@rivm-loculus-tools/common-frontend 0.1.3 → 0.2.0

package/dist/models/fasta.js

@@ -0,0 +1,8 @@
+//#region src/models/fasta.ts
+var e = /* @__PURE__ */ function(e) {
+	return e.ERROR = "ERROR", e.IDLE = "IDLE", e.LOADING = "LOADING", e.SUCCESS = "SUCCESS", e;
+}({});
+//#endregion
+export { e as LOADING_STATUS };
+
+//# sourceMappingURL=fasta.js.map

package/dist/models/fasta.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"fasta.js","names":["LOADING_STATUS","\"ERROR\"","\"IDLE\"","\"LOADING\"","\"SUCCESS\""],"sources":["../../src/models/fasta.ts"],"sourcesContent":["export enum LOADING_STATUS {\n  ERROR = 'ERROR',\n  IDLE = 'IDLE',\n  LOADING = 'LOADING',\n  SUCCESS = 'SUCCESS',\n}\n\nexport type FastaParseResult = {\n  error?: string;\n  expectedLength: number;\n  invalidSequences?: { id: string; length: number }[];\n  isAligned: boolean;\n  sequences: FastaSequence[];\n};\n\nexport type FastaSequence = {\n  accessionVersion: string;\n  header: string;\n  id: string;\n  length: number;\n  sequence: string;\n};\n"],"mappings":";AAAA,IAAYA,IAAL,yBAAA,GAAA;QACL,EAAAC,QAAA,SACA,EAAAC,OAAA,QACA,EAAAC,UAAA,WACA,EAAAC,UAAA;AACF,EAAA,CAAA,CAAA"}

package/dist/models/metadata.d.ts

@@ -0,0 +1,9 @@
+export interface MetadataParseResult {
+    columns: string[];
+    error?: string;
+    records: MetadataRecord[];
+    recordsByAccession: Record<string, MetadataRecord>;
+    recordsByColumn: Record<string, Record<string, MetadataRecord>>;
+    recordsBySampleId: Record<string, MetadataRecord>;
+}
+export type MetadataRecord = Record<string, string>;

package/dist/stores/fastaDataStore/fastaDataStore.d.ts

@@ -0,0 +1,32 @@
+import { StoreApi } from 'zustand';
+import { FastaParseResult, LOADING_STATUS } from '../../models/fasta';
+import { MetadataParseResult } from '../../models/metadata';
+export type FastaDataStore = FastaDataStoreActions & FastaDataStoreState;
+export interface FastaDataStoreActions {
+    resetDataset: () => void;
+    setColumnMatchCounts: (counts: Record<string, number>) => void;
+    setData: (fasta: string, tsv?: string) => Promise<{
+        fastaResult: FastaParseResult;
+        metadataResult?: MetadataParseResult;
+    }>;
+    setLoadingStatus: (status: LOADING_STATUS) => void;
+    setMatchKeyField: (field: null | string) => void;
+}
+export interface FastaDataStoreState {
+    columnMatchCounts: Record<string, number>;
+    loadingError: null | string;
+    loadingStatus: LOADING_STATUS;
+    matchKeyField: null | string;
+    parsedFasta: FastaParseResult | null;
+    parsedMetadata: MetadataParseResult | null;
+    rawFasta: string;
+    rawMetadata: string;
+}
+export declare const createFastaDataStoreInitialState: () => FastaDataStoreState;
+type Get<T extends FastaDataStore> = StoreApi<T>['getState'];
+type Set<T extends FastaDataStore> = StoreApi<T>['setState'];
+export declare const createFastaDataStoreActions: <T extends FastaDataStore>(kwArgs: {
+    get: Get<T>;
+    set: Set<T>;
+}) => FastaDataStoreActions;
+export {};

