AWiAsLvCZOA2rdnQ7Q==",
+          "dev": true,
+          "requires": {
+            "@babel/helper-get-function-arity": "^7.7.0",
+            "@babel/template": "^7.7.0",
+            "@babel/types": "^7.7.0"
+          }
+        },
+        "@babel/helper-get-function-arity": {
+          "version": "7.7.0",
+          "resolved": "https://registry.npmjs.org/@babel/helper-get-function-arity/-/helper-get-function-arity-7.7.0.tgz",
+          "integrity": "sha512-tLdojOTz4vWcEnHWHCuPN5P85JLZWbm5Fx5ZsMEMPhF3Uoe3O7awrbM2nQ04bDOUToH/2tH/ezKEOR8zEYzqyw==",
+          "dev": true,
+          "requires": {
+            "@babel/types": "^7.7.0"
           }
         },
         "@babel/helper-split-export-declaration": {
-          "version": "7.4.4",
-          "resolved": "https://registry.npmjs.org/@babel/helper-split-export-declaration/-/helper-split-export-declaration-7.4.4.tgz",
-          "integrity": "sha512-Ro/XkzLf3JFITkW6b+hNxzZ1n5OQ80NvIUdmHspih1XAhtN3vPTuUFT4eQnela+2MaZ5ulH+iyP513KJrxbN7Q==",
+          "version": "7.7.0",
+          "resolved": "https://registry.npmjs.org/@babel/helper-split-export-declaration/-/helper-split-export-declaration-7.7.0.tgz",
+          "integrity": "sha512-HgYSI8rH08neWlAH3CcdkFg9qX9YsZysZI5GD8LjhQib/mM0jGOZOVkoUiiV2Hu978fRtjtsGsW6w0pKHUWtqA==",
           "dev": true,
           "requires": {
-            "@babel/types": "^7.4.4"
+            "@babel/types": "^7.7.0"
           }
         },
         "@babel/parser": {
-          "version": "7.6.0",
-          "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.6.0.tgz",
-          "integrity": "sha512-+o2q111WEx4srBs7L9eJmcwi655eD8sXniLqMB93TBK9GrNzGrxDWSjiqz2hLU0Ha8MTXFIP0yd9fNdP+m43ZQ==",
+          "version": "7.7.3",
+          "resolved": "https://registry.npmjs.org/@babel/parser/-/parser-7.7.3.tgz",
+          "integrity": "sha512-bqv+iCo9i+uLVbI0ILzKkvMorqxouI+GbV13ivcARXn9NNEabi2IEz912IgNpT/60BNXac5dgcfjb94NjsF33A==",
           "dev": true
         },
+        "@babel/template": {
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+          "resolved": "https://registry.npmjs.org/@babel/template/-/template-7.7.0.tgz",
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@@ -6144,6 +7064,17 @@
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@@ -7576,32 +8526,86 @@
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-        "ansi-escapes": "^3.2.0",
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-        "figures": "^2.0.0",
-        "lodash": "^4.17.12",
-        "mute-stream": "0.0.7",
+        "figures": "^3.0.0",
+        "lodash": "^4.17.15",
+        "mute-stream": "0.0.8",
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-        "string-width": "^2.1.0",
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@@ -7609,6 +8613,14 @@
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+            }
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@@ -8209,6 +9221,19 @@
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             "realpath-native": "^1.1.0",
             "yargs": "^13.3.0"
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+          "dependencies": {
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+              "dev": true,
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+                "escape-string-regexp": "^1.0.5",
+                "supports-color": "^5.3.0"
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@@ -8273,6 +9298,19 @@
         "micromatch": "^3.1.10",
         "pretty-format": "^24.9.0",
         "realpath-native": "^1.1.0"
+      },
+      "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
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+          "dev": true,
+          "requires": {
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+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
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@@ -8288,6 +9326,19 @@
         "spawnd": "^4.0.0",
         "tree-kill": "^1.2.1",
         "wait-on": "^3.3.0"
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+      "dependencies": {
+        "chalk": {
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+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
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+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
+          }
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@@ -8300,6 +9351,19 @@
         "diff-sequences": "^24.9.0",
         "jest-get-type": "^24.9.0",
         "pretty-format": "^24.9.0"
+      },
+      "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
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+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
+          }
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@@ -8322,6 +9386,19 @@
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         "jest-util": "^24.9.0",
         "pretty-format": "^24.9.0"
+      },
+      "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
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+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
+          }
+        }
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@@ -8361,6 +9438,19 @@
         "cwd": "^0.10.0",
         "jest-dev-server": "^4.3.0",
         "merge-deep": "^3.0.2"
+      },
+      "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
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+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
+          }
+        }
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@@ -8419,6 +9509,19 @@
         "jest-util": "^24.9.0",
         "pretty-format": "^24.9.0",
         "throat": "^4.0.0"
+      },
+      "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
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+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
+          }
+        }
       }
     },
     "jest-leak-detector": {
@@ -8441,6 +9544,19 @@
         "jest-diff": "^24.9.0",
         "jest-get-type": "^24.9.0",
         "pretty-format": "^24.9.0"
+      },
+      "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
+          "integrity": "sha512-Mti+f9lpJNcwF4tWV8/OrTTtF1gZi+f8FqlyAdouralcFWFQWF2+NgCHShjkCb+IFBLq9buZwE1xckQU4peSuQ==",
+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
+          }
+        }
       }
     },
     "jest-message-util": {
@@ -8459,6 +9575,17 @@
         "stack-utils": "^1.0.1"
       },
       "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
+          "integrity": "sha512-Mti+f9lpJNcwF4tWV8/OrTTtF1gZi+f8FqlyAdouralcFWFQWF2+NgCHShjkCb+IFBLq9buZwE1xckQU4peSuQ==",
+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
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           "resolved": "https://registry.npmjs.org/slash/-/slash-2.0.0.tgz",
@@ -8509,6 +9636,19 @@
         "chalk": "^2.0.1",
         "jest-pnp-resolver": "^1.2.1",
         "realpath-native": "^1.1.0"
+      },
+      "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
+          "integrity": "sha512-Mti+f9lpJNcwF4tWV8/OrTTtF1gZi+f8FqlyAdouralcFWFQWF2+NgCHShjkCb+IFBLq9buZwE1xckQU4peSuQ==",
+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
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     "jest-resolve-dependencies": {
@@ -8549,6 +9689,17 @@
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       },
