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Fix bugs when changing datasets with URL queries defined #613

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merged 4 commits into from
Aug 5, 2018
Merged

Fix bugs when changing datasets with URL queries defined #613

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fd1fea4
fix URL bug where region didn't exist in new dataset
jameshadfield Aug 4, 2018
aee2daa
fix URL bug when changing datasets with a genotype selected
jameshadfield Aug 4, 2018
2cc26d5
fall back to default colorBy / geo resolutions when valid
jameshadfield Aug 5, 2018
79a3799
ensure filters are valid upon dataset load
jameshadfield Aug 5, 2018
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73 changes: 63 additions & 10 deletions src/actions/recomputeReduxState.js
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import queryString from "query-string";
import { numericToCalendar, calendarToNumeric } from "../util/dateHelpers";
import { reallySmallNumber, twoColumnBreakpoint } from "../util/globals";
import { reallySmallNumber, twoColumnBreakpoint, defaultColorBy, defaultGeoResolution } from "../util/globals";
import { calcBrowserDimensionsInitialState } from "../reducers/browserDimensions";
import { strainNameToIdx, calculateVisiblityAndBranchThickness } from "../util/treeVisibilityHelpers";
import { constructVisibleTipLookupBetweenTrees } from "../util/treeTangleHelpers";
Expand Down Expand Up @@ -260,7 +260,7 @@ const modifyStateViaTree = (state, tree, treeToo) => {
return state;
};

const checkAndCorrectErrorsInState = (state, metadata) => {
const checkAndCorrectErrorsInState = (state, metadata, query, tree) => {
/* The one (bigish) problem with this being in the reducer is that
we can't have any side effects. So if we detect and error introduced by
a URL QUERY (and correct it in state), we can't correct the URL */
Expand All @@ -269,19 +269,51 @@ const checkAndCorrectErrorsInState = (state, metadata) => {
if (!metadata.colorOptions) {
metadata.colorOptions = {};
}
if (Object.keys(metadata.colorOptions).indexOf(state.colorBy) === -1 && !state["colorBy"].startsWith("gt-")) {
const fallBackToDefaultColorBy = () => {
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]);
if (Object.keys(metadata.colorOptions).length > 0) {
state.colorBy = availableNonGenotypeColorBys[0];
state.defaults.colorBy = availableNonGenotypeColorBys[0];

if (metadata.defaults && metadata.defaults.colorBy && availableNonGenotypeColorBys.indexOf(metadata.defaults.colorBy) !== -1) {
console.warn("colorBy falling back to", metadata.defaults.colorBy);
state.colorBy = metadata.defaults.colorBy;
state.defaults.colorBy = metadata.defaults.colorBy;
} else if (availableNonGenotypeColorBys.length) {
if (availableNonGenotypeColorBys.indexOf(defaultColorBy) !== -1) {
state.colorBy = defaultColorBy;
state.defaults.colorBy = defaultColorBy;
} else {
console.error("Error detected trying to set colorBy to", state.colorBy, "falling back to", availableNonGenotypeColorBys[0]);
state.colorBy = availableNonGenotypeColorBys[0];
state.defaults.colorBy = availableNonGenotypeColorBys[0];
}
} else {
console.error("Error detected trying to set colorBy to", state.colorBy, " as there are no color options defined in the JSONs!");
state.colorBy = "none";
state.defaults.colorBy = "none";
}
delete query.c;
};
if (state["colorBy"].startsWith("gt-")) {
/* Check that the genotype is valid with the current data */
if (!metadata.annotations) {
fallBackToDefaultColorBy();
} else {
const [gene, pos] = state.colorBy.split("-")[1].split("_");
if (!(gene in metadata.annotations)) {
fallBackToDefaultColorBy();
} else if (gene === "nuc") {
if ((metadata.annotations[gene].end - metadata.annotations[gene].start) < pos) {
fallBackToDefaultColorBy();
}
} else if ((metadata.annotations[gene].end - metadata.annotations[gene].start)/3 < pos) {
fallBackToDefaultColorBy();
}
}
} else if (Object.keys(metadata.colorOptions).indexOf(state.colorBy) === -1) {
/* if it's a _non_ genotype colorBy AND it's not a valid option, fall back to the default */
fallBackToDefaultColorBy();
}

/* colorBy confidence */
Expand All @@ -297,8 +329,16 @@ const checkAndCorrectErrorsInState = (state, metadata) => {
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"]);
/* fallbacks: JSON defined default, then hardocded default, then any available */
if (metadata.defaults && metadata.defaults.geoResolution && availableGeoResultions.indexOf(metadata.defaults.geoResolution) !== -1) {
state.geoResolution = metadata.defaults.geoResolution;
} else if (availableGeoResultions.indexOf(defaultGeoResolution) !== -1) {
state.geoResolution = defaultGeoResolution;
} else {
state.geoResolution = availableGeoResultions[0];
}
console.error("Error detected. Setting geoResolution to ", state.geoResolution);
delete query.r; // no-op if query.r doesn't exist
}
} else {
console.warn("The meta.json did not include geo info.");
Expand All @@ -323,6 +363,19 @@ const checkAndCorrectErrorsInState = (state, metadata) => {
}
}

/* are filters valid? */
const activeFilters = Object.keys(state.filters).filter((f) => f.length);
const stateCounts = countTraitsAcrossTree(tree.nodes, activeFilters, false, true);
for (const filterType of activeFilters) {
const validValues = state.filters[filterType]
.filter((filterValue) => filterValue in stateCounts[filterType]);
state.filters[filterType] = validValues;
if (!validValues.length) {
delete query[`f_${filterType}`];
} else {
query[`f_${filterType}`] = validValues.join(",");
}
}
return state;
};

Expand Down Expand Up @@ -429,7 +482,7 @@ export const createStateFromQueryOrJSONs = ({
controls = modifyStateViaURLQuery(controls, query);
}

controls = checkAndCorrectErrorsInState(controls, metadata); /* must run last */
controls = checkAndCorrectErrorsInState(controls, metadata, query, tree); /* must run last */


/* calculate colours if loading from JSONs or if the query demands change */
Expand Down