do not hard-wire column names in annotations (#785)

* enforce column name uniqueness for obs and var

* parameterize the column name containing obs and var user-readable names

* use the new annotation index value from schema

* update f/e unit tests

* PR review suggestions

* lint

client/src/actions/index.js

@@ -21,24 +21,32 @@ const doInitialDataLoad = () =>
     dispatch({ type: "initial data load start" });
 
     try {
-      const requestJson = _(["config", "schema"])
+      /*
+      Step 1 - config & schema, all JSON
+      */
+      const requestJson = ["config", "schema"]
         .map(r => `${globals.API.prefix}${globals.API.version}${r}`)
-        .map(url => doJsonRequest(url))
-        .value();
-      const requestBinary = _([
-        "annotations/obs",
-        "annotations/var?annotation-name=name",
-        "layout/obs"
-      ])
-        .map(r => `${globals.API.prefix}${globals.API.version}${r}`)
-        .map(url => doBinaryRequest(url))
-        .value();
-
-      const results = await Promise.all(_.concat(requestJson, requestBinary));
-
+        .map(url => doJsonRequest(url));
+      const stepOneResults = await Promise.all(requestJson);
       /* set config defaults */
-      const config = { ...globals.configDefaults, ...results[0].config };
-      const [, schema, obsAnno, varAnno, obsLayout] = [...results];
+      const config = { ...globals.configDefaults, ...stepOneResults[0].config };
+      const schema = stepOneResults[1];
+
+      /*
+      Step 2 - dataframes, all binary.  NOTE: uses results of step 1.
+      */
+      /* only load names for var annotations, if possible*/
+      const varIndexName = schema?.schema?.annotations?.var?.index;
+      const varAnnotationsQuery = varIndexName
+        ? `?annotation-name=${varIndexName}`
+        : "";
+      const varAnnotationsURL = `annotations/var${varAnnotationsQuery}`;
+      const requestBinary = ["annotations/obs", varAnnotationsURL, "layout/obs"]
+        .map(r => `${globals.API.prefix}${globals.API.version}${r}`)
+        .map(url => doBinaryRequest(url));
+      const stepTwoResults = await Promise.all(requestBinary);
+      const [obsAnno, varAnno, obsLayout] = [...stepTwoResults];
+
       const universe = Universe.createUniverseFromResponse(
         config,
         schema,
@@ -91,6 +99,10 @@ needs expression data.
 Transparently utilizes cached data if it is already present.
 */
 async function _doRequestExpressionData(dispatch, getState, genes) {
+  const state = getState();
+  const { universe } = state;
+  const varIndexName = universe.schema.annotations.var.index;
+
   /* helper for this function only */
   const fetchData = async geneNames => {
     const res = await fetch(
@@ -100,7 +112,7 @@ async function _doRequestExpressionData(dispatch, getState, genes) {
         body: JSON.stringify({
           filter: {
             var: {
-              annotation_value: [{ name: "name", values: geneNames }]
+              annotation_value: [{ name: varIndexName, values: geneNames }]
             }
           }
         }),
@@ -123,8 +135,6 @@ async function _doRequestExpressionData(dispatch, getState, genes) {
     return Universe.convertDataFBStoObject(universe, data);
   };
 
-  const state = getState();
-  const { universe } = state;
   /* preload data already in cache */
   let expressionData = _.transform(
     genes,
@@ -241,6 +251,7 @@ const requestDifferentialExpression = (set1, set2, num_genes = 10) => async (
     */
     const state = getState();
     const { universe } = state;
+    const varIndexName = universe.schema.annotations.var.index;
 
     // Legal values are null, Array or TypedArray.  Null is initial state.
     if (!set1) set1 = [];
@@ -277,7 +288,7 @@ const requestDifferentialExpression = (set1, set2, num_genes = 10) => async (
     const data = await res.json();
     // result is [ [varIdx, ...], ... ]
     const topNGenes = _.map(data, r =>
-      universe.varAnnotations.at(r[0], "name")
+      universe.varAnnotations.at(r[0], varIndexName)
     );
 