       "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
+          "integrity": "sha512-Mti+f9lpJNcwF4tWV8/OrTTtF1gZi+f8FqlyAdouralcFWFQWF2+NgCHShjkCb+IFBLq9buZwE1xckQU4peSuQ==",
+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
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         "graceful-fs": {
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           "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.2.tgz",
@@ -8588,6 +9739,17 @@
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       },
       "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
+          "integrity": "sha512-Mti+f9lpJNcwF4tWV8/OrTTtF1gZi+f8FqlyAdouralcFWFQWF2+NgCHShjkCb+IFBLq9buZwE1xckQU4peSuQ==",
+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
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           "version": "4.2.2",
           "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.2.tgz",
@@ -8635,6 +9797,17 @@
         "semver": "^6.2.0"
       },
       "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
+          "integrity": "sha512-Mti+f9lpJNcwF4tWV8/OrTTtF1gZi+f8FqlyAdouralcFWFQWF2+NgCHShjkCb+IFBLq9buZwE1xckQU4peSuQ==",
+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
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           "version": "6.3.0",
           "resolved": "https://registry.npmjs.org/semver/-/semver-6.3.0.tgz",
@@ -8663,6 +9836,17 @@
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       },
       "dependencies": {
+        "chalk": {
+          "version": "2.4.2",
+          "resolved": "https://registry.npmjs.org/chalk/-/chalk-2.4.2.tgz",
+          "integrity": "sha512-Mti+f9lpJNcwF4tWV8/OrTTtF1gZi+f8FqlyAdouralcFWFQWF2+NgCHShjkCb+IFBLq9buZwE1xckQU4peSuQ==",
+          "dev": true,
+          "requires": {
+            "ansi-styles": "^3.2.1",
+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
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         "ci-info": {
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           "resolved": "https://registry.npmjs.org/ci-info/-/ci-info-2.0.0.tgz",
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+            "escape-string-regexp": "^1.0.5",
+            "supports-color": "^5.3.0"
+          },
+          "dependencies": {
+            "supports-color": {
+              "version": "5.5.0",
+              "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-5.5.0.tgz",
+              "integrity": "sha512-QjVjwdXIt408MIiAqCX4oUKsgU2EqAGzs2Ppkm4aQYbjm+ZEWEcW4SfFNTr4uMNZma0ey4f5lgLrkB0aX0QMow==",
+              "dev": true,
+              "requires": {
+                "has-flag": "^3.0.0"
+              }
+            }
+          }
+        },
+        "enhanced-resolve": {
+          "version": "4.1.0",
+          "resolved": "https://registry.npmjs.org/enhanced-resolve/-/enhanced-resolve-4.1.0.tgz",
+          "integrity": "sha512-F/7vkyTtyc/llOIn8oWclcB25KdRaiPBpZYDgJHgh/UHtpgT2p2eldQgtQnLtUvfMKPKxbRaQM/hHkvLHt1Vng==",
+          "dev": true,
+          "requires": {
+            "graceful-fs": "^4.1.2",
+            "memory-fs": "^0.4.0",
+            "tapable": "^1.0.0"
+          }
+        },
         "global-modules": {
           "version": "2.0.0",
           "resolved": "https://registry.npmjs.org/global-modules/-/global-modules-2.0.0.tgz",
@@ -13667,9 +14996,9 @@
       }
     },
     "webpack-dev-middleware": {
-      "version": "3.7.1",
-      "resolved": "https://registry.npmjs.org/webpack-dev-middleware/-/webpack-dev-middleware-3.7.1.tgz",
-      "integrity": "sha512-5MWu9SH1z3hY7oHOV6Kbkz5x7hXbxK56mGHNqHTe6d+ewxOwKUxoUJBs7QIaJb33lPjl9bJZ3X0vCoooUzC36A==",
+      "version": "3.7.2",
+      "resolved": "https://registry.npmjs.org/webpack-dev-middleware/-/webpack-dev-middleware-3.7.2.tgz",
+      "integrity": "sha512-1xC42LxbYoqLNAhV6YzTYacicgMZQTqRd27Sim9wn5hJrX3I5nxYy1SxSd4+gjUFsz1dQFj+yEe6zEVmSkeJjw==",
       "dev": true,
       "requires": {
         "memory-fs": "^0.4.1",
diff --git a/client/package.json b/client/package.json
index d7f980e3..8861b786 100644
--- a/client/package.json
+++ b/client/package.json
@@ -45,48 +45,48 @@
     "is-number": "^7.0.0",
     "lodash": "^4.17.15",
     "memoize-one": "^5.1.1",
-    "react": "^16.9.0",
+    "react": "^16.11.0",
     "react-autocomplete": "^1.7.2",
-    "react-dom": "^16.9.0",
+    "react-dom": "^16.11.0",
     "react-flip-toolkit": "7.0.6",
     "react-helmet": "^5.2.1",
-    "react-icons": "^3.7.0",
-    "react-redux": "^7.1.1",
+    "react-icons": "^3.8.0",
+    "react-redux": "^7.1.3",
     "redux": "^4.0.4",
     "redux-thunk": "^2.2.0",
     "regl": "^1.3.13"
   },
   "devDependencies": {
-    "@babel/core": "^7.6.0",
-    "@babel/plugin-proposal-class-properties": "^7.5.5",
-    "@babel/plugin-proposal-decorators": "^7.6.0",
+    "@babel/core": "^7.7.2",
+    "@babel/plugin-proposal-class-properties": "^7.7.0",
+    "@babel/plugin-proposal-decorators": "^7.7.0",
     "@babel/plugin-proposal-export-namespace-from": "^7.5.2",
     "@babel/plugin-proposal-function-bind": "^7.2.0",
     "@babel/plugin-proposal-nullish-coalescing-operator": "^7.4.4",
     "@babel/plugin-proposal-optional-chaining": "^7.6.0",
-    "@babel/plugin-transform-react-constant-elements": "^7.6.0",
-    "@babel/plugin-transform-runtime": "^7.6.0",
-    "@babel/preset-env": "^7.6.0",
-    "@babel/preset-react": "^7.0.0",
-    "@babel/register": "^7.6.0",
-    "@babel/runtime": "^7.6.0",
+    "@babel/plugin-transform-react-constant-elements": "^7.6.3",
+    "@babel/plugin-transform-runtime": "^7.6.2",
+    "@babel/preset-env": "^7.7.1",
+    "@babel/preset-react": "^7.7.0",
+    "@babel/register": "^7.7.0",
+    "@babel/runtime": "^7.7.2",
     "babel-eslint": "^10.0.3",
     "babel-jest": "^24.9.0",
     "babel-loader": "^8.0.6",
     "babel-preset-modern-browsers": "^14.0.0",
-    "chalk": "^2.4.2",
+    "chalk": "^3.0.0",
     "connect-history-api-fallback": "^1.6.0",
-    "copy-webpack-plugin": "^5.0.4",
+    "copy-webpack-plugin": "^5.0.5",
     "css-loader": "^3.2.0",
-    "eslint": "^6.4.0",
+    "eslint": "^6.6.0",
     "eslint-config-airbnb": "^18.0.1",
-    "eslint-config-prettier": "^6.3.0",
-    "eslint-loader": "^3.0.0",
+    "eslint-config-prettier": "^6.5.0",
+    "eslint-loader": "^3.0.2",
     "eslint-plugin-filenames": "^1.3.2",
     "eslint-plugin-import": "^2.18.2",
-    "eslint-plugin-jest": "^22.17.0",
+    "eslint-plugin-jest": "^23.0.4",
     "eslint-plugin-jsx-a11y": "^6.2.3",
-    "eslint-plugin-react": "^7.14.3",
+    "eslint-plugin-react": "^7.16.0",
     "express": "^4.17.1",
     "file-loader": "^4.2.0",
     "html-webpack-inline-source-plugin": "0.0.10",
@@ -95,16 +95,16 @@
     "jest-puppeteer": "^4.3.0",
     "json-loader": "^0.5.4",
     "mini-css-extract-plugin": "^0.8.0",
-    "puppeteer": "^1.20.0",
+    "puppeteer": "^2.0.0",
     "rimraf": "^3.0.0",
     "serve-favicon": "^2.3.0",
-    "start-server-and-test": "^1.10.2",
+    "start-server-and-test": "^1.10.6",
     "style-loader": "^1.0.0",
     "sw-precache-webpack-plugin": "^0.11.5",
-    "url-loader": "^2.1.0",
-    "webpack": "^4.40.2",
-    "webpack-cli": "^3.3.8",
-    "webpack-dev-middleware": "^3.7.1"
+    "url-loader": "^2.2.0",
+    "webpack": "^4.41.2",
+    "webpack-cli": "^3.3.10",
+    "webpack-dev-middleware": "^3.7.2"
   },
   "jest": {
     "testMatch": [

