Merge pull request #586 from nextstrain/meta-safety-checks

Meta safety checks

src/actions/loadData.js

@@ -103,9 +103,8 @@ const fetchDataAndDispatch = (dispatch, datasets, query, s3bucket, narrativeJSON
       values.forEach((v, i) => {
         if (v) data.JSONs[promisesOrder[i]] = v; // if statement removes undefinds
       });
-      // console.log(data);
-      if (!(data.JSONs.meta && data.JSONs.tree)) {
-        console.error("Tree & Meta JSONs could not be loaded.");
+      if (!data.JSONs.tree) {
+        console.error("Tree JSON could not be loaded.");
         dispatch(goTo404(`
           Auspice attempted to load JSONs for the dataset "${datasets.datapath.replace(/_/g, '/')}", but they couldn't be found.
         `));

src/actions/recomputeReduxState.js

@@ -147,7 +147,7 @@ const modifyStateViaMetadata = (state, metadata) => {
     // need authors in metadata.filters to include as filter
     // but metadata.author_info is generally required for app functioning
   } else {
-    console.error("the meta.json must include author_info");
+    console.warn("the meta.json did not include author_info");
   }
   if (metadata.filters) {
     metadata.filters.forEach((v) => {
@@ -179,8 +179,25 @@ const modifyStateViaMetadata = (state, metadata) => {
     }
   }
 
-  state.panelsAvailable = metadata.panels.slice();
-  state.panelsToDisplay = metadata.panels.slice();
+  if (metadata.panels) {
+    state.panelsAvailable = metadata.panels.slice();
+    state.panelsToDisplay = metadata.panels.slice();
+  } else {
+    state.panelsAvailable = ["tree"];
+    state.panelsToDisplay = ["tree"];
+  }
+
+  /* if metadata lacks geo, remove map from panels to display */
+  if (!metadata.geo) {
+    state.panelsAvailable = state.panelsAvailable.filter((item) => item !== "map");
+    state.panelsToDisplay = state.panelsToDisplay.filter((item) => item !== "map");
+  }
+
+  /* if metadata lacks annotations, remove entropy from panels to display */
+  if (!metadata.annotations) {
+    state.panelsAvailable = state.panelsAvailable.filter((item) => item !== "entropy");
+    state.panelsToDisplay = state.panelsToDisplay.filter((item) => item !== "entropy");
+  }
 
   /* if only map or only tree, then panelLayout must be full */
   /* note - this will be overwritten by the URL query */
@@ -189,13 +206,17 @@ const modifyStateViaMetadata = (state, metadata) => {
     state.canTogglePanelLayout = false;
   }
   /* annotations in metadata */
-  if (!metadata.annotations) {console.error("Metadata needs updating with annotations field. Rerun augur. FATAL.");}
-  for (const gene of Object.keys(metadata.annotations)) {
-    state.geneLength[gene] = metadata.annotations[gene].end - metadata.annotations[gene].start;
-    if (gene !== "nuc") {
-      state.geneLength[gene] /= 3;
+  if (metadata.annotations) {
+    for (const gene of Object.keys(metadata.annotations)) {
+      state.geneLength[gene] = metadata.annotations[gene].end - metadata.annotations[gene].start;
+      if (gene !== "nuc") {
+        state.geneLength[gene] /= 3;
+      }
     }
+  } else {
+    console.warn("The meta.json did not include annotations.");
   }
+
   return state;
 };
 
@@ -246,14 +267,22 @@ const checkAndCorrectErrorsInState = (state, metadata) => {
   a URL QUERY (and correct it in state), we can't correct the URL */
 
   /* colorBy */
+  if (!metadata.colorOptions) {
+    metadata.colorOptions = {};
+  }
   if (Object.keys(metadata.colorOptions).indexOf(state.colorBy) === -1 && !state["colorBy"].startsWith("gt-")) {
     const availableNonGenotypeColorBys = Object.keys(metadata.colorOptions);
     if (availableNonGenotypeColorBys.indexOf("gt") > -1) {
       availableNonGenotypeColorBys.splice(availableNonGenotypeColorBys.indexOf("gt"), 1);
     }
     console.error("Error detected trying to set colorBy to", state.colorBy, "(valid options are", Object.keys(metadata.colorOptions).join(", "), "). Setting to", availableNonGenotypeColorBys[0]);
-    state.colorBy = availableNonGenotypeColorBys[0];
-    state.defaults.colorBy = availableNonGenotypeColorBys[0];
+    if (Object.keys(metadata.colorOptions).length > 0) {
+      state.colorBy = availableNonGenotypeColorBys[0];
+      state.defaults.colorBy = availableNonGenotypeColorBys[0];
+    } else {
+      state.colorBy = "none";
+      state.defaults.colorBy = "none";
+    }
   }
 
