Experimental - manual annotations (#837)

* icons, partway

* redux for values

* onChange

* cancel

* annotations lifecycle for category names

* copy categorical

* edit category

* add Dataframe.withColsFrom

* render user annotations; default add/delete annotation category

* add label name to actions

* category name edit

* error checking improvements

* change schema field isUserAnnotation to writable

* always have an unassigned label; implement delete label

* implement add new label and edit label name

* label current cell selection

* fix select exact bug in crossfilter

* clean up categorical reducer

* fix tests

* remove debugging printf

* implement subset/reset for user annotations

* undo redo support for user annotations

* remove duplicate button from categories

* add modal

* remove obsolete duplicate annotation reducers

* remove old debugging printf

* connect modal to annotation create and dup

* initial full-stack wiring

* finish up end-to-end wiring

* fix existing unit tests

* fix pytests to match new schema API

* remove debugging printfs

* add label file rotation

* remove obsolete comment

* add fbs encode/decode tests

* add tests for writable annotations

* simplify code

* fix hashing bug with FBS encoding

* lint

* fix smoke tests

* improve error checking in Dataframe.withColsFrom

* add unit test for Dataframe.withColsFrom

* add unit test for Dataframe.columns and Dataframe.renameCol

* fix bug in FBS encode, add better error checks, refactor

* add FBS encode/decode test

* add clarifying comment

* clean up action type names; fix state inconsistency in crossfilter update

* change autosave timer to 2.5sec

* sort categorical metadata render order so it remains consistent

* add temporary autogenerated label for add-new-label operation

* fix hover-over label menu interference with cell highlighting

* remove debugging code

* add missing reducer cases & fix typo

* make dataframe memoize more general purpose

* add dev mode for annos

* fix error on select duplicate

* handle zero occupancy categories

* correctly maintain unclipped AND clipped world

* correctly handle zero length FBS matrix and label files

* ensure all writable categorical schema contains an unassigned category

* handle case where building occupancy stack for category with no members

* dialog for creating label, disable button if duplicate or empty

* visually separate writeable

* edit category

* fix edit category name

* remove debugging code

* fix edit annotation label

* visually define unassigned, change options

* Pull in requirements.txt from `master`

* label currently selected cells

* duplicate label

* lint

* fix pytest merge issues

* rename --label-file to --experimental-label-file

* remove debugging console log

* spelling error fix; fix bug found in PR review.

* lint

client/src/reducers/world.js

@@ -1,7 +1,22 @@
-import { World, ControlsHelpers } from "../util/stateManager";
+import { unassignedCategoryLabel } from "../globals";
+import {
+  World,
+  ControlsHelpers as CH,
+  AnnotationsHelpers as AH
+} from "../util/stateManager";
 import clip from "../util/clip";
 import quantile from "../util/quantile";
 
+/*
+important note: much of this code assumes that wriable (user) annotations
+will NOT contain scalar data (ie, will only contain categorical labelled
+data), and therefore will never need to be clipped.  Put another way, it
+assumes that for these annotations, the clipped & unclipped data is equal.
+
+If we ever start allowing user editable scalar data, this assumption will
+need to be revisited.
+*/
+
 const WorldReducer = (
   state = null,
   action,
@@ -9,16 +24,13 @@ const WorldReducer = (
   prevSharedState
 ) => {
   switch (action.type) {
-    case "initial data load complete (universe exists)": {
+    case "initial data load complete (universe exists)":
+    case "reset World to eq Universe": {
       const { universe } = nextSharedState;
       const world = World.createWorldFromEntireUniverse(universe);
       return world;
     }
 
-    case "reset World to eq Universe": {
-      return prevSharedState.resetCache.world;
-    }
-
     case "set World to current selection": {
       /* Set viewable world to be the currently selected data */
       const world = World.createWorldBySelection(
@@ -80,7 +92,7 @@ const WorldReducer = (
           Object.keys(action.expressionData)
         )
       ];
-      unclippedVarData = ControlsHelpers.pruneVarDataCache(
+      unclippedVarData = CH.pruneVarDataCache(
         unclippedVarData,
         allTheGenesWeNeed
       );
@@ -122,6 +134,135 @@ const WorldReducer = (
       };
     }
 
