wip

src/actions/recomputeReduxState.js → src/actions/recomputeReduxState.ts

@@ -16,14 +16,18 @@ import { entropyCreateState, genomeMap as createGenomeMap } from "../util/entrop
 import { calcNodeColor } from "../util/colorHelpers";
 import { calcColorScale, createVisibleLegendValues } from "../util/colorScale";
 import { computeMatrixFromRawData, checkIfNormalizableFromRawData } from "../util/processFrequencies";
-import { applyInViewNodesToTree } from "../actions/tree";
+import { applyInViewNodesToTree } from "./tree";
 import { validateScatterVariables } from "../util/scatterplotHelpers";
 import { isColorByGenotype, decodeColorByGenotype, encodeColorByGenotype, decodeGenotypeFilters, encodeGenotypeFilters, getCdsFromGenotype } from "../util/getGenotype";
 import { getTraitFromNode, getDivFromNode, collectGenotypeStates } from "../util/treeMiscHelpers";
 import { collectAvailableTipLabelOptions } from "../components/controls/choose-tip-label";
 import { hasMultipleGridPanels } from "./panelDisplay";
 import { strainSymbolUrlString } from "../middleware/changeURL";
 
+import { DatasetJson } from "../types/datasetJson";
+import { MetadataState } from "../reducers/metadata";
+import { ReduxRootState, AppDispatch } from "../store";
+
 export const doesColorByHaveConfidence = (controlsState, colorBy) =>
   controlsState.coloringsPresentOnTreeWithConfidence.has(colorBy);
 
@@ -118,8 +122,11 @@ const modifyStateViaURLQuery = (state, query) => {
   if (query.animate) {
     const params = query.animate.split(',');
     // console.log("start animation!", params);
-    window.NEXTSTRAIN.animationStartPoint = calendarToNumeric(params[0]);
-    window.NEXTSTRAIN.animationEndPoint = calendarToNumeric(params[1]);
+    // TS TODO FIX
+    if ('NEXTSTRAIN' in window) {
+      (window.NEXTSTRAIN as any).animationStartPoint = calendarToNumeric(params[0]);
+      (window.NEXTSTRAIN as any).animationEndPoint = calendarToNumeric(params[1]);
+    }
     state.dateMin = params[0];
     state.dateMax = params[1];
     state.dateMinNumeric = calendarToNumeric(params[0]);
@@ -380,7 +387,7 @@ const modifyControlsStateViaTree = (state, tree, treeToo, colorings) => {
   state.coloringsPresentOnTree = new Set();
   state.coloringsPresentOnTreeWithConfidence = new Set(); // subset of above
 
-  let coloringsToCheck = [];
+  let coloringsToCheck: string[] = [];
   if (colorings) {
     coloringsToCheck = Object.keys(colorings);
   }
@@ -444,7 +451,7 @@ const modifyControlsStateViaTree = (state, tree, treeToo, colorings) => {
   return state;
 };
 
-const checkAndCorrectErrorsInState = (state, metadata, genomeMap, query, tree, viewingNarrative) => {
+const checkAndCorrectErrorsInState = (state, metadata: MetadataState, genomeMap, query, tree, viewingNarrative) => {
   /* want to check that the (currently set) colorBy (state.colorBy) is valid,
    * and fall-back to an available colorBy if not
    */
@@ -597,7 +604,8 @@ const checkAndCorrectErrorsInState = (state, metadata, genomeMap, query, tree, v
       continue
     }
     /* delete filter names (e.g. country, region) which aren't observed on the tree */
-    if (!Object.keys(tree.totalStateCounts).includes(traitName) && traitName!==strainSymbol && traitName!==genotypeSymbol) {
+    // TS TODO - remove the following cast (and check code _was_ working as I thought it was...)
+    if (!Object.keys(tree.totalStateCounts).includes(traitName as string) && traitName!==strainSymbol && traitName!==genotypeSymbol) {
       delete state.filters[traitName];
       delete query[_queryKey(traitName)];
       continue
@@ -734,8 +742,8 @@ const convertColoringsListToDict = (coloringsList) => {
  *
  * A lot of this is simply changing augur's snake_case to auspice's camelCase
  */
-const createMetadataStateFromJSON = (json) => {
-  const metadata = {};
+const createMetadataStateFromJSON = (json: DatasetJson): MetadataState => {
+  const metadata: MetadataState = {};
   if (json.meta.colorings) {
     metadata.colorings = convertColoringsListToDict(json.meta.colorings);
   }
@@ -851,6 +859,18 @@ export const getNarrativePageFromQuery = (query, narrative) => {
   return n;
 };
 
