Graceful Failure for Firebrowse Errors

main/js/afterSubmit.js

@@ -37,7 +37,8 @@ const buildPlots = async function() {
 
   if (isEmpty(selectedTumorTypes) || isEmpty(allSelectedGenes) ) {
     console.log("user did not provide enough information for query");
-    window.alert("Please select at least one tumor type and gene.");
+    let message = "Please select at least one tumor type and gene to generate plots.";
+    handleDataFetchError(message);
     return null;
   }
 
@@ -86,7 +87,8 @@ const buildPlots = async function() {
   }
   else {
     //Set screen text to indicate that no plots were generated due to lack of patient barcodes
-    handleEmptyCohort();
+    message = "The gene mutation and/or metadata filter(s) produced a cohort with no patients. To see figures, please change the gene mutation and/or metadata filter(s).";
+    handleDataFetchError(message);
     return null;
   }
   expressionData = (expressionData || []).filter(
@@ -533,14 +535,15 @@ let downloadClinicalData = function(cohortID, clinicalData, barcodes_clin) {
   }
 }
 
-let handleEmptyCohort = function () {
-  let empty_cohort_message = "The gene mutation and/or metadata filter(s) produced a cohort with no patients. To see figures, please change the gene mutation and/or metadata filter(s)."
+let handleDataFetchError = function (message) {
   // Remove the loaders from heatmap, violin, and survival tabs
   document.getElementById("heatmapLoaderDiv").classList.remove("loader");
   document.getElementById("violinLoaderDiv").classList.remove("loader");
   document.getElementById("survivalLoaderDiv").classList.remove("loader");
   // Set text of each plot tab
-  d3.select("#heatmapLoaderDiv").html(empty_cohort_message);
-  d3.select("#violinLoaderDiv").html(empty_cohort_message);
-  d3.select("#survivalLoaderDiv").html(empty_cohort_message);
+  error_message_font_size = "16px";
+  error_message_font_color = "#8B0000";
+  d3.select("#heatmapLoaderDiv").html(message).style("color", error_message_font_color).style("font-size", error_message_font_size);
+  d3.select("#violinLoaderDiv").html(message).style("color", error_message_font_color).style("font-size", error_message_font_size);
+  d3.select("#survivalLoaderDiv").html(message).style("color", error_message_font_color).style("font-size", error_message_font_size);
 };

main/js/dataAcquisition/fetch.js

@@ -28,7 +28,7 @@ const _fetchFromFireBrowse = async function(endpoint, params, expectedKey) {
     const json = await response.json();
     return json;
   } catch(error) {
-    console.log(`${expectedKey} is empty, returning an object with empty ${expectedKey} `);
+    console.warn(`${expectedKey} is empty, returning an object with empty ${expectedKey} `);
     return minimalJson;
   }
 };
@@ -163,7 +163,11 @@ firebrowse.fetch = async function(endpoint, params, groupBy) {
       ProgressBar.setPercentage(i/paramsMatrix.length*100, "Fetching " + expectedKey);
       // Run a fetch and then collect the data into one common object.
       await _fetchFromFireBrowse(endpoint, paramsForThisCall, expectedKey)
-        .then(x => {results[expectedKey].push(...x[expectedKey])});
+        .then(x => {
+          // Verify retrieved data has expectedKey as a field
+          if(expectedKey in x)
+            results[expectedKey].push(...x[expectedKey])
+        });
     }
     ProgressBar.cleanUp();
     return results;
@@ -205,7 +209,12 @@ firebrowse.fetchClinicalFH = async function({cohorts, genes, barcodes, pageNum})
     groupBy.push({key: "tcga_participant_barcode", length: 50});
   }
   const data = await firebrowse.fetch("/Samples/Clinical_FH", params, groupBy);
-  return data.Clinical_FH;
+  // Check that firebrowse.fetch() returned properly formatted data
+  let data_field = "Clinical_FH";
+  if(data_field in data)
+    return data[data_field];
+  else
+    throw new Error("Clinical data could not be fetched from Firebrowse");
 };
 
 
@@ -219,8 +228,13 @@ firebrowse.fetchClinicalFH = async function({cohorts, genes, barcodes, pageNum})
  */
 firebrowse.fetchCohorts = async function() {
   const params = { format: "json" };
+  //Check that Firebrowse fetch returned properly formatted data
   const fetchResponse = await firebrowse.fetch("/Metadata/Cohorts", params);
-  return fetchResponse.Cohorts;
+  let data_field = "Cohorts";
+  if(data_field in fetchResponse)
+    return fetchResponse[data_field];
+  else
+    throw new Error("Cohort names could not be fetched from Firebrowse");
 };
 