From cf8f1a710d344b8241d6fb793c07701298b478dd Mon Sep 17 00:00:00 2001
From: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
Date: Mon, 18 Nov 2019 12:41:58 -0800
Subject: [PATCH 11/16] add padding to scatterplot shift (#1043)

---
 client/src/components/scatterplot/scatterplot.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/scatterplot/scatterplot.js b/client/src/components/scatterplot/scatterplot.js
index 781aa9b7..90016859 100644
--- a/client/src/components/scatterplot/scatterplot.js
+++ b/client/src/components/scatterplot/scatterplot.js
@@ -381,7 +381,7 @@ class Scatterplot extends React.PureComponent {
       <div
         style={{
           position: "fixed",
-          bottom: minimized ? -height + -margin.top : 0,
+          bottom: minimized ? -height + -margin.top - 2 : 0,
           borderRadius: "3px 3px 0px 0px",
           left: globals.leftSidebarWidth + globals.scatterplotMarginLeft,
           padding: "0px 20px 20px 0px",

From bd5f816d58eec2054312f0f2bd32ffebed9d584e Mon Sep 17 00:00:00 2001
From: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
Date: Mon, 18 Nov 2019 12:42:55 -0800
Subject: [PATCH 12/16] fix dataset title clipping (#1040)

---
 client/src/components/leftSidebar/topLeftLogoAndTitle.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/client/src/components/leftSidebar/topLeftLogoAndTitle.js b/client/src/components/leftSidebar/topLeftLogoAndTitle.js
index be56e531..51f9972f 100644
--- a/client/src/components/leftSidebar/topLeftLogoAndTitle.js
+++ b/client/src/components/leftSidebar/topLeftLogoAndTitle.js
@@ -74,7 +74,7 @@ class LeftSideBar extends React.Component {
             display: "inline-block",
             width: "190px",
             marginLeft: "7px",
-            height: "1.1em",
+            height: "1.2em",
             overflow: "hidden",
             wordBreak: "break-all"
           }}

From 5968da18b4894a8d9ed3ba42e24fd3b3dcb944d0 Mon Sep 17 00:00:00 2001
From: Severiano Badajoz <sbadajoz@chanzuckerberg.com>
Date: Mon, 18 Nov 2019 12:43:16 -0800
Subject: [PATCH 13/16] fix inconsistent sidebar value height(#1039)

---
 client/src/components/categorical/value.js | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/client/src/components/categorical/value.js b/client/src/components/categorical/value.js
index afcb4455..60b07e19 100644
--- a/client/src/components/categorical/value.js
+++ b/client/src/components/categorical/value.js
@@ -478,16 +478,19 @@ class CategoryValue extends React.Component {
                         data-testclass="handleDeleteValue"
                         data-testid={`handleDeleteValue-${metadataField}`}
                         onClick={this.handleDeleteValue}
-                        text={`Delete this label, and reassign all cells to type '${
-                          globals.unassignedCategoryLabel
-                        }'`}
+                        text={`Delete this label, and reassign all cells to type '${globals.unassignedCategoryLabel}'`}
                       />
                     ) : null}
                   </Menu>
                 }
               >
                 <Button
-                  style={{ marginLeft: 0, position: "relative", top: -1 }}
+                  style={{
+                    marginLeft: 0,
+                    position: "relative",
+                    top: -1,
+                    minHeight: 16
+                  }}
                   data-testclass="seeActions"
                   data-testid={`seeActions-${metadataField}`}
                   icon="more"

From 9a540a4f0a94f69daf1ccfc3df0336a58644f61f Mon Sep 17 00:00:00 2001
From: Bruce Martin <bruce@chanzuckerberg.com>
Date: Tue, 19 Nov 2019 11:11:19 -0800
Subject: [PATCH 14/16] fix erroneous state clearing (#1052)

---
 client/src/util/typedCrossfilter/crossfilter.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/client/src/util/typedCrossfilter/crossfilter.js b/client/src/util/typedCrossfilter/crossfilter.js
index 79244055..4bd12188 100644
--- a/client/src/util/typedCrossfilter/crossfilter.js
+++ b/client/src/util/typedCrossfilter/crossfilter.js
@@ -62,7 +62,7 @@ export default class ImmutableTypedCrossfilter {
 
   setData(data) {
     const { selectionCache } = this;
-    this.selectionCache = null;
+    this.selectionCache = {};
     return new ImmutableTypedCrossfilter(data, this.dimensions, selectionCache);
   }
 
@@ -159,7 +159,7 @@ export default class ImmutableTypedCrossfilter {
       select("blort", {mode: "range", lo: 0, hi: 999.99});
     */
     const { data, selectionCache } = this;
-    this.selectionCache = null;
+    this.selectionCache = {};
     const dimensions = { ...this.dimensions };
     const { dim, id, selection: oldSelection } = dimensions[name];
     const newSelection = dim.select(spec);

From ee62dd355faec6bd79fc7018639953fc1041aab8 Mon Sep 17 00:00:00 2001
From: Bruce Martin <bruce@chanzuckerberg.com>
Date: Thu, 21 Nov 2019 14:10:02 -0800
Subject: [PATCH 15/16] [WIP] JS lint and dead code removal (#1053)

* lint and dead code removal

* fix regressions
---
 .../components/brushableHistogram/index.js    |  64 +++++-----
 .../src/components/categorical/categorical.js |   4 +-
 client/src/components/categorical/category.js |  10 +-
 .../src/components/categorical/occupancy.js   |   4 +-
 client/src/components/categorical/value.js    |   5 +-
 .../src/components/continuous/continuous.js   |  11 +-
 .../src/components/framework/custom-icons.js  |  16 ---
 client/src/components/geneExpression/index.js | 113 +++++++++---------
 client/src/components/leftSidebar/index.js    |   2 -
 client/src/components/menubar/index.js        |  10 +-
 client/src/components/rightSidebar/index.js   |  12 +-
 client/src/reducers/centroidLabel.js          |  11 +-
 client/src/reducers/colors.js                 |   2 +-
 client/src/util/centroid.js                   |   3 +
 .../util/stateManager/annotationsHelpers.js   |   2 +-
 .../src/util/typedCrossfilter/crossfilter.js  |   4 +-
 16 files changed, 118 insertions(+), 155 deletions(-)
 delete mode 100644 client/src/components/framework/custom-icons.js

diff --git a/client/src/components/brushableHistogram/index.js b/client/src/components/brushableHistogram/index.js
index 58379b20..8f5755d1 100644
--- a/client/src/components/brushableHistogram/index.js
+++ b/client/src/components/brushableHistogram/index.js
@@ -44,7 +44,7 @@ class HistogramBrush extends React.PureComponent {
     return varData.col(field);
   }
 
-  calcHistogramCache = memoize((col, field) => {
+  calcHistogramCache = memoize(col => {
     /*
      recalculate expensive stuff, notably bins, summaries, etc.
     */
@@ -240,15 +240,23 @@ class HistogramBrush extends React.PureComponent {
     };
   }
 
-  drawHistogram(svgRef) {
-    const { field, world } = this.props;
-    const col = HistogramBrush.getColumn(world, field);
-    const histogramCache = this.calcHistogramCache(col, field);
-    const { x, y, bins } = histogramCache;
-    this._histogram = { x, y, bins, svgRef };
-  }
+  handleSetGeneAsScatterplotX = () => {
+    const { dispatch, field } = this.props;
+    dispatch({
+      type: "set scatterplot x",
+      data: field
+    });
+  };
 
-  handleColorAction() {
+  handleSetGeneAsScatterplotY = () => {
+    const { dispatch, field } = this.props;
+    dispatch({
+      type: "set scatterplot y",
+      data: field
+    });
+  };
+
+  handleColorAction = () => {
     const { dispatch, field, world, ranges } = this.props;
 
     if (world.obsAnnotations.hasCol(field)) {
@@ -260,9 +268,9 @@ class HistogramBrush extends React.PureComponent {
     } else if (world.varData.hasCol(field)) {
       dispatch(actions.requestSingleGeneExpressionCountsForColoringPOST(field));
     }
-  }
+  };
 
