All the zooms

docs-src/docs/advanced-functionality/view-settings.md

@@ -20,7 +20,7 @@ Each of these can be overridden by the JSON `display_defaults`, and then the vie
 * Default phylogeny distance measure is time, if available.
 * Default geographic resolution is "country", if available.
 * Default colouring is "country", if available.
-
+* Default branch labelling is "clade", if available.
 
 ## Dataset (JSON) configurable defaults
 
@@ -35,6 +35,7 @@ For instance, if you set `display_defaults.color_by` to `country`, but load the
 | `distance_measure`  | Phylogeny x-axis measure     | "div" or "num_date" |
 | `map_triplicate`    | Should the map repeat, so that you can pan further in each direction? | Boolean |
 | `layout`            | Tree layout        | "rect", "radial", "clock" or "unrooted |
+| `branch_label`      | Which set of branch labels are to be displayed | "aa", "lineage" |
 
 Furthermore, a JSON property `meta.panels` lists which panels auspice displays.
 If this is not included, then auspice tries to display as many as possible.
@@ -66,7 +67,9 @@ All URL queries modify the view away from the default settings -- if you change
 | `animate`  | Animation settings | |
 | `n`        | Narrative page number | `n=1` goes to the first page |
 | `s`        | Selected strain | `s=1_0199_PF` |
-| `clade`    | Labeled clade that tree is zoomed to | `clade=B3` (numeric values are buggy) |
+| `branchLabel` | Branch labels to display | `branchLabel=aa` |
+| `label`    | Labeled branch that tree is zoomed to | `label=clade:B3`, `label=lineage:relapse` |
+| `clade`    | _DEPRECATED_ Labeled clade that tree is zoomed to | `clade=B3` should now become `label=clade:B3` |
 
 
 **See this in action:**

src/actions/loadData.js

@@ -181,7 +181,8 @@ const fetchDataAndDispatch = async (dispatch, url, query, narrativeBlocks) => {
         query,
         narrativeBlocks,
         mainTreeName: secondTreeUrl ? mainDatasetUrl : null,
-        secondTreeName: secondTreeUrl ? secondTreeUrl : null
+        secondTreeName: secondTreeUrl ? secondTreeUrl : null,
+        dispatch
       })
     });
 
@@ -233,7 +234,7 @@ export const loadSecondTree = (secondTreeUrl, firstTreeUrl) => async (dispatch,
     return;
   }
   const oldState = getState();
-  const newState = createTreeTooState({treeTooJSON: secondJson.tree, oldState, originalTreeUrl: firstTreeUrl, secondTreeUrl: secondTreeUrl});
+  const newState = createTreeTooState({treeTooJSON: secondJson.tree, oldState, originalTreeUrl: firstTreeUrl, secondTreeUrl: secondTreeUrl, dispatch});
   dispatch({type: types.TREE_TOO_DATA, ...newState});
 };
 

src/actions/navigation.js

@@ -70,7 +70,7 @@ export const changePage = ({
   }
 
   /* the path (dataset) remains the same... but the state may be modulated by the query */
-  const newState = createStateFromQueryOrJSONs({oldState, query});
+  const newState = createStateFromQueryOrJSONs({oldState, query, dispatch});
   dispatch({
     type: URL_QUERY_CHANGE_WITH_COMPUTED_STATE,
     ...newState,
@@ -92,7 +92,7 @@ export const goTo404 = (errorMessage) => ({
 
 export const EXPERIMENTAL_showMainDisplayMarkdown = ({query, queryToDisplay}) =>
   (dispatch, getState) => {
-    const newState = createStateFromQueryOrJSONs({oldState: getState(), query});
+    const newState = createStateFromQueryOrJSONs({oldState: getState(), query, dispatch});
     newState.controls.panelsToDisplay = ["EXPERIMENTAL_MainDisplayMarkdown"];
     dispatch({
       type: URL_QUERY_CHANGE_WITH_COMPUTED_STATE,

src/actions/recomputeReduxState.js

@@ -100,6 +100,10 @@ const modifyStateViaURLQuery = (state, query) => {
   } else {
     state.animationPlayPauseButton = "Play";
   }
+  if (query.branchLabel) {
+    state.selectedBranchLabel = query.branchLabel;
+    // do not modify the default (only the JSON can do this)
+  }
   return state;
 };
 
@@ -164,8 +168,8 @@ const modifyStateViaMetadata = (state, metadata) => {
     console.warn("JSON did not include any filters");
   }
   if (metadata.displayDefaults) {
-    const keysToCheckFor = ["geoResolution", "colorBy", "distanceMeasure", "layout", "mapTriplicate"];
-    const expectedTypes = ["string", "string", "string", "string", "boolean"];
+    const keysToCheckFor = ["geoResolution", "colorBy", "distanceMeasure", "layout", "mapTriplicate", "selectedBranchLabel"];
+    const expectedTypes = ["string", "string", "string", "string", "boolean", "string"];
 
     for (let i = 0; i < keysToCheckFor.length; i += 1) {
       if (metadata.displayDefaults[keysToCheckFor[i]]) {
@@ -310,7 +314,13 @@ const modifyControlsStateViaTree = (state, tree, treeToo, colorings) => {
   state.distanceMeasure = state.branchLengthsToDisplay === "divOnly" ? "div" :
     state.branchLengthsToDisplay === "dateOnly" ? "num_date" : state.distanceMeasure;
 
