renaming backend, cellxgene to server, client respectively

client/src/actions/index.js

@@ -0,0 +1,232 @@
+// jshint esversion: 6
+import * as globals from "../globals";
+import store from "../reducers";
+import URI from "urijs";
+import _ from "lodash";
+
+const requestCells = (query = "") => {
+  return dispatch => {
+    dispatch({ type: "request cells started" });
+    return fetch(`${globals.API.prefix}${globals.API.version}cells${query}`, {
+      method: "get",
+      headers: new Headers({
+        "Content-Type": "application/json"
+      })
+    })
+      .then(res => res.json())
+      .then(
+        data => dispatch({ type: "request cells success", data }),
+        error => dispatch({ type: "request cells error", error })
+      );
+  };
+};
+
+/* SELECT */
+const regraph = () => {
+  return (dispatch, getState) => {
+    dispatch({ type: "regraph started" });
+
+    const state = getState();
+    const selectedMetadata = {};
+
+    _.each(state.controls.categoricalAsBooleansMap, (options, field) => {
+      let atLeastOneOptionDeselected = false;
+
+      _.each(options, (isActive, option) => {
+        if (!isActive) {
+          atLeastOneOptionDeselected = true;
+        }
+      });
+
+      if (atLeastOneOptionDeselected) {
+        _.each(options, (isActive, option) => {
+          if (isActive) {
+            if (selectedMetadata[field]) {
+              selectedMetadata[field].push(option);
+            } else if (!selectedMetadata[field]) {
+              selectedMetadata[field] = [option];
+            }
+          }
+        });
+      }
+    });
+
+    let uri = new URI();
+    uri.setSearch(selectedMetadata);
+    console.log(uri.search(), selectedMetadata);
+
+    dispatch(requestCells(uri.search())).then(res => {
+      if (res.error) {
+        dispatch({ type: "regraph error" });
+      } else {
+        dispatch({ type: "regraph success" });
+      }
+    });
+  };
+};
+
+const resetGraph = () => {
+  return (dispatch, getState) => {
+    dispatch({ type: "reset graph" });
+  };
+};
+
+const initialize = () => {
+  return (dispatch, getState) => {
+    dispatch({ type: "initialize started" });
+    fetch(`${globals.API.prefix}${globals.API.version}initialize`, {
+      method: "get",
+      headers: new Headers({
+        "Content-Type": "application/json"
+      })
+    })
+      .then(res => res.json())
+      .then(
+        data => dispatch({ type: "initialize success", data }),
+        error => dispatch({ type: "initialize error", error })
+      );
+  };
+};
+
+// This code defends against the case where /expression returns a cellname
+// never seen before (ie, not returned by /cells).   This should not happen
+// (see https://github.com/chanzuckerberg/cellxgene-rest-api/issues/34) but
+// occasionally does.
+//
+function cleanupExpressionResponse(data) {
+  const s = store.getState();
+  const metadata = s.controls.allCellsMetadataMap;
+  let errorFound = false;
+  data.data.cells = _.filter(data.data.cells, cell => {
+    if (!errorFound && !metadata[cell.cellname]) {
+      errorFound = true;
+      console.error(
+        "Warning: /expression REST API returned unexpected cell names -- discarding surprises."
+      );
+    }
+    return metadata[cell.cellname];
+  });
+
+  return data;
+}
+
+const requestGeneExpressionCounts = () => {
+  return (dispatch, getState) => {
+    dispatch({ type: "get expression started" });
+    fetch(`${globals.API.prefix}${globals.API.version}expression`, {
+      method: "get",
+      headers: new Headers({
+        accept: "application/json"
+      })
+    })
+      .then(res => res.json())
+      .then(data => cleanupExpressionResponse(data))
+      .then(
+        data => dispatch({ type: "get expression success", data }),
+        error => dispatch({ type: "get expression error", error })
+      );
+  };
+};
+
+const requestSingleGeneExpressionCountsForColoringPOST = gene => {
+  return (dispatch, getState) => {
+    dispatch({ type: "get single gene expression for coloring started" });
+    fetch(`${globals.API.prefix}${globals.API.version}expression`, {
+      method: "POST",
+      body: JSON.stringify({
+        genelist: [gene]
+      }),
+      headers: new Headers({
+        accept: "application/json",
+        "Content-Type": "application/json"
+      })
+    })
+      .then(res => res.json())
+      .then(data => cleanupExpressionResponse(data))
+      .then(
+        data =>
+          dispatch({
+            type: "color by expression",
+            gene: gene,
+            data
+          }),
+        error =>
+          dispatch({
+            type: "get single gene expression for coloring error",
+            error
+          })
+      );
+  };
+};
+
+const requestGeneExpressionCountsPOST = genes => {
+  return (dispatch, getState) => {
+    dispatch({ type: "get expression started" });
+    fetch(`${globals.API.prefix}${globals.API.version}expression`, {
+      method: "POST",
+      body: JSON.stringify({
+        genelist: genes
+      }),
+      headers: new Headers({
+        accept: "application/json",
+        "Content-Type": "application/json"
+      })
+    })
+      .then(res => res.json())
+      .then(data => cleanupExpressionResponse(data))
+      .then(
+        data => dispatch({ type: "get expression success", data }),
+        error => dispatch({ type: "get expression error", error })
+      );
+  };
+};
+
+const requestDifferentialExpression = (celllist1, celllist2, num_genes = 7) => {
+  return (dispatch, getState) => {
+    dispatch({ type: "request differential expression started" });
+    fetch(`${globals.API.prefix}${globals.API.version}diffexpression`, {
+      method: "POST",
+      body: JSON.stringify({
+        celllist1,
+        celllist2,
+        num_genes
+      }),
+      headers: new Headers({
+        accept: "application/json",
+        "Content-Type": "application/json"
+      })
+    })
+      .then(res => res.json())
+      .then(
+        data => {
+          /* kick off a secondary action to get all expression counts for all cells now that we know what the top expressed are */
+          dispatch(
+            requestGeneExpressionCountsPOST(
+              _.union(
+                data.data.celllist1.topgenes,
+                data.data.celllist2.topgenes
+              ) // ["GPM6B", "FEZ1", "TSPAN31", "PCSK1N", "TUBA1A", "GPM6A", "CLU", "FCER1G", "TYROBP", "C1QB", "CD74", "CYBA", "GPX1", "TMSB4X"]
+            )
+          );
+          /* then send the success case action through */
+          return dispatch({
+            type: "request differential expression success",
+            data
+          });
+        },
+        error =>
+          dispatch({ type: "request differential expression error", error })
+      );
+  };
+};
+
+export default {
+  initialize,
+  requestCells,
+  regraph,
+  resetGraph,
+  requestGeneExpressionCounts,
+  requestGeneExpressionCountsPOST,
+  requestSingleGeneExpressionCountsForColoringPOST,
+  requestDifferentialExpression
+};