-  removeHistogram() {
+  removeHistogram = () => {
     const {
       dispatch,
       field,
@@ -291,26 +299,14 @@ class HistogramBrush extends React.PureComponent {
         data: null
       });
     }
-  }
+  };
 
-  handleSetGeneAsScatterplotX() {
-    return () => {
-      const { dispatch, field } = this.props;
-      dispatch({
-        type: "set scatterplot x",
-        data: field
-      });
-    };
-  }
-
-  handleSetGeneAsScatterplotY() {
-    return () => {
-      const { dispatch, field } = this.props;
-      dispatch({
-        type: "set scatterplot y",
-        data: field
-      });
-    };
+  drawHistogram(svgRef) {
+    const { field, world } = this.props;
+    const col = HistogramBrush.getColumn(world, field);
+    const histogramCache = this.calcHistogramCache(col);
+    const { x, y, bins } = histogramCache;
+    this._histogram = { x, y, bins, svgRef };
   }
 
   renderAxesBrushBins(x, y, bins, svgRef, field) {
@@ -439,7 +435,7 @@ class HistogramBrush extends React.PureComponent {
               <ButtonGroup style={{ marginRight: 7 }}>
                 <Button
                   data-testid={`plot-x-${field}`}
-                  onClick={this.handleSetGeneAsScatterplotX(field).bind(this)}
+                  onClick={this.handleSetGeneAsScatterplotX}
                   active={scatterplotXXaccessor === field}
                   intent={scatterplotXXaccessor === field ? "primary" : "none"}
                 >
@@ -447,7 +443,7 @@ class HistogramBrush extends React.PureComponent {
                 </Button>
                 <Button
                   data-testid={`plot-y-${field}`}
-                  onClick={this.handleSetGeneAsScatterplotY(field).bind(this)}
+                  onClick={this.handleSetGeneAsScatterplotY}
                   active={scatterplotYYaccessor === field}
                   intent={scatterplotYYaccessor === field ? "primary" : "none"}
                 >
@@ -459,7 +455,7 @@ class HistogramBrush extends React.PureComponent {
           {isUserDefined ? (
             <Button
               minimal
-              onClick={this.removeHistogram.bind(this)}
+              onClick={this.removeHistogram}
               style={{
                 color: globals.blue,
                 cursor: "pointer",
@@ -475,7 +471,7 @@ class HistogramBrush extends React.PureComponent {
             hoverOpenDelay={globals.tooltipHoverOpenDelay}
           >
             <Button
-              onClick={this.handleColorAction.bind(this)}
+              onClick={this.handleColorAction}
               active={colorAccessor === field}
               intent={colorAccessor === field ? "primary" : "none"}
               data-testclass="colorby"
diff --git a/client/src/components/categorical/categorical.js b/client/src/components/categorical/categorical.js
index d9948a5d..37574027 100644
--- a/client/src/components/categorical/categorical.js
+++ b/client/src/components/categorical/categorical.js
@@ -83,7 +83,7 @@ class Categories extends React.Component {
 
   categoryNameErrorMessage = name => {
     const err = this.categoryNameError(name);
-    if (err == "duplicate") {
+    if (err === "duplicate") {
       return (
         <span>
           <span style={{ fontStyle: "italic" }}>{name}</span> already exists -
@@ -91,7 +91,7 @@ class Categories extends React.Component {
         </span>
       );
     }
-    if (err == "characters") {
+    if (err === "characters") {
       return (
         <span>
           <span style={{ fontStyle: "italic" }}>{name}</span> contains illegal
diff --git a/client/src/components/categorical/category.js b/client/src/components/categorical/category.js
index 078fc384..a966025d 100644
--- a/client/src/components/categorical/category.js
+++ b/client/src/components/categorical/category.js
@@ -149,7 +149,7 @@ class Category extends React.Component {
     or return an error type.
     */
     const { metadataField, universe } = this.props;
-    const obsByName = universe.schema.annotations.obsByName;
+    const { obsByName } = universe.schema.annotations;
 
     if (obsByName[metadataField].categories.indexOf(name) !== -1) {
       return "duplicate";
@@ -165,7 +165,7 @@ class Category extends React.Component {
   labelNameErrorMessage = name => {
     const { metadataField } = this.props;
     const err = this.labelNameError(name);
-    if (err == "duplicate") {
+    if (err === "duplicate") {
       return (
         <span>
           <span style={{ fontStyle: "italic" }}>{name}</span> already exists
@@ -174,7 +174,7 @@ class Category extends React.Component {
         </span>
       );
     }
-    if (err == "characters") {
+    if (err === "characters") {
       return (
         <span>
           <span style={{ fontStyle: "italic" }}>{name}</span> contains illegal
@@ -242,8 +242,7 @@ class Category extends React.Component {
       colorAccessor,
       categoricalSelection,
       isUserAnno,
-      annotations,
-      universe
+      annotations
     } = this.props;
     const { isTruncated } = categoricalSelection[metadataField];
 
@@ -288,7 +287,6 @@ class Category extends React.Component {
                 type="checkbox"
               />
               <span className="bp3-control-indicator" />
-              {""}
             </label>
             <span
               data-testid={`category-expand-${metadataField}`}
diff --git a/client/src/components/categorical/occupancy.js b/client/src/components/categorical/occupancy.js
index 68f6e269..fdf7a2b1 100644
--- a/client/src/components/categorical/occupancy.js
+++ b/client/src/components/categorical/occupancy.js
@@ -144,7 +144,9 @@ class Occupancy extends React.Component {
       categoryIndex
     } = this.props;
 
-    this.canvas?.getContext("2d").clearRect(0, 0, this._WIDTH, this._HEIGHT);
+    const { canvas } = this;
+    if (canvas)
+      canvas.getContext("2d").clearRect(0, 0, this._WIDTH, this._HEIGHT);
 
     const colorByIsCatagoricalData = !!categoricalSelection[colorAccessor];
 
diff --git a/client/src/components/categorical/value.js b/client/src/components/categorical/value.js
index 60b07e19..090550df 100644
--- a/client/src/components/categorical/value.js
+++ b/client/src/components/categorical/value.js
@@ -9,13 +9,12 @@ import {
   MenuItem,
   Popover,
   Position,
-  Icon,
-  PopoverInteractionKind
+  PopoverInteractionKind,
+  Tooltip
 } from "@blueprintjs/core";
 import Occupancy from "./occupancy";
 import * as globals from "../../globals";
 import styles from "./categorical.css";
-import { Tooltip } from "@blueprintjs/core";
 
 import { AnnotationsHelpers } from "../../util/stateManager";
 
diff --git a/client/src/components/continuous/continuous.js b/client/src/components/continuous/continuous.js
index ef3b4409..3e9c8831 100644
--- a/client/src/components/continuous/continuous.js
+++ b/client/src/components/continuous/continuous.js
@@ -25,7 +25,7 @@ class Continuous extends React.Component {
 
   componentDidUpdate() {}
 
-  handleColorAction(key) {
+  handleColorAction = key => {
     return () => {
       const { dispatch, obsAnnotations } = this.props;
       const summary = obsAnnotations.col(key).summarize();
@@ -35,7 +35,7 @@ class Continuous extends React.Component {
         rangeForColorAccessor: summary
       });
     };
-  }
+  };
 