 /** Get the number of mRNASeq samples per cohort.
@@ -242,8 +256,12 @@ firebrowse.fetchCounts = async function(cohorts) {
     data_type: "mrnaseq",
     totals: "true",
   };
-  const fetchResponse = await firebrowse.fetch("/Metadata/Counts", params);
-  return fetchResponse.Counts;
+  const data = await firebrowse.fetch("/Metadata/Counts", params);
+  let data_field = "Counts"
+  if(data_field in data)
+    return data[data_field];
+  else
+    throw new Error("Cohort counts could not be fetched from Firebrowse");
 };
 
 firebrowse.fetchMutationMAF = async function ({cohorts, genes}) {
@@ -275,7 +293,11 @@ firebrowse.fetchMutationMAF = async function ({cohorts, genes}) {
   else {
     data = await firebrowse.fetch("/Analyses/Mutation/MAF", params, groupBy);
   }
-  return data.MAF;
+  let data_field = "MAF"
+  if(data_field in data)
+    return data[data_field];
+  else
+    throw new Error("Could not fetch MAF mutation data from Firehose");
 };
 
 
@@ -324,7 +346,12 @@ firebrowse.fetchmRNASeq = async function({cohorts, genes, barcodes}) {
     groupBy.push({key: "tcga_participant_barcode", length: 400});
   }
   const data = await firebrowse.fetch("/Samples/mRNASeq", params, groupBy);
-  return data.mRNASeq;
+  let data_field = "mRNASeq"
+  if(data_field in data)
+    return data[data_field];
+  else
+    throw new Error("Could not fetch mRNASeq expression data from Firehose");
+
 };
 
 // Prevent any changes to this object.

main/js/fillSelectBoxes.js

@@ -12,31 +12,35 @@
  * @returns {undefined}
  */
 const fillCancerTypeSelectBox = async function () {
-  const cancerTypesQuery = await firebrowse.fetchCohorts();
-  const cancerTypesQueryNoFPPP = cancerTypesQuery.reduce((acc, item) => item.cohort !== 'FPPP' ? [...acc, item] : acc, []);
-  cancerTypesQueryNoFPPP.sort();
-  let selectBox = document.getElementById("cancerTypeMultipleSelection");
-  for (let i = 0; i < cancerTypesQueryNoFPPP.length; i++) {
-    let currentOption = document.createElement("option");
-    currentOption.value = cancerTypesQueryNoFPPP[i]["cohort"];
-    currentOption.text =
-      "(" +
-      cancerTypesQueryNoFPPP[i]["cohort"] +
-      ") " +
-      cancerTypesQueryNoFPPP[i]["description"];
-    currentOption.id = cancerTypesQueryNoFPPP[i]["cohort"];
-    selectBox.appendChild(currentOption);
-  }
-  let cancerTypeSelectedOptions = localStorage
-    .getItem("cancerTypeSelectedOptions") || null
-  if (cancerTypeSelectedOptions) {
-    cancerTypeSelectedOptions = cancerTypeSelectedOptions.split(",");
-    $(".cancerTypeMultipleSelection").val(cancerTypeSelectedOptions);
-    $(".cancerTypeMultipleSelection").trigger('change');
-  }
-
-  return true;
+  try {
+    const cancerTypesQuery = await firebrowse.fetchCohorts();
+    const cancerTypesQueryNoFPPP = cancerTypesQuery.reduce((acc, item) => item.cohort !== 'FPPP' ? [...acc, item] : acc, []);
+    cancerTypesQueryNoFPPP.sort();
+    let selectBox = document.getElementById("cancerTypeMultipleSelection");
+    for (let i = 0; i < cancerTypesQueryNoFPPP.length; i++) {
+      let currentOption = document.createElement("option");
+      currentOption.value = cancerTypesQueryNoFPPP[i]["cohort"];
+      currentOption.text =
+        "(" +
+        cancerTypesQueryNoFPPP[i]["cohort"] +
+        ") " +
+        cancerTypesQueryNoFPPP[i]["description"];
+      currentOption.id = cancerTypesQueryNoFPPP[i]["cohort"];
+      selectBox.appendChild(currentOption);
+    }
+    let cancerTypeSelectedOptions = localStorage
+      .getItem("cancerTypeSelectedOptions") || null
+    if (cancerTypeSelectedOptions) {
+      cancerTypeSelectedOptions = cancerTypeSelectedOptions.split(",");
+      $(".cancerTypeMultipleSelection").val(cancerTypeSelectedOptions);
+      $(".cancerTypeMultipleSelection").trigger('change');
+    }
 
