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/util/actionHelpers.js

@@ -30,22 +30,27 @@ export function catchErrorsWrap(fn, dispatchToUser = false) {
   };
 }
 
-/*
-Wrapper to perform async fetch with some modest error handling
-and decoding.
-*/
-const doFetch = async (url, acceptType) => {
+/**
+ * Wrapper to perform async fetch with some modest error handling
+ * and decoding.  Arguments are identical to standard fetch.
+ */
+export const doFetch = async (url, init = {}) => {
   try {
-    const res = await fetch(url, {
+    // add defaults to the fetch init param.
+    init = {
       method: "get",
-      headers: new Headers({
-        Accept: acceptType,
-      }),
       credentials: "include",
-    });
-    if (res.ok && res.headers.get("Content-Type").includes(acceptType)) {
+      ...init,
+    };
+    const acceptType = init.headers?.get("Accept");
+    const res = await fetch(url, init);
+    if (
+      res.ok &&
+      (!acceptType || res.headers.get("Content-Type").includes(acceptType))
+    ) {
       return res;
     }
+
     // else an error
     const msg = `Unexpected HTTP response ${res.status}, ${res.statusText}`;
     dispatchNetworkErrorMessageToUser(msg);
@@ -61,16 +66,22 @@ const doFetch = async (url, acceptType) => {
 /*
 Wrapper to perform an async fetch and JSON decode response.
 */
-export const doJsonRequest = async (url) => {
-  const res = await doFetch(url, "application/json");
+export const doJsonRequest = async (url, init = {}) => {
+  const res = await doFetch(url, {
+    ...init,
+    headers: new Headers({ Accept: "application/json" }),
+  });
   return res.json();
 };
 
 /*
 Wrapper to perform an async fetch for binary data.
 */
-export const doBinaryRequest = async (url) => {
-  const res = await doFetch(url, "application/octet-stream");
+export const doBinaryRequest = async (url, init = {}) => {
+  const res = await doFetch(url, {
+    ...init,
+    headers: new Headers({ Accept: "application/octet-stream" }),
+  });
   return res.arrayBuffer();
 };
 

client/src/util/nameCreators.js

@@ -8,6 +8,9 @@ have a obsAnnotation named X, but we are using that for layout. So
 we namespace, and abstract to avoid proliferating strings throughout the
 codebase.
 
+It is _no longer_ used to remove collisions in the crossfilter or
+anno matrix namespaces. It is still used by the component tier.
+
 */
 
 const makeDimensionName = (namespace, key) => `${namespace}_${key}`;
@@ -18,12 +21,15 @@ export const diffexpDimensionName = (key) =>
   makeDimensionName("varData_diffexp", key);
 export const userDefinedDimensionName = (key) =>
   makeDimensionName("varData_userDefined", key);
+export const geneSetSummaryDimensionName = (key) =>
+  makeDimensionName("geneSetSummary", key);
 
 /*
     continuousNamespace = {
     isObs: true,
     isDiffExp: false,
-    isUserDefined: false
+    isUserDefined: false,
+    isGeneSet: false,
   }
 
   ie., makeContinuousDimensionName(continuousNamespace = {isObs: true}, "total_reads")
@@ -37,6 +43,8 @@ export const makeContinuousDimensionName = (continuousNamespace, key) => {
     name = diffexpDimensionName(key);
   } else if (continuousNamespace.isUserDefined) {
     name = userDefinedDimensionName(key);
+  } else if (continuousNamespace.isGeneSetSummary) {
+    name = geneSetSummaryDimensionName(key);
   } else {
     throw new Error("unknown continuous dimension");
   }

client/src/util/stateManager/colorHelpers.js

@@ -25,9 +25,11 @@ export function createColorQuery(colorMode, colorByAccessor, schema) {
       return [
         "X",
         {
-          field: "var",
-          column: varIndex,
-          value: colorByAccessor,
+          where: {
+            field: "var",
+            column: varIndex,
+            value: colorByAccessor,
+          },
         },
       ];
     }

client/src/util/stateManager/index.js

@@ -4,8 +4,16 @@ This is all VERY tightly integrated with reducers and actions, and
 exists to support those concepts.
 */
 
-export * as ColorHelpers from "./colorHelpers";
-export * as ControlsHelpers from "./controlsHelpers";
-export * as AnnotationsHelpers from "./annotationsHelpers";
-export * as SchemaHelpers from "./schemaHelpers";
-export * as MatrixFBS from "./matrix";
+import * as ColorHelpers from "./colorHelpers";
+import * as ControlsHelpers from "./controlsHelpers";
+import * as AnnotationsHelpers from "./annotationsHelpers";
+import * as SchemaHelpers from "./schemaHelpers";
+import * as MatrixFBS from "./matrix";
+
+export {
+  ColorHelpers,
+  ControlsHelpers,
+  AnnotationsHelpers,
+  SchemaHelpers,
+  MatrixFBS,
+};