   render() {
     const { obsAnnotations, schema } = this.props;
@@ -54,10 +54,11 @@ class Continuous extends React.Component {
       <div>
         {this.hasContinuous ? (
           <p
-            style={Object.assign({}, globals.leftSidebarSectionHeading, {
+            style={{
+              ...globals.leftSidebarSectionHeading,
               marginTop: 40,
               paddingLeft: globals.leftSidebarSectionPadding
-            })}
+            }}
           >
             Continuous metadata
           </p>
@@ -84,7 +85,7 @@ class Continuous extends React.Component {
                     isObs
                     zebra={zebra % 2 === 0}
                     ranges={summary}
-                    handleColorAction={this.handleColorAction(key).bind(this)}
+                    handleColorAction={this.handleColorAction(key)}
                   />
                 );
               }
diff --git a/client/src/components/framework/custom-icons.js b/client/src/components/framework/custom-icons.js
deleted file mode 100644
index a6a41335..00000000
--- a/client/src/components/framework/custom-icons.js
+++ /dev/null
@@ -1,16 +0,0 @@
-/* https://github.com/palantir/blueprint/issues/2348 */
-
-<defs>
-<clipPath id="clip0">
-<rect width="16" height="16" fill="white"/>
-</clipPath>
-</defs>
-<g clip-path="url(#clip0)">
-<rect width="16" height="16" fill="white"/>
-<path d="M1.33415 8.75877C0.939491 8.36411 0.727699 7.82249 0.749957 7.2648L0.926361 2.84501C0.967947 1.80308 1.80308 0.967947 2.84501 0.926361L7.2648 0.749958C7.82249 0.727699 8.36411 0.939492 8.75877 1.33415L14.3595 6.93485C15.1405 7.7159 15.1405 8.98223 14.3595 9.76328L9.76328 14.3595C8.98223 15.1405 7.7159 15.1405 6.93485 14.3595L1.33415 8.75877Z" fill="black"/>
-<circle cx="4.5" cy="4.5" r="1.5" fill="white"/>
-<circle cx="4.5" cy="11.5" r="3.75" stroke="white" stroke-width="0.5"/>
-<circle cx="4.5" cy="11.5" r="3.5" fill="black"/>
-<line x1="4.5" y1="10" x2="4.5" y2="13" stroke="white"/>
-<line x1="3" y1="11.5" x2="6" y2="11.5" stroke="white"/>
-</g>
diff --git a/client/src/components/geneExpression/index.js b/client/src/components/geneExpression/index.js
index 49d2fd36..2af9455a 100644
--- a/client/src/components/geneExpression/index.js
+++ b/client/src/components/geneExpression/index.js
@@ -24,7 +24,7 @@ import {
 
 import { memoize } from "../../util/dataframe/util";
 
-const renderGene = (fuzzySortResult, { handleClick, modifiers, query }) => {
+const renderGene = (fuzzySortResult, { handleClick, modifiers }) => {
   if (!modifiers.matchesPredicate) {
     return null;
   }
@@ -89,6 +89,59 @@ class GeneExpression extends React.Component {
   // eslint-disable-next-line react/sort-comp
   _memoGenesToUpper = memoize(this._genesToUpper, arr => arr);
 
+  handleBulkAddClick = () => {
+    const { world, dispatch, userDefinedGenes } = this.props;
+    const varIndexName = world.schema.annotations.var.index;
+    const { bulkAdd } = this.state;
+
+    /*
+      test:
+      Apod,,, Cd74,,    ,,,    Foo,    Bar-2,,
+    */
+    if (bulkAdd !== "") {
+      const genes = _.pull(_.uniq(bulkAdd.split(/[ ,]+/)), "");
+      if (genes.length === 0) {
+        return keepAroundErrorToast("Must enter a gene name.");
+      }
+      const worldGenes = world.varAnnotations.col(varIndexName).asArray();
+
+      // These gene lists are unique enough where memoization is useless
+      const upperGenes = this._genesToUpper(genes);
+      const upperUserDefinedGenes = this._genesToUpper(userDefinedGenes);
+
+      const upperWorldGenes = this._memoGenesToUpper(worldGenes);
+
+      dispatch({ type: "bulk user defined gene start" });
+
+      Promise.all(
+        [...upperGenes.keys()].map(upperGene => {
+          if (upperUserDefinedGenes.get(upperGene) !== undefined) {
+            return keepAroundErrorToast("That gene already exists");
+          }
+
+          const indexOfGene = upperWorldGenes.get(upperGene);
+
+          if (indexOfGene === undefined) {
+            return keepAroundErrorToast(
+              `${
+                genes[upperGenes.get(upperGene)]
+              } doesn't appear to be a valid gene name.`
+            );
+          }
+          return dispatch(
+            actions.requestUserDefinedGene(worldGenes[indexOfGene])
+          );
+        })
+      ).then(
+        () => dispatch({ type: "bulk user defined gene complete" }),
+        () => dispatch({ type: "bulk user defined gene error" })
+      );
+    }
+
+    this.setState({ bulkAdd: "" });
+    return undefined;
+  };
+
   placeholderGeneNames() {
     /*
     return a string containing gene name suggestions for use as a user hint.
@@ -145,58 +198,6 @@ class GeneExpression extends React.Component {
     }
   }
 
-  handleBulkAddClick() {
-    const { world, dispatch, userDefinedGenes } = this.props;
-    const varIndexName = world.schema.annotations.var.index;
-    const { bulkAdd } = this.state;
-
-    /*
-      test:
-      Apod,,, Cd74,,    ,,,    Foo,    Bar-2,,
-    */
-    if (bulkAdd !== "") {
-      const genes = _.pull(_.uniq(bulkAdd.split(/[ ,]+/)), "");
-      if (genes.length === 0) {
-        return keepAroundErrorToast("Must enter a gene name.");
-      }
-      const worldGenes = world.varAnnotations.col(varIndexName).asArray();
-
-      // These gene lists are unique enough where memoization is useless
-      const upperGenes = this._genesToUpper(genes);
-      const upperUserDefinedGenes = this._genesToUpper(userDefinedGenes);
-
-      const upperWorldGenes = this._memoGenesToUpper(worldGenes);
-
-      dispatch({ type: "bulk user defined gene start" });
-
-      Promise.all(
-        [...upperGenes.keys()].map(upperGene => {
-          if (upperUserDefinedGenes.get(upperGene) !== undefined) {
-            return keepAroundErrorToast("That gene already exists");
-          }
-
-          const indexOfGene = upperWorldGenes.get(upperGene);
-
-          if (indexOfGene === undefined) {
-            return keepAroundErrorToast(
-              `${
-                genes[upperGenes.get(upperGene)]
-              } doesn't appear to be a valid gene name.`
-            );
-          }
-          return dispatch(
-            actions.requestUserDefinedGene(worldGenes[indexOfGene])
-          );
-        })
-      ).then(
-        () => dispatch({ type: "bulk user defined gene complete" }),
-        () => dispatch({ type: "bulk user defined gene error" })
-      );
-    }
-
-    this.setState({ bulkAdd: "" });
-  }
-
   render() {
     const {
       world,
@@ -261,7 +262,7 @@ class GeneExpression extends React.Component {
                 }}
                 initialContent={<MenuItem disabled text="Enter a gene…" />}
                 inputProps={{ "data-testid": "gene-search" }}
-                inputValueRenderer={g => {
+                inputValueRenderer={() => {
                   return "";
                 }}
                 itemListPredicate={filterGenes}
@@ -276,7 +277,7 @@ class GeneExpression extends React.Component {
               />
               <Button
                 className="bp3-button bp3-intent-primary"
-                data-testid={"add-gene"}
+                data-testid="add-gene"
                 loading={userDefinedGenesLoading}
                 onClick={() => this.handleClick(activeItem)}
               >
@@ -308,7 +309,7 @@ class GeneExpression extends React.Component {
                     />
                     <Button
                       intent="primary"
-                      onClick={this.handleBulkAddClick.bind(this)}
+                      onClick={this.handleBulkAddClick}
                       loading={userDefinedGenesLoading}
                     >
                       Add genes
diff --git a/client/src/components/leftSidebar/index.js b/client/src/components/leftSidebar/index.js
index fc5fc3e7..b83fa9b8 100644
--- a/client/src/components/leftSidebar/index.js
+++ b/client/src/components/leftSidebar/index.js
@@ -2,8 +2,6 @@
 import React from "react";
 import { connect } from "react-redux";
 import Categorical from "../categorical/categorical";
-import Continuous from "../continuous/continuous";
-import GeneExpression from "../geneExpression";
 import * as globals from "../../globals";
 import DynamicScatterplot from "../scatterplot/scatterplot";
 import TopLeftLogoAndTitle from "./topLeftLogoAndTitle";
diff --git a/client/src/components/menubar/index.js b/client/src/components/menubar/index.js
index 2382aa37..ad6fd404 100644
--- a/client/src/components/menubar/index.js
+++ b/client/src/components/menubar/index.js
@@ -266,11 +266,10 @@ class MenuBar extends React.Component {
     const haveBothCellSets =
       !!differential.celllist1 && !!differential.celllist2;
 
