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https://github.com/chanzuckerberg/cellxgene.git
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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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@@ -34,28 +34,34 @@ const aSchemaResponse = {
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type: "float32"
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},
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annotations: {
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obs: [
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{ name: "name", type: "string" },
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{ name: "field1", type: "int32" },
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{ name: "field2", type: "float32" },
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{ name: "field3", type: "boolean" },
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{
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name: "field4",
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type: "categorical",
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categories: field4Categories
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}
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],
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var: [
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{ name: "name", type: "string" },
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{ name: "fieldA", type: "int32" },
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{ name: "fieldB", type: "float32" },
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{ name: "fieldC", type: "boolean" },
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{
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name: "fieldD",
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type: "categorical",
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categories: fieldDCategories
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}
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]
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obs: {
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index: "name",
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columns: [
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{ name: "name", type: "string" },
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{ name: "field1", type: "int32" },
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{ name: "field2", type: "float32" },
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{ name: "field3", type: "boolean" },
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{
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name: "field4",
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type: "categorical",
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categories: field4Categories
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}
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]
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},
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var: {
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index: "name",
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columns: [
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{ name: "name", type: "string" },
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{ name: "fieldA", type: "int32" },
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{ name: "fieldB", type: "float32" },
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{ name: "fieldC", type: "boolean" },
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{
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name: "fieldD",
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type: "categorical",
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categories: fieldDCategories
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}
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]
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}
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},
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layout: {
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obs: [{ name: "umap", type: "float32", dims: ["umap_0", "umap_1"] }],
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@@ -53,7 +53,7 @@ describe("createUniverseFromResponse", () => {
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expect(universe.obsAnnotations.dims).toEqual([
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nObs,
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REST.schema.schema.annotations.obs.length
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REST.schema.schema.annotations.obs.columns.length
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]);
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expect(universe.obsLayout.dims).toEqual([nObs, 2]);
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expect(universe.obsLayout.colIndex.keys()).toEqual(
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@@ -61,7 +61,7 @@ describe("createUniverseFromResponse", () => {
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);
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expect(universe.varAnnotations.dims).toEqual([
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nVar,
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REST.schema.schema.annotations.var.length
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REST.schema.schema.annotations.var.columns.length
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]);
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expect(universe.varData.isEmpty()).toBeTruthy();
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});
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@@ -155,14 +155,18 @@ describe("createObsDimensionMap", () => {
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const { crossfilter } = defaultBigBang();
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const annotationNames = _.map(
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REST.schema.schema.annotations.obs,
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REST.schema.schema.annotations.obs.columns,
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c => c.name
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);
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const schemaByObsName = _.keyBy(REST.schema.schema.annotations.obs, "name");
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const obsIndexColName = REST.schema.schema.annotations.obs.index;
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const schemaByObsName = _.keyBy(
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REST.schema.schema.annotations.obs.columns,
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"name"
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);
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expect(crossfilter).toBeDefined();
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annotationNames.forEach(name => {
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const dim = crossfilter.dimensions[obsAnnoDimensionName(name)];
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if (name === "name") {
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if (name === obsIndexColName) {
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expect(dim).toBeUndefined();
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} else {
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const { type } = schemaByObsName[name];
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