   /* colorBy confidence */
@@ -266,10 +295,14 @@ const checkAndCorrectErrorsInState = (state, metadata) => {
   }
 
   /* geoResolution */
-  const availableGeoResultions = Object.keys(metadata.geo);
-  if (availableGeoResultions.indexOf(state["geoResolution"]) === -1) {
-    state["geoResolution"] = availableGeoResultions[0];
-    console.error("Error detected. Setting geoResolution to ", state["geoResolution"]);
+  if (metadata.geo) {
+    const availableGeoResultions = Object.keys(metadata.geo);
+    if (availableGeoResultions.indexOf(state["geoResolution"]) === -1) {
+      state["geoResolution"] = availableGeoResultions[0];
+      console.error("Error detected. Setting geoResolution to ", state["geoResolution"]);
+    }
+  } else {
+    console.warn("The meta.json did not include geo info.");
   }
 
   /* temporalConfidence */
@@ -284,8 +317,12 @@ const checkAndCorrectErrorsInState = (state, metadata) => {
   }
 
   /* if colorBy is a genotype then we need to set mutType */
-  const maybeMutType = determineColorByGenotypeType(state.colorBy);
-  if (maybeMutType) state.mutType = maybeMutType;
+  if (state.colorBy) {
+    const maybeMutType = determineColorByGenotypeType(state.colorBy);
+    if (maybeMutType) {
+      state.mutType = maybeMutType;
+    }
+  }
 
   return state;
 };
@@ -348,21 +385,24 @@ export const createStateFromQueryOrJSONs = ({
   /* first task is to create metadata, entropy, controls & tree partial state */
   if (JSONs) {
     if (JSONs.narrative) narrative = JSONs.narrative;
-    /* ceate metadata state */
+    /* create metadata state */
     metadata = JSONs.meta;
+    if (metadata === undefined) {
+      metadata = {};
+    }
     if (Object.prototype.hasOwnProperty.call(metadata, "loaded")) {
       console.error("Metadata JSON must not contain the key \"loaded\". Ignoring.");
     }
     metadata.colorOptions = metadata.color_options;
     delete metadata.color_options;
     metadata.loaded = true;
     /* entropy state */
-    entropy = entropyCreateStateFromJsons(JSONs.meta);
+    entropy = entropyCreateStateFromJsons(metadata);
     /* new tree state(s) */
-    tree = treeJsonToState(JSONs.tree, JSONs.meta.vaccine_choices);
+    tree = treeJsonToState(JSONs.tree, metadata.vaccine_choices);
     tree.debug = "LEFT";
     if (JSONs.treeToo) {
-      treeToo = treeJsonToState(JSONs.treeToo, JSONs.meta.vaccine_choices);
+      treeToo = treeJsonToState(JSONs.treeToo, metadata.vaccine_choices);
       treeToo.debug = "RIGHT";
     }
     /* new controls state - don't apply query yet (or error check!) */
@@ -415,9 +455,11 @@ export const createStateFromQueryOrJSONs = ({
   }
 
   /* calculate entropy in view */
-  const [entropyBars, entropyMaxYVal] = calcEntropyInView(tree.nodes, tree.visibility, controls.mutType, entropy.geneMap, entropy.showCounts);
-  entropy.bars = entropyBars;
-  entropy.maxYVal = entropyMaxYVal;
+  if (entropy.loaded) {
+    const [entropyBars, entropyMaxYVal] = calcEntropyInView(tree.nodes, tree.visibility, controls.mutType, entropy.geneMap, entropy.showCounts);
+    entropy.bars = entropyBars;
+    entropy.maxYVal = entropyMaxYVal;
+  }
 
   /* potentially calculate frequency (or update it!)
   this needs to come after the colorscale & tree is set */

src/components/download/helperFunctions.js

@@ -83,15 +83,17 @@ export const authorCSV = (dispatch, filePrefix, metadata, tree) => {
     }
   });
   const body = [];
-  for (const author of Object.keys(metadata.author_info)) {
-    body.push([
-      prettyString(author, {camelCase: false}),
-      metadata.author_info[author].n,
-      prettyString(metadata.author_info[author].title, {removeComma: true}),
-      prettyString(metadata.author_info[author].journal, {removeComma: true}),
-      isPaperURLValid(metadata.author_info[author]) ? formatURLString(metadata.author_info[author].paper_url) : "unknown",
-      authors[author].join(" ")
-    ]);
+  if (metadata.author_info) {
+    for (const author of Object.keys(metadata.author_info)) {
+      body.push([
+        prettyString(author, {camelCase: false}),
+        metadata.author_info[author].n,
+        prettyString(metadata.author_info[author].title, {removeComma: true}),
+        prettyString(metadata.author_info[author].journal, {removeComma: true}),
+        isPaperURLValid(metadata.author_info[author]) ? formatURLString(metadata.author_info[author].paper_url) : "unknown",
+        authors[author].join(" ")
+      ]);
+    }
   }
 