-    const tipMessage =
-      "See top 10 differentially expressed genes" +
-      (diffexpMayBeSlow
-        ? " (CAUTION: large dataset - may take longer or fail)"
-        : "");
+    const slowMsg = diffexpMayBeSlow
+      ? " (CAUTION: large dataset - may take longer or fail)"
+      : "";
+    const tipMessage = `See top 10 differentially expressed genes${slowMsg}`;
 
     return (
       <div className="bp3-button-group" style={{ marginRight: 10 }}>
@@ -318,7 +317,6 @@ class MenuBar extends React.Component {
   render() {
     const {
       dispatch,
-      differential,
       crossfilter,
       resettingInterface,
       libraryVersions,
diff --git a/client/src/components/rightSidebar/index.js b/client/src/components/rightSidebar/index.js
index 54a59a34..04a0b91d 100644
--- a/client/src/components/rightSidebar/index.js
+++ b/client/src/components/rightSidebar/index.js
@@ -12,17 +12,7 @@ import * as globals from "../../globals";
 }))
 class RightSidebar extends React.Component {
   render() {
-    const {
-      responsive,
-      scatterplotXXaccessor,
-      scatterplotYYaccessor
-    } = this.props;
-
-    /*
-    this magic number should be made less fragile,
-    if cellxgene logo or tabs change, this must as well
-    */
-    const logoRelatedPadding = 50;
+    const { responsive } = this.props;
 
     return (
       <div
diff --git a/client/src/reducers/centroidLabel.js b/client/src/reducers/centroidLabel.js
index c1060fb6..9a1d7ada 100644
--- a/client/src/reducers/centroidLabel.js
+++ b/client/src/reducers/centroidLabel.js
@@ -1,5 +1,3 @@
-import calcCentroid from "../util/centroid";
-
 const initialState = {
   metadataField: "",
   categoryIndex: -1,
@@ -8,7 +6,7 @@ const initialState = {
 };
 
 const CentroidLabel = (state = initialState, action, sharedNextState) => {
-  const { categoricalSelection, world, layoutChoice } = sharedNextState;
+  const { categoricalSelection } = sharedNextState;
   const { metadataField, categoryIndex } = action;
   const categoryField =
     categoricalSelection?.[metadataField]?.categoryValues[categoryIndex];
@@ -19,12 +17,7 @@ const CentroidLabel = (state = initialState, action, sharedNextState) => {
         metadataField,
         categoryIndex,
         categoryField,
-        centroidXY: null /* calcCentroid(  This function call is computationally heavy and also leading to large GC. Before reimplementation, look into optimization and memoization
-          world,
-          metadataField,
-          categoryField,
-          layoutChoice.currentDimNames
-        ) */
+        centroidXY: null
       };
 
     case "category value mouse hover end":
diff --git a/client/src/reducers/colors.js b/client/src/reducers/colors.js
index 723f299b..b314a87f 100644
--- a/client/src/reducers/colors.js
+++ b/client/src/reducers/colors.js
@@ -55,7 +55,7 @@ const ColorsReducer = (
 
     case "annotation: delete category": {
       const { colorAccessor } = state;
-      if (action.metadataField != colorAccessor) {
+      if (action.metadataField !== colorAccessor) {
         return state;
       }
       /* else reset */
diff --git a/client/src/util/centroid.js b/client/src/util/centroid.js
index 2cb1b60e..486ad6f3 100644
--- a/client/src/util/centroid.js
+++ b/client/src/util/centroid.js
@@ -3,6 +3,8 @@ import quantile from "./quantile";
 /*
   Centroid coordinate calculation
 */
+
+/* Unused - please cleanup
 const calcMeanCentroid = (world, annoName, annoValue, layoutDimNames) => {
   const centroid = { x: 0, y: 0, size: 0 };
   const annoArray = world.obsAnnotations.col(annoName).asArray();
@@ -24,6 +26,7 @@ const calcMeanCentroid = (world, annoName, annoValue, layoutDimNames) => {
 
   return [centroid.x, centroid.y];
 };
+*/
 
 const calcMedianCentroid = (world, annoName, annoValue, layoutDimNames) => {
   const centroidX = [];
diff --git a/client/src/util/stateManager/annotationsHelpers.js b/client/src/util/stateManager/annotationsHelpers.js
index 4310781c..4fc0954e 100644
--- a/client/src/util/stateManager/annotationsHelpers.js
+++ b/client/src/util/stateManager/annotationsHelpers.js
@@ -138,7 +138,7 @@ export function allHaveLabelByMask(df, colName, label, mask) {
 	const col = df.col(colName);
 	if (!col) return false;
 	if (df.length !== mask.length)
-		throw new InternalError("mismatch on mask length");
+		throw new RangeError("mismatch on mask length");
 
 	for (let i = 0; i < df.length; i += 1) {
 		if (mask[i]) {
diff --git a/client/src/util/typedCrossfilter/crossfilter.js b/client/src/util/typedCrossfilter/crossfilter.js
index 4bd12188..67a2b487 100644
--- a/client/src/util/typedCrossfilter/crossfilter.js
+++ b/client/src/util/typedCrossfilter/crossfilter.js
@@ -108,7 +108,7 @@ export default class ImmutableTypedCrossfilter {
     };
 
     return new ImmutableTypedCrossfilter(data, dimensions, {
-      bitArray: bitArray
+      bitArray
     });
   }
 
@@ -128,7 +128,7 @@ export default class ImmutableTypedCrossfilter {
     }
 
     return new ImmutableTypedCrossfilter(data, dimensions, {
-      bitArray: bitArray
+      bitArray
     });
   }
 

From c2ededfc62eab66f214df331051cfe543c0053db Mon Sep 17 00:00:00 2001
From: Colin Megill <colinmegill@gmail.com>
Date: Thu, 21 Nov 2019 19:08:29 -0500
Subject: [PATCH 16/16] Anno editing label/category error states (#1048)

* anno error states

* label validation should not treat empty string as error

* disable Submit if no label or category entered

* edit category name error states

* flex start

* pr cleanup

* label name validation fixes

* PR comment responses
---
 .../src/components/categorical/categorical.js |  19 ++-
 client/src/components/categorical/category.js | 141 ++++++++++++++----
 client/src/components/categorical/value.js    | 134 +++++++++++++----
 3 files changed, 227 insertions(+), 67 deletions(-)

diff --git a/client/src/components/categorical/categorical.js b/client/src/components/categorical/categorical.js
index 37574027..53ff7f3b 100644
--- a/client/src/components/categorical/categorical.js
+++ b/client/src/components/categorical/categorical.js
@@ -64,9 +64,11 @@ class Categories extends React.Component {
 
   categoryNameError = name => {
     /*
-    return false if this is a LEGAL/acceptable category name,
+    return false if this is a LEGAL/acceptable category name or NULL/empty string,
     or return an error type.
     */
+    if (!name) return false;
+
     const { categoricalSelection } = this.props;
     const allCategoryNames = Object.keys(categoricalSelection);
 
