Ontologies (#1110)

* add sample ontologies file

* add ontologies reducer

* Move select category to own component

* Dialog and Input factored out

* refactoring categorical, partway

* validationn

* anno

* suggest  populates input

* frontend for ontology working

* initial implementation of back-end support for ontologies

* edit is now dialog again

* autosuggest working on edit

* part way through create arbitrary label

* handle choice in function

* pass duplicate cat  prop

* editing works

* update test to match new CLI params

* fix occupancy alignment

* edit category as dialogue

* secondary button

* remove stubbed out ontologies

* add label setting upon new label creation

* Update legal characters for labels (#1119)

* Allow any term in the ontology (bypass legal name check)

* Add hyphens and parens to legal characters in names

* improve performance for large ontologies

* correctly handle case where ontologies are disabled

* fix logic error in CLI

Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com>

* PR cleanup 1

* lint

* validate user generated labels

* finish hooking up connected suggest component

* protect against undefined callbacks

* Fix illegal characters error message

* break out npm run commands

* fix error detection on label edit

Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com>
Co-authored-by: Sidney Bell <sidneymbell@users.noreply.github.com>

client/src/reducers/annotations.js

@@ -31,7 +31,6 @@ const Annotations = (
 ) => {
   switch (action.type) {
     case "configuration load complete": {
-      const DefaultDataCollectionName = null;
       const dataCollectionName =
         action.config.parameters?.["annotations-data-collection-name"] ?? null;
       const dataCollectionNameIsReadOnly =

client/src/reducers/crossfilter.js

@@ -165,9 +165,16 @@ const CrossfilterReducerBase = (
       return state.delDimension(obsAnnoDimensionName(action.metadataField));
     }
 
+    case "annotation: add new label to category":
     case "annotation: label current cell selection":
     case "annotation: label edited":
     case "annotation: delete label": {
+      if (
+        action.type === "annotation: add new label to category" &&
+        !action.assignSelectedCells
+      )
+        return state;
+
       /* we need to reindex the dimension.  For now, just drop it and add another */
       const name = action.metadataField;
       const dimName = obsAnnoDimensionName(name);

client/src/reducers/index.js

@@ -18,6 +18,7 @@ import controls from "./controls";
 import resetCache from "./resetCache";
 import annotations from "./annotations";
 import autosave from "./autosave";
+import ontology from "./ontology";
 import centroidLabels from "./centroidLabels";
 import pointDialation from "./pointDilation";
 
@@ -28,6 +29,7 @@ const Reducer = undoable(
     ["config", config],
     ["universe", universe],
     ["world", world],
+    ["ontology", ontology],
     ["annotations", annotations],
     ["layoutChoice", layoutChoice],
     ["categoricalSelection", categoricalSelection],
@@ -45,15 +47,15 @@ const Reducer = undoable(
   ]),
   [
     "universe",
-    "categoricalSelection",
     "world",
+    "categoricalSelection",
     "continuousSelection",
     "graphSelection",
     "crossfilter",
-    "layoutChoice",
+    "colors",
     "controls",
     "differential",
-    "colors",
+    "layoutChoice",
     "centroidLabels",
     "annotations"
   ],

client/src/reducers/ontology.js

@@ -0,0 +1,29 @@
+// jshint esversion: 6
+const Ontology = (
+  state = {
+    enabled: false, // are ontology terms enabled?
+    terms: null, // an array of term names, eg, ['cell', 'lung cell', ...]
+    termSet: null, // a Set object containing all terms, for fast lookup
+    loading: true
+  },
+  action
+) => {
+  switch (action.type) {
+    case "configuration load complete":
+      const enabled =
+        action.config?.parameters?.annotations_cell_ontology_enabled ?? false;
+      const terms = action.config?.parameters?.annotations_cell_ontology_terms;
+      const termSet = new Set(terms);
+      return {
+        ...state,
+        loading: false,
+        enabled,
+        terms,
+        termSet
+      };
+    default:
+      return state;
+  }
+};
+
+export default Ontology;

client/src/reducers/universe.js

@@ -136,13 +136,27 @@ const Universe = (state = null, action, nextSharedState, prevSharedState) => {
           "user annotations require a non-zero length string name"
         );
 