package/dist/stores/fastaDataStore/index.js

@@ -0,0 +1,57 @@
+import { MetaDataUtil as e } from "../../utils/MetaDataUtil/index.js";
+import { FastaUtil as t } from "../../utils/FastaUtil/index.js";
+import { LOADING_STATUS as n } from "../../models/fasta.js";
+//#region src/stores/fastaDataStore/fastaDataStore.ts
+var r = () => ({
+	columnMatchCounts: {},
+	loadingError: null,
+	loadingStatus: n.IDLE,
+	matchKeyField: null,
+	parsedFasta: null,
+	parsedMetadata: null,
+	rawFasta: "",
+	rawMetadata: ""
+}), i = (i) => {
+	let { get: a, set: o } = i, s = (e) => o(e);
+	return {
+		resetDataset: () => s(r()),
+		setColumnMatchCounts: (e) => s({ columnMatchCounts: e }),
+		setData: async (r, i) => {
+			let o = t.parseFasta(r);
+			if (o.error) throw s({
+				loadingError: o.error,
+				loadingStatus: n.ERROR
+			}), Error(o.error);
+			s({
+				parsedFasta: o,
+				rawFasta: r
+			});
+			let c;
+			if (i) {
+				if (c = e.parseTsv(i), c.error) throw s({
+					loadingError: c.error,
+					loadingStatus: n.ERROR
+				}), Error(c.error);
+				s({
+					parsedMetadata: c,
+					rawMetadata: i
+				});
+				let t = o.sequences.map((e) => e.id), { bestColumn: r, matchCounts: l } = e.findBestMatchingColumn(c.columns, c.recordsByColumn, t);
+				a().setColumnMatchCounts(l), a().setMatchKeyField(r);
+			}
+			return s({
+				loadingError: null,
+				loadingStatus: n.SUCCESS
+			}), Promise.resolve({
+				fastaResult: o,
+				metadataResult: c
+			});
+		},
+		setLoadingStatus: (e) => s({ loadingStatus: e }),
+		setMatchKeyField: (e) => s({ matchKeyField: e })
+	};
+};
+//#endregion
+export { i as createFastaDataStoreActions, r as createFastaDataStoreInitialState };
+
+//# sourceMappingURL=index.js.map