-  state.selectedBranchLabel = tree.availableBranchLabels.indexOf("clade") !== -1 ? "clade" : "none";
+  /* if clade is available as a branch label, then set this as the "default". This
+  is largely due to historical reasons. Note that it *can* and *will* be overridden
+  by JSON display_defaults and URL query */
+  if (tree.availableBranchLabels.indexOf("clade") !== -1) {
+    state.defaults.selectedBranchLabel = "clade";
+    state.selectedBranchLabel = "clade";
+  }
 
   state.temporalConfidence = getTraitFromNode(tree.nodes[0], "num_date", {confidence: true}) ?
     {exists: true, display: true, on: false} :
@@ -395,6 +405,13 @@ const checkAndCorrectErrorsInState = (state, metadata, query, tree) => {
     console.warn("JSONs did not include `geoResolutions`");
   }
 
+  /* show label */
+  if (state.selectedBranchLabel && !tree.availableBranchLabels.includes(state.selectedBranchLabel)) {
+    console.error("Can't set selected branch label to ", state.selectedBranchLabel);
+    state.selectedBranchLabel = "none";
+    state.defaults.selectedBranchLabel = "none";
+  }
+
   /* temporalConfidence */
   if (state.temporalConfidence.exists) {
     if (state.layout !== "rect") {
@@ -436,7 +453,7 @@ const checkAndCorrectErrorsInState = (state, metadata, query, tree) => {
   return state;
 };
 
-const modifyTreeStateVisAndBranchThickness = (oldState, tipSelected, cladeSelected, controlsState) => {
+const modifyTreeStateVisAndBranchThickness = (oldState, tipSelected, zoomSelected, controlsState, dispatch) => {
   /* calculate new branch thicknesses & visibility */
   let tipSelectedIdx = 0;
   /* check if the query defines a strain to be selected */
@@ -445,16 +462,21 @@ const modifyTreeStateVisAndBranchThickness = (oldState, tipSelected, cladeSelect
     tipSelectedIdx = strainNameToIdx(oldState.nodes, tipSelected);
     oldState.selectedStrain = tipSelected;
   }
-  if (cladeSelected) {
-    const cladeSelectedIdx = cladeSelected === 'root' ? 0 : getIdxMatchingLabel(oldState.nodes, "clade", cladeSelected);
-    oldState.selectedClade = cladeSelected;
+  if (zoomSelected) {
+    // Check and fix old format 'clade=B' - in this case selectionClade is just 'B'
+    const [labelName, labelValue] = zoomSelected.split(":");
+    const cladeSelectedIdx = getIdxMatchingLabel(oldState.nodes, labelName, labelValue, dispatch);
+    oldState.selectedClade = zoomSelected;
     newIdxRoot = applyInViewNodesToTree(cladeSelectedIdx, oldState); // tipSelectedIdx, oldState);
+  } else {
+    oldState.selectedClade = undefined;
+    newIdxRoot = applyInViewNodesToTree(0, oldState); // tipSelectedIdx, oldState);
   }
   const visAndThicknessData = calculateVisiblityAndBranchThickness(
     oldState,
     controlsState,
     {dateMinNumeric: controlsState.dateMinNumeric, dateMaxNumeric: controlsState.dateMaxNumeric},
-    {tipSelectedIdx, validIdxRoot: newIdxRoot}
+    {tipSelectedIdx}
   );
 
   const newState = Object.assign({}, oldState, visAndThicknessData);
@@ -546,6 +568,7 @@ const createMetadataStateFromJSON = (json) => {
       color_by: "colorBy",
       geo_resolution: "geoResolution",
       distance_measure: "distanceMeasure",
+      branch_label: "selectedBranchLabel",
       map_triplicate: "mapTriplicate",
       layout: "layout"
     };
@@ -574,7 +597,8 @@ export const createStateFromQueryOrJSONs = ({
   narrativeBlocks = false,
   mainTreeName = false,
   secondTreeName = false,
-  query
+  query,
+  dispatch
 }) => {
   let tree, treeToo, entropy, controls, metadata, narrative, frequencies;
   /* first task is to create metadata, entropy, controls & tree partial state */
@@ -642,7 +666,7 @@ export const createStateFromQueryOrJSONs = ({
 
 
   /* calculate colours if loading from JSONs or if the query demands change */
-  if (json || controls.colorBy !== oldState.colorBy) {
+  if (json || controls.colorBy !== oldState.controls.colorBy) {
     const colorScale = calcColorScale(controls.colorBy, controls, tree, treeToo, metadata);
     const nodeColors = calcNodeColor(tree, colorScale);
     controls.colorScale = colorScale;
@@ -651,16 +675,31 @@ export const createStateFromQueryOrJSONs = ({
     tree.nodeColors = nodeColors;
   }
 
