mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-27 22:38:12 +08:00
do not hard-wire column names in annotations (#785)
* enforce column name uniqueness for obs and var * parameterize the column name containing obs and var user-readable names * use the new annotation index value from schema * update f/e unit tests * PR review suggestions * lint
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@@ -56,13 +56,14 @@ function topNCategories(summary) {
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export function createCategoricalSelection(maxCategoryItems, world) {
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const res = {};
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const obsIndexName = world.schema.annotations.obs.index;
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_.forEach(world.obsAnnotations.colIndex.keys(), key => {
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const summary = world.obsAnnotations.col(key).summarize();
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if (summary.categories) {
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const isColorField = key.includes("color") || key.includes("Color");
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const isSelectableCategory =
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!isColorField &&
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key !== "name" &&
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key !== obsIndexName &&
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summary.categories.length < maxCategoryItems;
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if (isSelectableCategory) {
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const [categoryValues, categoryValueCounts] = topNCategories(summary);
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@@ -124,7 +124,7 @@ function reconcileSchemaCategoriesWithSummary(universe) {
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cases, add a 'categories' field to the schema so it is accessible.
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*/
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universe.schema.annotations.obs.forEach(s => {
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universe.schema.annotations.obs.columns.forEach(s => {
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if (
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s.type === "string" ||
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s.type === "boolean" ||
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@@ -179,10 +179,10 @@ export function createUniverseFromResponse(
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/* Index schema for ease of use */
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universe.schema.annotations.obsByName = fromEntries(
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universe.schema.annotations.obs.map(v => [v.name, v])
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universe.schema.annotations.obs.columns.map(v => [v.name, v])
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);
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universe.schema.annotations.varByName = fromEntries(
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universe.schema.annotations.var.map(v => [v.name, v])
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universe.schema.annotations.var.columns.map(v => [v.name, v])
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);
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universe.schema.layout.obsByName = fromEntries(
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universe.schema.layout.obs.map(v => [v.name, v])
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@@ -213,8 +213,9 @@ export function convertDataFBStoObject(universe, arrayBuffer) {
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throw new Error("Unexpected non-floating point response from server.");
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}
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const varIndexName = universe.schema.annotations.var.index;
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for (let c = 0; c < colIdx.length; c += 1) {
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const varName = universe.varAnnotations.at(colIdx[c], "name");
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const varName = universe.varAnnotations.at(colIdx[c], varIndexName);
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result[varName] = columns[c];
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}
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return result;
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@@ -263,10 +263,14 @@ function deduceDimensionType(attributes, fieldName) {
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export function createObsDimensions(crossfilter, world, XYdimNames) {
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/*
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create and return a crossfilter with a dimension for every obs annotation
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for which we have a supported type, *except* 'name'
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for which we have a supported type, *except* for the index column, indicated
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by schema.annotations.obs.index.
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*/
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const { schema, obsLayout, obsAnnotations } = world;
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const annoList = schema.annotations.obs.filter(anno => anno.name !== "name");
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const indexName = schema.annotations.obs.index;
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const annoList = schema.annotations.obs.columns.filter(
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anno => anno.name !== indexName
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);
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crossfilter = annoList.reduce((xfltr, anno) => {
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const dimType = deduceDimensionType(anno, anno.name);
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const colData = obsAnnotations.col(anno.name).asArray();
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