     /*

client/src/components/continuous/continuous.js

@@ -66,7 +66,8 @@ class Continuous extends React.Component {
           ? _.map(obsAnnotations.colIndex.keys(), key => {
               const isColorField =
                 key.includes("color") || key.includes("Color");
-              if (key === "name" || isColorField) return null;
+              if (key === schema.annotations.obs.index || isColorField)
+                return null;
 
               const summary = obsAnnotations.col(key).summarize();
               const nonFiniteExtent =

client/src/components/geneExpression/index.js

@@ -85,7 +85,8 @@ class GeneExpression extends React.Component {
     */
     const { world } = this.props;
     const { varAnnotations } = world;
-    const geneNames = varAnnotations.col("name").asArray();
+    const varIndexName = world.schema.annotations.var.index;
+    const geneNames = varAnnotations.col(varIndexName).asArray();
     if (geneNames.length > 0) {
       const placeholder = [];
       let len = geneNames.length;
@@ -107,6 +108,7 @@ class GeneExpression extends React.Component {
 
   handleClick(g) {
     const { world, dispatch, userDefinedGenes } = this.props;
+    const varIndexName = world.schema.annotations.var.index;
     const gene = g.target;
     if (userDefinedGenes.indexOf(gene) !== -1) {
       postUserErrorToast("That gene already exists");
@@ -114,7 +116,9 @@ class GeneExpression extends React.Component {
       postUserErrorToast(
         "That's too many genes, you can have at most 15 user defined genes"
       );
-    } else if (world.varAnnotations.col("name").indexOf(gene) === undefined) {
+    } else if (
+      world.varAnnotations.col(varIndexName).indexOf(gene) === undefined
+    ) {
       postUserErrorToast("That doesn't appear to be a valid gene name.");
     } else {
       dispatch({ type: "single user defined gene start" });
@@ -127,6 +131,7 @@ class GeneExpression extends React.Component {
 
   handleBulkAddClick() {
     const { world, dispatch, userDefinedGenes } = this.props;
+    const varIndexName = world.schema.annotations.var.index;
     const { bulkAdd } = this.state;
 
     /*
@@ -145,7 +150,9 @@ class GeneExpression extends React.Component {
           if (userDefinedGenes.indexOf(gene) !== -1) {
             return keepAroundErrorToast("That gene already exists");
           }
-          if (world.varAnnotations.col("name").indexOf(gene) === undefined) {
+          if (
+            world.varAnnotations.col(varIndexName).indexOf(gene) === undefined
+          ) {
             return keepAroundErrorToast(
               `${gene} doesn't appear to be a valid gene name.`
             );
@@ -168,7 +175,7 @@ class GeneExpression extends React.Component {
       userDefinedGenesLoading,
       differential
     } = this.props;
-
+    const varIndexName = world?.schema?.annotations?.var?.index;
     const { tab, bulkAdd } = this.state;
 
     return (
@@ -243,7 +250,7 @@ class GeneExpression extends React.Component {
                 itemRenderer={renderGene.bind(this)}
                 items={
                   world && world.varAnnotations
-                    ? world.varAnnotations.col("name").asArray()
+                    ? world.varAnnotations.col(varIndexName).asArray()
                     : ["No genes"]
                 }
                 popoverProps={{ minimal: true }}
@@ -322,7 +329,7 @@ class GeneExpression extends React.Component {
           <ExpressionButtons />
           {differential.diffExp
             ? _.map(differential.diffExp, (value, index) => {
-                const name = world.varAnnotations.at(value[0], "name");
+                const name = world.varAnnotations.at(value[0], varIndexName);
                 const values = world.varData.col(name);
                 if (!values) {
                   return null;

client/src/reducers/controls.js

@@ -93,9 +93,10 @@ const Controls = (
     }
     case "request differential expression success": {
       const { world } = prevSharedState;
+      const varIndexName = world.schema.annotations.var.index;
       const _diffexpGenes = [];
       action.data.forEach(d => {
-        _diffexpGenes.push(world.varAnnotations.at(d[0], "name"));
+        _diffexpGenes.push(world.varAnnotations.at(d[0], varIndexName));
       });
       return {
         ...state,