@@ -83,6 +85,7 @@ class Categories extends React.Component {
 
   categoryNameErrorMessage = name => {
     const err = this.categoryNameError(name);
+    if (err === false) return null;
     if (err === "duplicate") {
       return (
         <span>
@@ -167,7 +170,6 @@ class Categories extends React.Component {
                       autoFocus
                       value={newCategoryText}
                       intent={
-                        newCategoryText &&
                         this.categoryNameError(newCategoryText)
                           ? "warning"
                           : "none"
@@ -180,11 +182,9 @@ class Categories extends React.Component {
                     <p
                       style={{
                         marginTop: 7,
-                        visibility:
-                          newCategoryText &&
-                          this.categoryNameError(newCategoryText)
-                            ? "visible"
-                            : "hidden",
+                        visibility: this.categoryNameError(newCategoryText)
+                          ? "visible"
+                          : "hidden",
                         color: Colors.ORANGE3
                       }}
                     >
@@ -227,7 +227,10 @@ class Categories extends React.Component {
                     </Tooltip>
                     <Button
                       onClick={this.handleCreateUserAnno}
-                      disabled={this.categoryNameError(newCategoryText)}
+                      disabled={
+                        !newCategoryText ||
+                        this.categoryNameError(newCategoryText)
+                      }
                       intent="primary"
                       type="submit"
                     >
diff --git a/client/src/components/categorical/category.js b/client/src/components/categorical/category.js
index a966025d..3329c7c3 100644
--- a/client/src/components/categorical/category.js
+++ b/client/src/components/categorical/category.js
@@ -35,7 +35,7 @@ class Category extends React.Component {
     this.state = {
       isChecked: true,
       isExpanded: false,
-      newCategoryText: "",
+      newCategoryText: props.metadataField,
       newLabelText: ""
     };
   }
@@ -116,9 +116,19 @@ class Category extends React.Component {
   };
 
   handleEditCategory = () => {
-    const { dispatch, metadataField } = this.props;
+    const { dispatch, metadataField, categoricalSelection } = this.props;
     const { newCategoryText } = this.state;
 
+    const allCategoryNames = _.keys(categoricalSelection);
+
+    if (
+      (allCategoryNames.indexOf(newCategoryText) > -1 &&
+        newCategoryText !== metadataField) ||
+      newCategoryText === ""
+    ) {
+      return;
+    }
+
     dispatch({
       type: "annotation: category edited",
       metadataField,
@@ -145,26 +155,27 @@ class Category extends React.Component {
 
   labelNameError = name => {
     /*
-    return false if this is a LEGAL/acceptable category name,
+    return false if this is a LEGAL/acceptable category name or NULL/empty string,
     or return an error type.
     */
-    const { metadataField, universe } = this.props;
-    const { obsByName } = universe.schema.annotations;
+    let error = false;
+    if (name) {
+      const { metadataField, universe } = this.props;
+      const { obsByName } = universe.schema.annotations;
 
-    if (obsByName[metadataField].categories.indexOf(name) !== -1) {
-      return "duplicate";
+      if (obsByName[metadataField].categories.indexOf(name) !== -1) {
+        error = "duplicate";
+      } else if (!AnnotationsHelpers.isLegalAnnotationName(name)) {
+        error = "characters";
+      }
     }
-
-    if (!AnnotationsHelpers.isLegalAnnotationName(name)) {
-      return "characters";
-    }
-
-    return false;
+    return error;
   };
 
   labelNameErrorMessage = name => {
     const { metadataField } = this.props;
     const err = this.labelNameError(name);
+    if (err === false) return null;
     if (err === "duplicate") {
       return (
         <span>
@@ -185,6 +196,83 @@ class Category extends React.Component {
     return err;
   };
 
+  categoryNameErrorMessage = () => {
+    const { newCategoryText } = this.state;
+    const err = this.editedCategoryNameError();
+    if (err === false) return null;
+
+    let markup = null;
+
+    if (err === "empty_string") {
+      markup = (
+        <span
+          style={{
+            display: "block",
+            fontStyle: "italic",
+            fontSize: 12,
+            marginTop: 5,
+            color: Colors.ORANGE3
+          }}
+        >
+          {"Category name cannot be blank"}
+        </span>
+      );
+    } else if (err === "already_exists") {
+      markup = (
+        <span
+          style={{
+            display: "block",
+            fontStyle: "italic",
+            fontSize: 12,
+            marginTop: 5,
+            color: Colors.ORANGE3
+          }}
+        >
+          {"Category name must be unique"}
+        </span>
+      );
+    } else if (err === "characters") {
+      markup = (
+        <span
+          style={{
+            display: "block",
+            fontStyle: "italic",
+            fontSize: 12,
+            marginTop: 5,
+            color: Colors.ORANGE3
+          }}
+        >
+          {"Only alphanumeric and underscore allowed"}
+        </span>
+      );
+    }
+
+    return markup;
+  };
+
+  editedCategoryNameError = () => {
+    const { metadataField, categoricalSelection } = this.props;
+    const { newCategoryText } = this.state;
+    const allCategoryNames = _.keys(categoricalSelection);
+
+    const isEmptyString = newCategoryText === "";
+    const categoryNameAlreadyExists =
+      allCategoryNames.indexOf(newCategoryText) > -1;
+    const sameName = newCategoryText === metadataField;
+
+    let error = false;
+
+    if (isEmptyString) {
+      error = "empty_string";
+    } else if (categoryNameAlreadyExists && !sameName) {
+      error = "already_exists";
+    } else if (!AnnotationsHelpers.isLegalAnnotationName(newCategoryText)) {
+      error = "characters";
+    }
+
+    return error;
+  };
+
   toggleAll() {
     const { dispatch, metadataField } = this.props;
     dispatch({
@@ -251,6 +339,7 @@ class Category extends React.Component {
       ...cat.categoryValueIndices
     ]);
     const optTuplesAsKey = _.map(optTuples, t => t[0]).join(""); // animation
+    const allCategoryNames = _.keys(categoricalSelection);
 