-      /* add the new label to the annotation */
+      /* add the new label to the annotation schema */
       const schema = AnnotationsHelpers.addObsAnnoCategory(
         state.schema,
         annotationName,
         newLabelName
       );
-      return { ...state, schema };
+
+      /* if so requested, label the current selection */
+      const { world, crossfilter } = prevSharedState;
+      const { metadataField, newLabelText } = action;
+      const obsAnnotations = !action.assignSelectedCells
+        ? state.obsAnnotations
+        : setLabelOnCurrentSelection(
+            state,
+            world,
+            crossfilter,
+            metadataField,
+            newLabelText
+          );
+
+      return { ...state, schema, obsAnnotations };
     }
 
     case "annotation: label edited": {
@@ -208,23 +222,11 @@ const Universe = (state = null, action, nextSharedState, prevSharedState) => {
     case "annotation: label current cell selection": {
       const { metadataField, label } = action;
       const { world, crossfilter } = prevSharedState;
-
-      /*
-      selection state is relative to world.  We need to convert it
-      to a mask for Universe before applying it.
-      */
-      const worldMask = crossfilter.allSelectedMask();
-      const mask = World.worldEqUniverse(world, state)
-        ? worldMask
-        : AnnotationsHelpers.worldToUniverseMask(
-            worldMask,
-            world.obsAnnotations,
-            state.nObs
-          );
-      const obsAnnotations = AnnotationsHelpers.setLabelByMask(
-        state.obsAnnotations,
+      const obsAnnotations = setLabelOnCurrentSelection(
+        state,
+        world,
+        crossfilter,
         metadataField,
-        mask,
         label
       );
       return { ...state, obsAnnotations };
@@ -236,4 +238,39 @@ const Universe = (state = null, action, nextSharedState, prevSharedState) => {
   }
 };
 
+function setLabelOnCurrentSelection(
+  universe,
+  world,
+  crossfilter,
+  metadataField,
+  label
+) {
+  /*
+  Set category `metadataField` to value `label` for anything currently selected.
+  Used by several action type reducers.
+
+  Returns the new obsAnnotations dataframe.
+  */
+
+  /*
+  selection state is relative to world.  We need to convert it
+  to a mask for Universe before applying it.
+  */
+  const worldMask = crossfilter.allSelectedMask();
+  const mask = World.worldEqUniverse(world, universe)
+    ? worldMask
+    : AnnotationsHelpers.worldToUniverseMask(
+        worldMask,
+        world.obsAnnotations,
+        universe.nObs
+      );
+  const obsAnnotations = AnnotationsHelpers.setLabelByMask(
+    universe.obsAnnotations,
+    metadataField,
+    mask,
+    label
+  );
+  return obsAnnotations;
+}
+
 export default Universe;

client/src/reducers/world.js

@@ -196,6 +196,21 @@ const WorldReducer = (
     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;
+      const { metadataField, newLabelText } = action;
+      const { crossfilter } = prevSharedState;
+
+      if (action.assignSelectedCells) {
+        return {
+          ...state,
+          schema,
+          ...setLabelOnCurrentSelection(
+            state,
+            crossfilter,
+            metadataField,
+            newLabelText
+          )
+        };
+      }
       return { ...state, schema };
     }
 
@@ -246,21 +261,10 @@ const WorldReducer = (
     case "annotation: label current cell selection": {
       const { metadataField, label } = action;
       const { crossfilter } = prevSharedState;
-      const mask = crossfilter.allSelectedMask();
-      const unclipped = {
-        ...state.unclipped,
-        obsAnnotations: AnnotationsHelpers.setLabelByMask(
-          state.unclipped.obsAnnotations,
-          metadataField,
-          mask,
-          label
-        )
+      return {
+        ...state,
+        ...setLabelOnCurrentSelection(state, crossfilter, metadataField, label)
       };
-      const obsAnnotations = state.obsAnnotations.replaceColData(
-        metadataField,
-        unclipped.obsAnnotations.col(metadataField).asArray()
-      );
-      return { ...state, obsAnnotations, unclipped };
     }
 
     default: {
@@ -269,4 +273,27 @@ const WorldReducer = (
   }
 };
 
+function setLabelOnCurrentSelection(world, crossfilter, metadataField, label) {
+  /*
+  Set category `metadataField` to value `label` for anything currently selected.
+  Used by several action type reducers.
+  */
+  const mask = crossfilter.allSelectedMask();
+  const unclipped = {
+    ...world.unclipped,
+    obsAnnotations: AnnotationsHelpers.setLabelByMask(
+      world.unclipped.obsAnnotations,
+      metadataField,
+      mask,
+      label
+    )
+  };
+  const obsAnnotations = world.obsAnnotations.replaceColData(
+    metadataField,
+    unclipped.obsAnnotations.col(metadataField).asArray()
+  );
+
+  return { obsAnnotations, unclipped };
+}
+
 export default WorldReducer;