/* Helpers for schema management TODO: all this would be much more natural if done with a framework like immutable.js */ import cloneDeep from "lodash.clonedeep"; import fromEntries from "../fromEntries"; import catLabelSort from "../catLabelSort"; import { RawSchema, Schema, EmbeddingSchema, AnnotationColumnSchema, } from "../../common/types/schema"; /* System wide schema assumptions: - schema and data wil be consistent (eg, for user-created annotations) - schema will be internally self-consistent (eg, index matches columns) */ export function indexEntireSchema(schema: RawSchema): Schema { /* Index schema for ease of use */ (schema as Schema).annotations.obsByName = fromEntries( schema.annotations?.obs?.columns?.map((v) => [v.name, v]) || [] ); (schema as Schema).annotations.varByName = fromEntries( schema.annotations?.var?.columns?.map((v) => [v.name, v]) || [] ); (schema as Schema).layout.obsByName = fromEntries( schema.layout?.obs?.map((v) => [v.name, v]) || [] ); (schema as Schema).layout.varByName = fromEntries( schema.layout?.var?.map((v) => [v.name, v]) || [] ); return schema as Schema; } function _copyObsAnno(schema: Schema): Schema { /* redux copy conventions - WARNING, only for modifying obs annotations */ return { ...schema, annotations: { ...schema.annotations, obs: cloneDeep(schema.annotations.obs), }, }; } function _copyObsLayout(schema: Schema): Schema { return { ...schema, layout: { ...schema.layout, obs: cloneDeep(schema.layout.obs), }, }; } function _reindexObsAnno(schema: Schema): Schema { /* reindex obs annotations ONLY */ schema.annotations.obsByName = fromEntries( schema.annotations.obs.columns.map((v) => [v.name, v]) ); return schema; } function _reindexObsLayout(schema: Schema) { schema.layout.obsByName = fromEntries( schema.layout.obs.map((v) => [v.name, v]) ); return schema; } export function removeObsAnnoColumn(schema: Schema, name: string): Schema { const newSchema = _copyObsAnno(schema); newSchema.annotations.obs.columns = schema.annotations.obs.columns.filter( (v) => v.name !== name ); return _reindexObsAnno(newSchema); } export function addObsAnnoColumn( schema: Schema, _: string, defn: AnnotationColumnSchema ): Schema { const newSchema = _copyObsAnno(schema); newSchema.annotations.obs.columns.push(defn); return _reindexObsAnno(newSchema); } export function removeObsAnnoCategory( schema: Schema, name: string, category: string ): Schema { /* remove a category from a categorical annotation */ const categories = schema.annotations.obsByName[name]?.categories; if (!categories) { throw new Error("column does not exist or is not categorical"); } const idx = categories.indexOf(category); if (idx === -1) throw new Error("category does not exist"); const newSchema = _reindexObsAnno(_copyObsAnno(schema)); /* remove category. Do not need to resort as this can't change presentation order */ newSchema.annotations.obsByName[name].categories?.splice(idx, 1); return newSchema; } // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. export function addObsAnnoCategory(schema: any, name: any, category: any) { /* add a category to a categorical annotation */ const categories = schema.annotations.obsByName[name]?.categories; if (!categories) throw new Error("column does not exist or is not categorical"); const idx = categories.indexOf(category); if (idx !== -1) throw new Error("category already exists"); const newSchema = _reindexObsAnno(_copyObsAnno(schema)); /* add category, retaining presentation sort order */ const catAnno = newSchema.annotations.obsByName[name]; catAnno.categories = catLabelSort(catAnno.writable, [ ...(catAnno.categories || []), category, ]); return newSchema; } export function addObsLayout(schema: Schema, layout: EmbeddingSchema): Schema { /* add or replace a layout */ const newSchema = _copyObsLayout(schema); newSchema.layout.obs.push(layout); return _reindexObsLayout(newSchema); } export function removeObsLayout(schema: Schema, name: string): Schema { /* remove a layout */ const newSchema = _copyObsLayout(schema); newSchema.layout.obs = schema.layout.obs.filter((v) => v.name !== name); return _reindexObsLayout(newSchema); }