client/src/reducers/crossfilter.js

@@ -90,8 +90,9 @@ const CrossfilterReducer = (
 
     case "request differential expression success": {
       const { world } = prevSharedState;
+      const varIndexName = world.schema.annotations.var.index;
       const genes = _.map(action.data, d =>
-        world.varAnnotations.at(d[0], "name")
+        world.varAnnotations.at(d[0], varIndexName)
       );
       const crossfilter = _.reduce(
         genes,
@@ -109,10 +110,11 @@ const CrossfilterReducer = (
 
     case "clear differential expression": {
       const { world } = prevSharedState;
+      const varIndexName = world.schema.annotations.var.index;
       const crossfilter = _.reduce(
         action.diffExp,
         (xfltr, values) => {
-          const name = world.varAnnotations.at(values[0], "name");
+          const name = world.varAnnotations.at(values[0], varIndexName);
           return xfltr.delDimension(diffexpDimensionName(name));
         },
         state

client/src/util/stateManager/controlsHelpers.js

@@ -56,13 +56,14 @@ function topNCategories(summary) {
 
 export function createCategoricalSelection(maxCategoryItems, world) {
   const res = {};
+  const obsIndexName = world.schema.annotations.obs.index;
   _.forEach(world.obsAnnotations.colIndex.keys(), key => {
     const summary = world.obsAnnotations.col(key).summarize();
     if (summary.categories) {
       const isColorField = key.includes("color") || key.includes("Color");
       const isSelectableCategory =
         !isColorField &&
-        key !== "name" &&
+        key !== obsIndexName &&
         summary.categories.length < maxCategoryItems;
       if (isSelectableCategory) {
         const [categoryValues, categoryValueCounts] = topNCategories(summary);

client/src/util/stateManager/universe.js

@@ -124,7 +124,7 @@ function reconcileSchemaCategoriesWithSummary(universe) {
   cases, add a 'categories' field to the schema so it is accessible.
   */
 
-  universe.schema.annotations.obs.forEach(s => {
+  universe.schema.annotations.obs.columns.forEach(s => {
     if (
       s.type === "string" ||
       s.type === "boolean" ||
@@ -179,10 +179,10 @@ export function createUniverseFromResponse(
 
   /* Index schema for ease of use */
   universe.schema.annotations.obsByName = fromEntries(
-    universe.schema.annotations.obs.map(v => [v.name, v])
+    universe.schema.annotations.obs.columns.map(v => [v.name, v])
   );
   universe.schema.annotations.varByName = fromEntries(
-    universe.schema.annotations.var.map(v => [v.name, v])
+    universe.schema.annotations.var.columns.map(v => [v.name, v])
   );
   universe.schema.layout.obsByName = fromEntries(
     universe.schema.layout.obs.map(v => [v.name, v])
@@ -213,8 +213,9 @@ export function convertDataFBStoObject(universe, arrayBuffer) {
     throw new Error("Unexpected non-floating point response from server.");
   }
 
+  const varIndexName = universe.schema.annotations.var.index;
   for (let c = 0; c < colIdx.length; c += 1) {
-    const varName = universe.varAnnotations.at(colIdx[c], "name");
+    const varName = universe.varAnnotations.at(colIdx[c], varIndexName);
     result[varName] = columns[c];
   }
   return result;

client/src/util/stateManager/world.js

@@ -263,10 +263,14 @@ function deduceDimensionType(attributes, fieldName) {
 export function createObsDimensions(crossfilter, world, XYdimNames) {
   /*
   create and return a crossfilter with a dimension for every obs annotation
-  for which we have a supported type, *except* 'name'
+  for which we have a supported type, *except* for the index column, indicated
+  by schema.annotations.obs.index.
   */
   const { schema, obsLayout, obsAnnotations } = world;
-  const annoList = schema.annotations.obs.filter(anno => anno.name !== "name");
+  const indexName = schema.annotations.obs.index;
+  const annoList = schema.annotations.obs.columns.filter(
+    anno => anno.name !== indexName
+  );
   crossfilter = annoList.reduce((xfltr, anno) => {
     const dimType = deduceDimensionType(anno, anno.name);
     const colData = obsAnnotations.col(anno.name).asArray();