+    case "annotation: create category": {
+      const name = action.data;
+      const { universe } = nextSharedState;
+      const { schema } = universe;
+
+      /*
+      if world !== universe, we have to subset the newly created annotation,
+      else, just use it as is.
+      */
+      let newAnnotation = null;
+      if (!World.worldEqUniverse(state, universe)) {
+        newAnnotation = universe.obsAnnotations
+          .subset(state.obsAnnotations.rowIndex.keys(), [name], null)
+          .icol(0)
+          .asArray();
+      } else {
+        newAnnotation = universe.obsAnnotations.col(name).asArray();
+      }
+      const obsAnnotations = state.obsAnnotations.withCol(
+        name,
+        newAnnotation,
+        state.obsAnnotations.rowIndex
+      );
+      const unclipped = {
+        ...state.unclipped,
+        obsAnnotations: state.unclipped.obsAnnotations.withCol(
+          name,
+          newAnnotation,
+          state.unclipped.obsAnnotations.rowIndex
+        )
+      };
+      return { ...state, schema, obsAnnotations, unclipped };
+    }
+
+    case "annotation: category edited": {
+      /* change the name of an obs annotation */
+      const name = action.metadataField;
+      const newName = action.newCategoryText;
+      const { schema } = nextSharedState.universe;
+      const obsAnnotations = state.obsAnnotations.renameCol(name, newName);
+      const unclipped = {
+        ...state.unclipped,
+        obsAnnotations: state.unclipped.obsAnnotations.renameCol(name, newName)
+      };
+      return { ...state, schema, obsAnnotations, unclipped };
+    }
+
+    case "annotation: delete category": {
+      /* remove a category from obs annotation */
+      const { schema } = nextSharedState.universe;
+      const name = action.metadataField;
+      const obsAnnotations = state.obsAnnotations.dropCol(name);
+      const unclipped = {
+        ...state.unclipped,
+        obsAnnotations: state.unclipped.obsAnnotations.dropCol(name)
+      };
+      return { ...state, schema, obsAnnotations, unclipped };
+    }
+
+    case "annotation: add new label to category": {
+      /* add a new label to the schema - schema updated by universe reducer, we just need to note it */
+      const { schema } = nextSharedState.universe;
+      return { ...state, schema };
+    }
+
+    case "annotation: label edited": {
+      const { schema } = nextSharedState.universe;
+      const { metadataField } = action;
+      const oldLabelName = action.label;
+      const newLabelName = action.editedLabel;
+
+      /* set all values to to new label */
+      const unclipped = {
+        ...state.unclipped,
+        obsAnnotations: AH.setLabelByValue(
+          state.unclipped.obsAnnotations,
+          metadataField,
+          oldLabelName,
+          newLabelName
+        )
+      };
+      const obsAnnotations = state.obsAnnotations.replaceColData(
+        metadataField,
+        unclipped.obsAnnotations.col(metadataField).asArray()
+      );
+      return { ...state, schema, obsAnnotations, unclipped };
+    }
+
+    case "annotation: delete label": {
+      const { schema } = nextSharedState.universe;
+      const { label, metadataField } = action;
+
+      /* set all values to unassigned in obsAnnotations */
+      const unclipped = {
+        ...state.unclipped,
+        obsAnnotations: AH.setLabelByValue(
+          state.unclipped.obsAnnotations,
+          metadataField,
+          label,
+          unassignedCategoryLabel
+        )
+      };
+      const obsAnnotations = state.obsAnnotations.replaceColData(
+        metadataField,
+        unclipped.obsAnnotations.col(metadataField).asArray()
+      );
+      return { ...state, schema, obsAnnotations, unclipped };
+    }
+
+    case "annotation: label current cell selection": {
+      const { metadataField, label } = action;
+      const { crossfilter } = prevSharedState;
+      const mask = crossfilter.allSelectedMask();
+      const unclipped = {
+        ...state.unclipped,
+        obsAnnotations: AH.setLabelByMask(
+          state.unclipped.obsAnnotations,
+          metadataField,
+          mask,
+          label
+        )
+      };
+      const obsAnnotations = state.obsAnnotations.replaceColData(
+        metadataField,
+        unclipped.obsAnnotations.col(metadataField).asArray()
+      );
+      return { ...state, obsAnnotations, unclipped };
+    }
+
     default: {
       return state;
     }