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improve type handling for non-string annotation data (#465)
* improve type handling for non-string annotation data * improve clarity of code
This commit is contained in:
committed by
Charlotte Weaver
parent
2b5094665f
commit
138d30909a
@@ -48,6 +48,12 @@ Example:
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NOTE: will not summarize the required 'name' annotation, as that is
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specified as unique per element.
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TODO: XXX - this data structure coerces all metadata categories into a string
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(ie, stores values as an Object property in the `options` field). This looses
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information (eg, type) for category types which are not strings. Consider an
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alterative data structure that does not use the object property for non-string
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data types (and does not use _.countBy to summarize).
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*/
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function summarizeDimension(schema, annotations) {
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return _(schema)
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@@ -58,11 +64,13 @@ function summarizeDimension(schema, annotations) {
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const continuous = type === "int32" || type === "float32";
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if (!continuous) {
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const categories = _.uniq(_.flatMap(annotations, name));
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const options = _.countBy(annotations, name);
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const numOptions = _.size(options);
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return {
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numOptions,
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options
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options,
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categories
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};
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}
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@@ -161,6 +161,32 @@ function RESTv02LayoutResponseToInternal(response) {
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return layout;
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}
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function reconcileSchemaCategoriesWithSummary(universe) {
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/*
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where we treat types as (essentially) categorical metadata, update
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the schema with data-derived categories (in addition to those in
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the server declared schema).
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For example, boolean defined fields in the schema do not contain
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explicit declaration of categories (nor do string fields). In these
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cases, add a 'categories' field to the schema so it is accessible.
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*/
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_.forEach(universe.schema.annotations.obs, s => {
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if (
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s.type === "string" ||
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s.type === "boolean" ||
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s.type === "categorical"
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) {
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const categories = _.union(
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_.get(s, "categories", []),
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_.get(universe.summary.obs[s.name], "categories", [])
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);
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s.categories = categories;
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}
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});
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}
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export function createUniverseFromRestV02Response(
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configResponse,
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schemaResponse,
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@@ -199,6 +225,7 @@ export function createUniverseFromRestV02Response(
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universe.varAnnotations
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);
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reconcileSchemaCategoriesWithSummary(universe);
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return finalize(universe);
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}
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