+/* TS TODO */
+interface CreateStateArgs {
+  json: DatasetJson | false;
+  secondTreeDataset: any;
+  oldState: ReduxRootState | false;
+  narrativeBlocks: any; /* if in a narrative this argument is set */
+  mainTreeName: string | false;
+  secondTreeName: string | false;
+  query?: any;
+  dispatch: any; /* redux should define this for us... */
+}
+
 export const createStateFromQueryOrJSONs = ({
   json = false, /* raw json data - completely nuke existing redux state */
   secondTreeDataset = false,
@@ -860,8 +880,9 @@ export const createStateFromQueryOrJSONs = ({
   secondTreeName = false,
   query,
   dispatch
-}) => {
-  let tree, treeToo, entropy, controls, metadata, narrative, frequencies, measurements;
+}: CreateStateArgs) => {
+  let tree, treeToo, entropy, controls, narrative, frequencies, measurements;
+  let metadata: MetadataState;
   /* first task is to create metadata, entropy, controls & tree partial state */
   if (json) {
     /* create metadata state */
@@ -905,6 +926,8 @@ export const createStateFromQueryOrJSONs = ({
     measurements = {...oldState.measurements};
     controls = restoreQueryableStateToDefaults(controls);
     controls = modifyStateViaMetadata(controls, metadata, entropy.genomeMap);
+  } else {
+    // can this _ever_ occur? If it does then `metadata` is undefined...
   }
 
   /* For the creation of state, we want to parse out URL query parameters
@@ -936,7 +959,7 @@ export const createStateFromQueryOrJSONs = ({
 
 
   /* calculate colours if loading from JSONs or if the query demands change */
-  if (json || controls.colorBy !== oldState.controls.colorBy) {
+  if (json || controls.colorBy !== oldState?.controls.colorBy) { // TODO - why elvis operator not working here?
     const colorScale = calcColorScale(controls.colorBy, controls, tree, treeToo, metadata);
     const nodeColors = calcNodeColor(tree, colorScale);
     controls.colorScale = colorScale;

src/reducers/metadata.js → src/reducers/metadata.ts

@@ -1,19 +1,49 @@
 import { colorOptions } from "../util/globals";
 import * as types from "../actions/types";
+import { DatasetJsonRootSequence, DatasetJson, DatasetJsonMeta } from "../types/datasetJson";
+
+/**
+ * A lot of to-dos here...
+ * Does it make sense to have two state types, a non-loaded one and
+ * a loaded one (discriminated type based on loaded: boolean) to give
+ * more assurances? Otherwise most properties are potential undefineds.
+ * (TS still helpful here tho)
+ */
+export interface MetadataState {
+  loaded: boolean;
+  rootSequence?: DatasetJsonRootSequence;
+  identicalGenomeMapAcrossBothTrees: boolean;
+  rootSequenceSecondTree?: DatasetJsonRootSequence;
+  colorOptions: any; // TODO XXX
+  colorings?: any; // TODO XXX
+  geoResolutions?: DatasetJsonMeta['geo_resolutions'];
+  buildUrl?: DatasetJsonMeta['build_url'] | false;
+  displayDefaults?: Record<string,any>; // TODO XXX
+  panels?: DatasetJsonMeta['panels'];
+  mainTreeNumTips?: number;
+  title?: DatasetJsonMeta['title'];
+  version?: DatasetJson['version'];
+  filters?: DatasetJsonMeta['filters'];
+  dataProvenance?: DatasetJsonMeta['data_provenance'];
+  maintainers?: DatasetJsonMeta['maintainers'];
+  description?: DatasetJsonMeta['description'];
+  updated?: DatasetJsonMeta['updated'];
+}
+
 
 /* The metadata reducer holds data that is
  * (a) mostly derived from the dataset JSON
  * (b) rarely changes
  */
 
-const Metadata = (state = {
+const Metadata = (state:MetadataState = {
   loaded: false, /* see comment in the sequences reducer for explanation */
-  metadata: null,
+  // metadata: null,
   rootSequence: undefined,
   identicalGenomeMapAcrossBothTrees: false,
   rootSequenceSecondTree: undefined,
   colorOptions // this can't be removed as the colorScale currently runs before it should
-}, action) => {
+}, action): MetadataState => {
   switch (action.type) {
     case types.DATA_INVALID:
       return Object.assign({}, state, {
@@ -22,6 +52,7 @@ const Metadata = (state = {
     case types.URL_QUERY_CHANGE_WITH_COMPUTED_STATE:
     case types.TREE_TOO_DATA:
     case types.CLEAN_START:
+      console.log("incoming!", action.metadata)
       return action.metadata;
     case types.ADD_EXTRA_METADATA: {
       const colorings = Object.assign({}, state.colorings, action.newColorings);
@@ -54,7 +85,8 @@ const Metadata = (state = {
   }
 };
 
-function getBuildUrlFromGetAvailableJson(availableData) {
+// TODO - can we replace the returned 'false' with 'undefined'?
+function getBuildUrlFromGetAvailableJson(availableData): (false | undefined | string) {
   if (!availableData) return undefined;
   /* check if the current dataset is present in the getAvailable data
   We currently parse the URL (pathname) for the current dataset but this

src/store.ts

@@ -47,7 +47,7 @@ if (process.env.NODE_ENV !== 'production' && module.hot) {
 }
 
 // Infer types from the store.
-export type RootState = ReturnType<typeof store.getState>
+export type ReduxRootState = ReturnType<typeof store.getState>
 export type AppDispatch = typeof store.dispatch
 
 export default store;