+  /* parse the query.label / query.clade */
   if (query.clade) {
-    tree = modifyTreeStateVisAndBranchThickness(tree, undefined, query.clade, controls);
-  } else { /* if not specifically given in URL, zoom to root */
-    tree = modifyTreeStateVisAndBranchThickness(tree, undefined, undefined, controls);
+    if (!query.label && query.clade !== "root") {
+      query.label = `clade:${query.clade}`;
+    }
+    delete query.clade;
   }
-  tree = modifyTreeStateVisAndBranchThickness(tree, query.s, undefined, controls);
+  if (query.label) {
+    if (!query.label.includes(":")) {
+      console.error("Defined a label without ':' separator.");
+      delete query.label;
+    }
+    if (!tree.availableBranchLabels.includes(query.label.split(":")[0])) {
+      console.error(`Label name ${query.label.split(":")[0]} doesn't exist`);
+      delete query.label;
+    }
+  }
+
+  /* if query.label is undefined then we intend to zoom to the root */
+  tree = modifyTreeStateVisAndBranchThickness(tree, query.s, query.label, controls, dispatch);
+
   if (treeToo && treeToo.loaded) {
     treeToo.nodeColorsVersion = tree.nodeColorsVersion;
     treeToo.nodeColors = calcNodeColor(treeToo, controls.colorScale);
-    treeToo = modifyTreeStateVisAndBranchThickness(treeToo, query.s, undefined, controls);
+    treeToo = modifyTreeStateVisAndBranchThickness(treeToo, query.s, undefined, controls, dispatch);
     controls = modifyControlsViaTreeToo(controls, treeToo.name);
     treeToo.tangleTipLookup = constructVisibleTipLookupBetweenTrees(tree.nodes, treeToo.nodes, tree.visibility, treeToo.visibility);
   }
@@ -695,7 +734,8 @@ export const createTreeTooState = ({
   treeTooJSON, /* raw json data */
   oldState,
   originalTreeUrl,
-  secondTreeUrl /* treeToo URL */
+  secondTreeUrl, /* treeToo URL */
+  dispatch
 }) => {
   /* TODO: reconsile choices (filters, colorBys etc) with this new tree */
   /* TODO: reconcile query with visibility etc */
@@ -707,7 +747,7 @@ export const createTreeTooState = ({
   treeToo.debug = "RIGHT";
   controls = modifyControlsStateViaTree(controls, tree, treeToo, oldState.metadata.colorings);
   controls = modifyControlsViaTreeToo(controls, secondTreeUrl);
-  treeToo = modifyTreeStateVisAndBranchThickness(treeToo, tree.selectedStrain, undefined, controls);
+  treeToo = modifyTreeStateVisAndBranchThickness(treeToo, tree.selectedStrain, undefined, controls, dispatch);
 
   /* calculate colours if loading from JSONs or if the query demands change */
   const colorScale = calcColorScale(controls.colorBy, controls, tree, treeToo, oldState.metadata);

src/actions/tree.js

@@ -21,7 +21,7 @@ export const applyInViewNodesToTree = (idx, tree) => {
     } else {
       applyToChildren(tree.nodes[validIdxRoot].shell, (d) => {d.inView = true;});
     }
-  } else if (idx !== tree.idxOfInViewRootNode) { /* if shell isn't set yet - have set clade in URL */
+  } else {
     tree.nodes.forEach((d) => {
       d.inView = false;
     });
@@ -92,7 +92,7 @@ export const updateVisibleTipsAndBranchThicknesses = (
       tree,
       controls,
       {dateMinNumeric: controls.dateMinNumeric, dateMaxNumeric: controls.dateMaxNumeric},
-      {tipSelectedIdx: tipIdx1, validIdxRoot: rootIdxTree1}
+      {tipSelectedIdx: tipIdx1}
     );
     const dispatchObj = {
       type: types.UPDATE_VISIBILITY_AND_BRANCH_THICKNESS,
@@ -113,7 +113,7 @@ export const updateVisibleTipsAndBranchThicknesses = (
         treeToo,
         controls,
         {dateMinNumeric: controls.dateMinNumeric, dateMaxNumeric: controls.dateMaxNumeric},
-        {tipSelectedIdx: tipIdx2, validIdxRoot: rootIdxTree2}
+        {tipSelectedIdx: tipIdx2}
       );
       dispatchObj.tangleTipLookup = constructVisibleTipLookupBetweenTrees(tree.nodes, treeToo.nodes, data.visibility, dataToo.visibility);
       dispatchObj.visibilityToo = dataToo.visibility;

src/components/main/utils.js

@@ -22,11 +22,9 @@ export const calcPanelDims = (grid, panels, narrativeIsDisplayed, availableWidth
     }
     /* widths */
     if (panels.includes("map") && panels.includes("tree") && !grid) {
-      console.warn("narrative mode specified full display but we have both map & tree");
       bigWidthFraction = 0.5;
     }
     if (grid && (!panels.includes("map") || !panels.includes("tree"))) {
-      console.warn("narrative mode specified grid display but we are not showing both map & tree");
       bigWidthFraction = 1;
     }
   }