   body.forEach((line) => { lineArray.push(line.join(",")); });

src/components/info/info.js

@@ -115,8 +115,10 @@ class Info extends React.Component {
   }
 
   getNumSelectedAuthors() {
-    if (!Object.prototype.hasOwnProperty.call(this.props.filters, "authors") || this.props.filters.authors.length === 0) {
-      return Object.keys(this.props.metadata.author_info).length;
+    if (this.props.metadata.author_info) {
+      if (!Object.prototype.hasOwnProperty.call(this.props.filters, "authors") || this.props.filters.authors.length === 0) {
+        return Object.keys(this.props.metadata.author_info).length;
+      }
     }
     return this.props.filters.authors.length;
   }

src/components/tree/infoPanels/click.js

@@ -84,7 +84,17 @@ const TipClickedPanel = ({tip, goAwayCallback, metadata}) => {
   const url = validAttr(tip.n.attr, "url") ? formatURL(tip.n.attr.url) : false;
   const uncertainty = "num_date_confidence" in tip.n.attr && tip.n.attr.num_date_confidence[0] !== tip.n.attr.num_date_confidence[1];
   const author = tip.n.attr.authors || undefined;
-  const authorInfo = metadata.author_info;
+  let authorInfo = {
+    author: {
+      n: null,
+      title: null,
+      journal: null,
+      paper_url: null
+    }
+  };
+  if (metadata.author_info) {
+    authorInfo = metadata.author_info;
+  }
   return (
     <div style={styles.container} onClick={() => goAwayCallback(tip)}>
       <div className={"panel"} style={infoPanelStyles.panel} onClick={(e) => stopProp(e)}>

src/util/colorScale.js

@@ -8,7 +8,7 @@ import { getExtraVals } from "./colorHelpers";
 import { parseEncodedGenotype } from "./getGenotype";
 import { setGenotype, orderOfGenotypeAppearance } from "./setGenotype";
 
-const unknownColor = "#DDDDDD";
+const unknownColor = "#AAAAAA";
 
 const getMinMaxFromTree = (nodes, nodesToo, attr) => {
   const arr = nodesToo ? nodes.concat(nodesToo) : nodes.slice();
@@ -80,7 +80,24 @@ const createLegendBounds = (legendValues) => {
 
 
 export const calcColorScale = (colorBy, controls, tree, treeToo, metadata) => {
-  // console.log(`calcColorScale for ${colorBy}. TreeToo? ${!!treeToo}`)
+
+  if (colorBy === "none") {
+    console.warn("ColorScale fallthrough for colorBy set to none");
+    const colorScale = () => unknownColor;
+    const genotype = null;
+    const legendValues = ["unknown"];
+    const legendBounds = createLegendBounds(legendValues);
+    return {
+      scale: colorScale,
+      continuous: false,
+      colorBy: colorBy,
+      version: controls.colorScale === undefined ? 1 : controls.colorScale.version + 1,
+      legendValues,
+      legendBounds,
+      genotype
+    };
+  }
+
   let genotype;
   if (colorBy.slice(0, 3) === "gt-" && controls.geneLength) {
     genotype = parseEncodedGenotype(colorBy, controls.geneLength);

src/util/entropy.js

@@ -100,7 +100,9 @@ const calcEntropy = (nodes, visibility, geneMap, isAA) => {
     if (isAA) {
       if (node.aa_muts) {
         for (const prot in node.aa_muts) { // eslint-disable-line
-          node.aa_muts[prot].forEach(assignFn, [prot, state]);
+          if (arrayOfProts.includes(prot)) {
+            node.aa_muts[prot].forEach(assignFn, [prot, state]);
+          }
         }
       }
     } else if (node.muts && node.muts.length) {

src/util/entropyCreateStateFromJsons.js

@@ -33,12 +33,20 @@ const processAnnotations = (annotations) => {
 };
 
 export const entropyCreateStateFromJsons = (metaJSON) => {
-  /* TODO check that metadata defines the entropy panel */
-  const annotations = getAnnotations(metaJSON.annotations);
+  if (metaJSON.annotations) {
+    const annotations = getAnnotations(metaJSON.annotations);
+    return {
+      showCounts: false,
+      loaded: true,
+      annotations,
+      geneMap: processAnnotations(annotations)
+    };
+  }
+  const annotations = [];
   return {
     showCounts: false,
-    loaded: true,
+    loaded: false,
     annotations,
-    geneMap: processAnnotations(annotations)
+    geneMap: {}
   };
 };