     return (
       <div
@@ -271,7 +360,7 @@ class Category extends React.Component {
             style={{
               display: "flex",
               justifyContent: "flex-start",
-              alignItems: "baseline"
+              alignItems: "flex-start"
             }}
           >
             <label className="bp3-control bp3-checkbox">
@@ -332,7 +421,7 @@ class Category extends React.Component {
                     rightElement={
                       <Button
                         minimal
-                        disabled={newCategoryText.length === 0}
+                        disabled={this.editedCategoryNameError()}
                         style={{ position: "relative", top: -1 }}
                         type="button"
                         icon="small-tick"
@@ -342,6 +431,7 @@ class Category extends React.Component {
                       />
                     }
                   />
+                  {this.categoryNameErrorMessage()}
                 </form>
               ) : (
                 metadataField
@@ -385,10 +475,7 @@ class Category extends React.Component {
                           autoFocus
                           value={newLabelText}
                           intent={
-                            // universe.schema.annotations.obsByName[
-                            //   metadataField
-                            // ].categories.indexOf(newLabelText) !== -1
-                            newLabelText && this.labelNameError(newLabelText)
+                            this.labelNameError(newLabelText)
                               ? "warning"
                               : "none"
                           }
@@ -400,13 +487,9 @@ class Category extends React.Component {
                         <p
                           style={{
                             marginTop: 7,
-                            visibility:
-                              // universe.schema.annotations.obsByName[
-                              //   metadataField
-                              // ].categories.indexOf(newLabelText) !== -1
-                              newLabelText && this.labelNameError(newLabelText)
-                                ? "visible"
-                                : "hidden",
+                            visibility: this.labelNameError(newLabelText)
+                              ? "visible"
+                              : "hidden",
                             color: Colors.ORANGE3
                           }}
                         >
@@ -423,11 +506,7 @@ class Category extends React.Component {
                         </Tooltip>
                         <Button
                           disabled={
-                            newLabelText.length === 0 ||
-                            // universe.schema.annotations.obsByName[
-                            //   metadataField
-                            // ].categories.indexOf(newLabelText) !== -1
-                            this.labelNameError(newLabelText)
+                            !newLabelText || this.labelNameError(newLabelText)
                           }
                           onClick={this.handleAddNewLabelToCategory}
                           intent="primary"
diff --git a/client/src/components/categorical/value.js b/client/src/components/categorical/value.js
index 090550df..16a74480 100644
--- a/client/src/components/categorical/value.js
+++ b/client/src/components/categorical/value.js
@@ -31,19 +31,26 @@ class CategoryValue extends React.Component {
   constructor(props) {
     super(props);
     this.state = {
-      editedLabelText: ""
+      editedLabelText: String(
+        props.categoricalSelection[props.metadataField].categoryValues[
+          props.categoryIndex
+        ]
+      ).valueOf()
     };
   }
 
-  handleDeleteValue = () => {
-    const {
-      dispatch,
-      metadataField,
-      categoryIndex,
-      categoricalSelection
-    } = this.props;
+  getLabel = () => {
+    const { metadataField, categoryIndex, categoricalSelection } = this.props;
     const category = categoricalSelection[metadataField];
     const label = category.categoryValues[categoryIndex];
+
+    return label;
+  };
+
+  handleDeleteValue = () => {
+    const { dispatch, metadataField } = this.props;
+    const label = this.getLabel();
+
     dispatch({
       type: "annotation: delete label",
       metadataField,
@@ -52,14 +59,8 @@ class CategoryValue extends React.Component {
   };
 
   handleAddCurrentSelectionToThisLabel = () => {
-    const {
-      dispatch,
-      metadataField,
-      categoryIndex,
-      categoricalSelection
-    } = this.props;
-    const category = categoricalSelection[metadataField];
-    const label = category.categoryValues[categoryIndex];
+    const { dispatch, metadataField, categoryIndex } = this.props;
+    const label = this.getLabel();
     dispatch({
       type: "annotation: label current cell selection",
       metadataField,
@@ -69,15 +70,9 @@ class CategoryValue extends React.Component {
   };
 
   handleEditValue = () => {
-    const {
-      dispatch,
-      metadataField,
-      categoryIndex,
-      categoricalSelection
-    } = this.props;
+    const { dispatch, metadataField, categoryIndex } = this.props;
     const { editedLabelText } = this.state;
-    const category = categoricalSelection[metadataField];
-    const label = category.categoryValues[categoryIndex];
+    const label = this.getLabel();
     dispatch({
       type: "annotation: label edited",
       editedLabel: editedLabelText,
@@ -85,7 +80,80 @@ class CategoryValue extends React.Component {
       categoryIndex,
       label
     });
-    this.setState({ editedLabelText: "" });
+  };
+
+  valueNameErrorMessage = () => {
+    const { editedLabelText } = this.state;
+    const err = this.valueNameError();
+    if (!err) return null;
+
+    let markup = null;
+
+    if (err === "empty_string") {
+      markup = (
+        <span
+          style={{
+            fontStyle: "italic",
+            fontSize: 12,
+            marginTop: 5,
+            color: Colors.ORANGE3
+          }}
+        >
+          {"Label cannot be blank"}
+        </span>
+      );
+    } else if (err === "duplicate") {
+      markup = (
+        <span
+          style={{
+            fontStyle: "italic",
+            fontSize: 12,
+            marginTop: 5,
+            color: Colors.ORANGE3
+          }}
+        >
+          {"Label must be unique"}
+        </span>
+      );
+    } else if (err === "characters") {
+      markup = (
+        <span
+          style={{
+            fontStyle: "italic",
+            fontSize: 12,
+            marginTop: 5,
+            color: Colors.ORANGE3
+          }}
+        >
+          {"Only alphanumeric and underscore allowed"}
+        </span>
+      );
+    }
+    return markup;
+  };
+
+  valueNameError = () => {
+    const { editedLabelText } = this.state;
+    const { categoricalSelection, metadataField, categoryIndex } = this.props;
+
+    let err = null;
+
+    const category = categoricalSelection[metadataField];
+    const displayString = String(
+      category.categoryValues[categoryIndex]
+    ).valueOf();
+
+    if (editedLabelText === "") {
+      err = "empty_string";
+    } else if (
+      category.categoryValues.indexOf(editedLabelText) > -1 &&
+      editedLabelText !== displayString
+    ) {
+      err = "duplicate";
+    } else if (!AnnotationsHelpers.isLegalAnnotationName(editedLabelText)) {
+      err = "characters";
+    }
+    return err;
   };
 
   activateEditLabelMode = () => {
@@ -115,7 +183,7 @@ class CategoryValue extends React.Component {
     });
   };
 
-  shouldComponentUpdate = nextProps => {
+  shouldComponentUpdate = (nextProps, nextState) => {
     /*
     Checks to see if at least one of the following changed:
     * world state
@@ -125,7 +193,7 @@ class CategoryValue extends React.Component {
 
     If and only if true, update the component
     */
-    const { props } = this;
+    const { props, state } = this;
     const { metadataField, categoryIndex, categoricalSelection } = props;
     const { categoricalSelection: newCategoricalSelection } = nextProps;
 
@@ -141,13 +209,15 @@ class CategoryValue extends React.Component {
     const colorAccessorChange = props.colorAccessor !== nextProps.colorAccessor;
     const annotationsChange = props.annotations !== nextProps.annotations;
     const crossfilterChange = props.crossfilter !== nextProps.crossfilter;
+    const editingLabel = state.editedLabelText !== nextState.editedLabelText;
 
     return (
       valueSelectionChange ||
       worldChange ||
       colorAccessorChange ||
       annotationsChange ||
-      crossfilterChange
+      crossfilterChange ||
+      editingLabel
     );
   };
 
@@ -222,6 +292,8 @@ class CategoryValue extends React.Component {
       flippedProps
     } = this.props;
 
+    const { editedLabelText } = this.state;
+
     if (!categoricalSelection) return null;
 
     const category = categoricalSelection[metadataField];
@@ -347,6 +419,9 @@ class CategoryValue extends React.Component {
               <form
                 onSubmit={e => {
                   e.preventDefault();
+                  if (this.valueNameError()) {
+                    return;
+                  }
                   this.handleEditValue();
                 }}
               >
@@ -357,6 +432,7 @@ class CategoryValue extends React.Component {
                   }}
                   small
                   autoFocus
+                  intent={this.valueNameError() ? "warning" : "none"}
                   onChange={e => {
                     this.setState({ editedLabelText: e.target.value });
                   }}
@@ -365,6 +441,7 @@ class CategoryValue extends React.Component {
                     <Button
                       minimal
                       style={{ position: "relative", top: -1 }}
+                      disabled={this.valueNameError()}
                       type="button"
                       icon="small-tick"
                       data-testclass="submitEdit"
@@ -373,6 +450,7 @@ class CategoryValue extends React.Component {
                     />
                   }
                 />
+                {this.valueNameErrorMessage()}
               </form>
             ) : null}
             {/*