+    return true;
+  } catch (err) {
+    message = "Could not fetch the cancer types from Firebrowse";
+    handleDataFetchError(message);
+  }
 };
 
 /////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
@@ -67,53 +71,58 @@ let displayNumberSamples = async function () {
     .select2("data")
     .map((cohortInfo) => cohortInfo.text.match(/\(([^)]+)\)/)[1]);
   if (myCohort.length != 0) {
-    // get counts of samples for selected tumor types:
-    numbersOfSamples = await firebrowse.fetchCounts(myCohort);
-    let formatted_numbersOfSamples = numbersOfSamples.map(x => {
-      const container = {};
-      container.cohort = x.cohort.substring(0, numbersOfSamples[0].cohort.indexOf('-'));
-      container.mrnaseq = x.mrnaseq;
-      return container;
-    });
-    // order counts array based on order in which tumor types were selected:
-    function orderThings (array, order, key) {
-      array.sort(function (a, b) {
-        var A = a[key], B = b[key];
-        if (order.indexOf(A) > order.indexOf(B)) {
-          return 1;
+    try {
+      // get counts of samples for selected tumor types:
+      numbersOfSamples = await firebrowse.fetchCounts(myCohort);
+      let formatted_numbersOfSamples = numbersOfSamples.map(x => {
+        const container = {};
+        container.cohort = x.cohort.substring(0, numbersOfSamples[0].cohort.indexOf('-'));
+        container.mrnaseq = x.mrnaseq;
+        return container;
+      });
+      // order counts array based on order in which tumor types were selected:
+      function orderThings (array, order, key) {
+        array.sort(function (a, b) {
+          var A = a[key], B = b[key];
+          if (order.indexOf(A) > order.indexOf(B)) {
+            return 1;
+          } else {
+            return -1;
+          }
+        });
+        return array;
+      };
+      orderedCountQuery = orderThings(formatted_numbersOfSamples, myCohort, 'cohort')
+      // build label:
+      let numSamplesLabel = "";
+      let para;
+      for (let i = 0; i < orderedCountQuery.length; i++) {
+        if (numSamplesLabel == "") {
+          numSamplesLabel += orderedCountQuery[i].cohort + ": " + orderedCountQuery[i].mrnaseq;
+          para = document.createElement("P");
+          para.setAttribute(
+            "style",
+            'text-align: center; color: #4db6ac; font-family: Georgia, "Times New Roman", Times, serif'
+          );
+          para.setAttribute("id", "numSamplesText");
+          para.innerText = "Number of samples: " + numSamplesLabel;
+          cancerQuerySelectBox.appendChild(para);
         } else {
-          return -1;
+          document.getElementById("numSamplesText").remove();
+          numSamplesLabel += ", " + orderedCountQuery[i].cohort +
+                  ": " + orderedCountQuery[i].mrnaseq;
+          para.setAttribute(
+            "style",
+            'text-align: center; color: #4db6ac; font-family: Georgia, "Times New Roman", Times, serif'
+          );
+          para.setAttribute("id", "numSamplesText");
+          para.innerText = "Number of samples: " + numSamplesLabel;
+          cancerQuerySelectBox.appendChild(para);
         }
-      });
-      return array;
-    };
-    orderedCountQuery = orderThings(formatted_numbersOfSamples, myCohort, 'cohort')
-    // build label:
-    let numSamplesLabel = "";
-    let para;
-    for (let i = 0; i < orderedCountQuery.length; i++) {
-      if (numSamplesLabel == "") {
-        numSamplesLabel += orderedCountQuery[i].cohort + ": " + orderedCountQuery[i].mrnaseq;
-        para = document.createElement("P");
-        para.setAttribute(
-          "style",
-          'text-align: center; color: #4db6ac; font-family: Georgia, "Times New Roman", Times, serif'
-        );
-        para.setAttribute("id", "numSamplesText");
-        para.innerText = "Number of samples: " + numSamplesLabel;
-        cancerQuerySelectBox.appendChild(para);
-      } else {
-        document.getElementById("numSamplesText").remove();
-        numSamplesLabel += ", " + orderedCountQuery[i].cohort +
-                 ": " + orderedCountQuery[i].mrnaseq;
-        para.setAttribute(
-          "style",
-          'text-align: center; color: #4db6ac; font-family: Georgia, "Times New Roman", Times, serif'
-        );
-        para.setAttribute("id", "numSamplesText");
-        para.innerText = "Number of samples: " + numSamplesLabel;
-        cancerQuerySelectBox.appendChild(para);
       }
+    } catch(err) {
+      message = "Could not fetch the cancer type counts from Firebrowse";
+      handleDataFetchError(message);
     }
   }
 };