package/dist/stores/fastaDataStore/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","names":["createFastaDataStoreInitialState","LOADING_STATUS","createFastaDataStoreActions","kwArgs","setBaseState","set","partial","counts","parsedFasta","FastaUtil","fasta","parsedMetadata","tsv","MetaDataUtil","fastaIds","s","get","matchCounts","bestColumn","status","field"],"sources":["../../../src/stores/fastaDataStore/fastaDataStore.ts"],"sourcesContent":["import type { StoreApi } from 'zustand';\n\nimport type { FastaParseResult } from '../../models/fasta';\nimport { LOADING_STATUS } from '../../models/fasta';\nimport type { MetadataParseResult } from '../../models/metadata';\nimport { FastaUtil } from '../../utils/FastaUtil';\nimport { MetaDataUtil } from '../../utils/MetaDataUtil';\n\nexport type FastaDataStore = FastaDataStoreActions & FastaDataStoreState;\n\nexport interface FastaDataStoreActions {\n  resetDataset: () => void;\n  setColumnMatchCounts: (counts: Record<string, number>) => void;\n  setData: (fasta: string, tsv?: string) => Promise<{ fastaResult: FastaParseResult; metadataResult?: MetadataParseResult }>;\n  setLoadingStatus: (status: LOADING_STATUS) => void;\n  setMatchKeyField: (field: null | string) => void;\n}\n\nexport interface FastaDataStoreState {\n  columnMatchCounts: Record<string, number>;\n  loadingError: null | string;\n  loadingStatus: LOADING_STATUS;\n  matchKeyField: null | string;\n  parsedFasta: FastaParseResult | null;\n  parsedMetadata: MetadataParseResult | null;\n  rawFasta: string;\n  rawMetadata: string;\n}\n\nexport const createFastaDataStoreInitialState = (): FastaDataStoreState => ({\n  columnMatchCounts: {},\n  loadingError: null,\n  loadingStatus: LOADING_STATUS.IDLE,\n  matchKeyField: null,\n  parsedFasta: null,\n  parsedMetadata: null,\n  rawFasta: '',\n  rawMetadata: '',\n});\n\n\ntype Get<T extends FastaDataStore> = StoreApi<T>['getState'];\ntype Set<T extends FastaDataStore> = StoreApi<T>['setState'];\n\nexport const createFastaDataStoreActions = <T extends FastaDataStore>(kwArgs: { get: Get<T>; set: Set<T> }): FastaDataStoreActions => {\n  const { get, set } = kwArgs;\n  const setBaseState = (partial: Partial<FastaDataStoreState>) => set(partial as Partial<T>);\n\n  return {\n    resetDataset: () => setBaseState(createFastaDataStoreInitialState()),\n    setColumnMatchCounts: (counts: Record<string, number>) => setBaseState({ columnMatchCounts: counts }),\n    setData: async (fasta: string, tsv?: string) => {\n      const parsedFasta = FastaUtil.parseFasta(fasta);\n\n      if (parsedFasta.error) {\n        setBaseState({\n          loadingError: parsedFasta.error,\n          loadingStatus: LOADING_STATUS.ERROR,\n        });\n        throw new Error(parsedFasta.error);\n      }\n\n      setBaseState({\n        parsedFasta,\n        rawFasta: fasta,\n      });\n\n      let parsedMetadata: MetadataParseResult | undefined;\n      if (tsv) {\n        parsedMetadata = MetaDataUtil.parseTsv(tsv);\n        if (parsedMetadata.error) {\n          setBaseState({\n            loadingError: parsedMetadata.error,\n            loadingStatus: LOADING_STATUS.ERROR,\n          });\n          throw new Error(parsedMetadata.error);\n        }\n\n        setBaseState({\n          parsedMetadata,\n          rawMetadata: tsv,\n        });\n\n        const fastaIds = parsedFasta.sequences.map((s) => s.id);\n        const { bestColumn, matchCounts } = MetaDataUtil.findBestMatchingColumn(\n          parsedMetadata.columns,\n          parsedMetadata.recordsByColumn,\n          fastaIds,\n        );\n        get().setColumnMatchCounts(matchCounts);\n        get().setMatchKeyField(bestColumn);\n      }\n\n      setBaseState({\n        loadingError: null,\n        loadingStatus: LOADING_STATUS.SUCCESS,\n      });\n      return Promise.resolve({ fastaResult: parsedFasta, metadataResult: parsedMetadata });\n    },\n    setLoadingStatus: (status: LOADING_STATUS) => setBaseState({ loadingStatus: status }),\n    setMatchKeyField: (field: null | string) => setBaseState({ matchKeyField: field }),\n  };\n};\n"],"mappings":";;;;AA6BA,IAAaA,WAA+D;CAC1E,mBAAmB,CAAC;CACpB,cAAc;CACd,eAAeC,EAAe;CAC9B,eAAe;CACf,aAAa;CACb,gBAAgB;CAChB,UAAU;CACV,aAAa;AACf,IAMaC,KAAyD,MAAgE;CACpI,IAAM,EAAE,QAAK,WAAQC,GACfC,KAAgB,MAA0CC,EAAIC,CAAqB;CAEzF,OAAO;EACL,oBAAoBF,EAAaJ,EAAiC,CAAC;EACnE,uBAAuB,MAAmCI,EAAa,EAAE,mBAAmBG,EAAO,CAAC;EACpG,SAAS,OAAO,GAAe,MAAiB;GAC9C,IAAMC,IAAcC,EAAU,WAAWC,CAAK;GAE9C,IAAIF,EAAY,OAKd,MAJAJ,EAAa;IACX,cAAcI,EAAY;IAC1B,eAAeP,EAAe;GAChC,CAAC,GACS,MAAMO,EAAY,KAAK;GAGnC,EAAa;IACX;IACA,UAAUE;GACZ,CAAC;GAED,IAAIC;GACJ,IAAIC,GAAK;IAEP,IADA,IAAiBC,EAAa,SAASD,CAAG,GACtCD,EAAe,OAKjB,MAJAP,EAAa;KACX,cAAcO,EAAe;KAC7B,eAAeV,EAAe;IAChC,CAAC,GACS,MAAMU,EAAe,KAAK;IAGtC,EAAa;KACX;KACA,aAAaC;IACf,CAAC;IAED,IAAME,IAAWN,EAAY,UAAU,KAAK,MAAMO,EAAE,EAAE,GAChD,EAAE,eAAY,mBAAgBF,EAAa,uBAC/CF,EAAe,SACfA,EAAe,iBACfG,CACF;IAEA,AADAE,EAAI,CAAC,CAAC,qBAAqBC,CAAW,GACtCD,EAAI,CAAC,CAAC,iBAAiBE,CAAU;GACnC;GAMA,OAJAd,EAAa;IACX,cAAc;IACd,eAAeH,EAAe;GAChC,CAAC,GACM,QAAQ,QAAQ;IAAE,aAAaO;IAAa,gBAAgBG;GAAe,CAAC;EACrF;EACA,mBAAmB,MAA2BP,EAAa,EAAE,eAAee,EAAO,CAAC;EACpF,mBAAmB,MAAyBf,EAAa,EAAE,eAAegB,EAAM,CAAC;CACnF;AACF"}