gene set summary progress (#2127)

* revert removal of cache control headers

* checkpoint work on revising summary route

* add summary query support to annoMatrix

* summarize route cleanup

* add mising file

* clean up summarize route

* add summary histogram

* update deps

* lint

* more lint

* lint

* manage crossfiler during gene set state changes

* remove obsolete debugging code

* correctly perform async watch in histogram

* better error handling

client/src/actions/annotation.js

@@ -396,9 +396,9 @@ export const saveGenesetsAction = () => async (dispatch, getState) => {
   const { lastTid, genesets } = state.genesets;
 
   const genesetsAreAvailable =
-    config?.parameters?.["annotations_genesets"] ?? false;
+    config?.parameters?.annotations_genesets ?? false;
   const genesetsReadonly =
-    config?.parameters?.["annotations_genesets_readonly"] ?? true;
+    config?.parameters?.annotations_genesets_readonly ?? true;
   if (!genesetsAreAvailable || genesetsReadonly) {
     // our non-save was completed!
     return dispatch({

client/src/actions/geneset.js

@@ -0,0 +1,126 @@
+/*
+Action creators for gene sets
+
+Primarily used to keep the crossfilter and underlying data in sync with the UI.
+
+The behavior manifest in these action creators:
+
+    Delete a gene set, will
+      * drop index & clear selection state on the gene set summary
+      * drop index & clear selection state of each gene in the geneset
+
+    Delete a gene from a gene set, will:
+      * drop index & clear selection state on the gene set summary
+      * drop index & clear selection state on the gene
+
+    Add a gene to a gene set, will:
+      * drop index & clear selection state on the gene set summary
+      * will NOT touch the selection state for the gene
+  
+Note that crossfilter indices are lazy created, as needed.
+*/
+
+export const genesetDelete = (genesetName) => (dispatch, getState) => {
+  const state = getState();
+  const { genesets } = state;
+  const gs = genesets?.genesets?.get(genesetName) ?? {};
+  const geneSymbols = Array.from(gs.genes.keys());
+  const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
+  dispatch({
+    type: "geneset: delete",
+    genesetName,
+    obsCrossfilter,
+    annoMatrix: obsCrossfilter.annoMatrix,
+  });
+};
+
+export const genesetAddGenes = (genesetName, genes) => (dispatch, getState) => {
+  const state = getState();
+  const { obsCrossfilter: prevObsCrossfilter } = state;
+  const obsCrossfilter = dropGenesetSummaryDimension(
+    prevObsCrossfilter,
+    state,
+    genesetName
+  );
+  dispatch({
+    type: "continuous metadata histogram cancel",
+    continuousNamespace: { isGeneSetSummary: true },
+    selection: genesetName,
+  });
+  return dispatch({
+    type: "geneset: add genes",
+    genesetName,
+    genes,
+    obsCrossfilter,
+    annoMatrix: obsCrossfilter.annoMatrix,
+  });
+};
+
+export const genesetDeleteGenes = (genesetName, geneSymbols) => (
+  dispatch,
+  getState
+) => {
+  const state = getState();
+  const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
+  return dispatch({
+    type: "geneset: delete genes",
+    genesetName,
+    geneSymbols,
+    obsCrossfilter,
+    annoMatrix: obsCrossfilter.annoMatrix,
+  });
+};
+
+/*
+Private
+*/
+
+function dropGenesetSummaryDimension(obsCrossfilter, state, genesetName) {
+  const { annoMatrix, genesets } = state;
+  const varIndex = annoMatrix.schema.annotations?.var?.index;
+  const gs = genesets?.genesets?.get(genesetName) ?? {};
+  const genes = Array.from(gs.genes.keys());
+  const query = {
+    summarize: {
+      method: "mean",
+      field: "var",
+      column: varIndex,
+      values: genes,
+    },
+  };
+  return obsCrossfilter.dropDimension("X", query);
+}
+
+function dropGeneDimension(obsCrossfilter, state, gene) {
+  const { annoMatrix } = state;
+  const varIndex = annoMatrix.schema.annotations?.var?.index;
+  const query = {
+    where: {
+      field: "var",
+      column: varIndex,
+      value: gene,
+    },
+  };
+  return obsCrossfilter.dropDimension("X", query);
+}
+
+function dropGeneset(dispatch, state, genesetName, geneSymbols) {
+  const { obsCrossfilter: prevObsCrossfilter } = state;
+  const obsCrossfilter = geneSymbols.reduce(
+    (crossfilter, gene) => dropGeneDimension(crossfilter, state, gene),
+    dropGenesetSummaryDimension(prevObsCrossfilter, state, genesetName)
+  );
+  dispatch({
+    type: "continuous metadata histogram cancel",
+    continuousNamespace: { isGeneSetSummary: true },
+    selection: genesetName,
+  });
+  geneSymbols.forEach((g) =>
+    dispatch({
+      type: "continuous metadata histogram cancel",
+      continuousNamespace: { isUserDefined: true },
+      selection: g,
+    })
+  );
+  return obsCrossfilter;
+}

client/src/actions/index.js

@@ -13,6 +13,7 @@ import * as selnActions from "./selection";
 import * as annoActions from "./annotation";
 import * as viewActions from "./viewStack";
 import * as embActions from "./embedding";
+import * as genesetActions from "./geneset";
 
 /*
 return promise fetching user-configured colors
@@ -58,7 +59,7 @@ async function genesetsFetch(dispatch, config) {
     genesets: [],
     tid: 0,
   };
-  if (config?.parameters?.["annotations_genesets"] ?? false) {
+  if (config?.parameters?.annotations_genesets ?? false) {
     fetchJson("genesets").then((response) => {
       dispatch({
         type: "geneset: initial load",
@@ -111,7 +112,7 @@ const doInitialDataLoad = () =>
       });
       dispatch({ type: "initial data load complete" });
 
-      const defaultEmbedding = config?.parameters?.["default_embedding"];
+      const defaultEmbedding = config?.parameters?.default_embedding;
       const layoutSchema = schema?.schema?.layout?.obs ?? [];
       if (
         defaultEmbedding &&
@@ -269,4 +270,7 @@ export default {
   needToSaveObsAnnotations: annoActions.needToSaveObsAnnotations,
   layoutChoiceAction: embActions.layoutChoiceAction,
   setCellSetFromSelection: selnActions.setCellSetFromSelection,
+  genesetDelete: genesetActions.genesetDelete,
+  genesetAddGenes: genesetActions.genesetAddGenes,
+  genesetDeleteGenes: genesetActions.genesetDeleteGenes,
 };