@gen-epix/ui-client-casedb 4.0.2 → 4.1.0

package/dist/_chunks/UploadUtil.js

@@ -4,11 +4,10 @@ import { t as i } from "./format.js";
 import { CaseTypeUtil as a, t as o } from "../utils/CaseTypeUtil/index.js";
 import { CASEDB_QUERY_KEY as s } from "../constants/query.js";
 import { CaseUtil as c, t as l } from "../utils/CaseUtil/index.js";
-import { FileUtil as u } from "../utils/FileUtil/index.js";
-import { UploadError as d } from "../classes/errors/index.js";
-import { lazy as f, object as p, string as m } from "yup";
-import { t as h } from "i18next";
-import { CaseDbCaseApi as g, CaseDbColType as _, CaseDbEtlStatus as v, CaseDbReadsFileFormat as y, CaseDbSeqFileFormat as b, CaseDbUploadAction as x } from "@gen-epix/api-casedb";
+import { UploadError as u } from "../classes/errors/index.js";
+import { lazy as d, object as f, string as p } from "yup";
+import { t as m } from "i18next";
+import { CaseDbCaseApi as h, CaseDbColType as g, CaseDbEtlStatus as _, CaseDbFileCompression as v, CaseDbReadsFileFormat as y, CaseDbSeqFileFormat as b, CaseDbUploadAction as x } from "@gen-epix/api-casedb";
 import { QueryClientService as S } from "@gen-epix/ui-client-common/classes/services/QueryClientService";
 import { ValidationUtil as C } from "@gen-epix/ui-core/utils/ValidationUtil";
 import { ObjectUtil as w } from "@gen-epix/ui-core/utils/ObjectUtil";
@@ -2660,11 +2659,12 @@ function ui(e, t, n) {
 //#region src/utils/UploadUtil/UploadUtil.ts
 var di = /* @__PURE__ */ e(l(), 1), fi = /* @__PURE__ */ e(o(), 1), pi = class e {
 	static caseDateColumnAliases = [
-		"_case_date",
-		"case date",
-		"case_date",
-		"casedate",
-		"case.date"
+		"_timed_at",
+		"timed at",
+		"timed_at",
+		"timedat",
+		"case.timed_at",
+		"timed_at_date"
 	];
 	static caseIdColumnAliases = [
 		"_case_id",
@@ -2688,7 +2688,7 @@ var di = /* @__PURE__ */ e(l(), 1), fi = /* @__PURE__ */ e(o(), 1), pi = class e
 	}
 	static async createCases(e) {
 		let { assemblyProtocolId: t, casesForVerificationFromSourceData: n, completeCaseType: r, createdInDataCollectionId: i, mappedColumns: a, sampleIdColId: o, selectedValidatedCases: s, sequenceMapping: l, sequencingProtocolId: u, signal: d } = e, { col: f, sampleIdentifierIssuerId: p } = a.find((e) => e.col?.id === o) ?? {};
-		return (await g.getInstance().uploadCases({
+		return (await h.getInstance().uploadCases({
 			case_batch: { cases: s.map((e) => {
 				let a = e.id, o = [], s = [], d = f ? c.getRowValue(e.validated_content, f, r)?.raw : null, m = n.find((t) => t.id === e.id);
 				return d && (l[e.id]?.sequenceFileNames && Object.entries(l[e.id].sequenceFileNames).forEach(([e, n]) => {
@@ -2730,15 +2730,15 @@ var di = /* @__PURE__ */ e(l(), 1), fi = /* @__PURE__ */ e(o(), 1), pi = class e
 	static async createCasesAndUploadFiles(t) {
 		let { onComplete: n, onError: r, onProgress: i } = t;
 		try {
-			i(0, h("Creating cases..."));
+			i(0, m("Creating cases..."));
 			let r = await e.createCases(t);
-			if (r.status === v.FAILED) throw new d(h("Failed to create cases during upload."), r);
+			if (r.status === _.FAILED) throw new u(m("Failed to create cases during upload."), r);
 			return await e.uploadFilesForCases({
 				...t,
 				caseBatchUploadResult: r,
 				endPercentage: 99,
 				startPercentage: 1
-			}), i(100, h("Upload complete.")), await S.getInstance().invalidateQueryKeys(S.getInstance().getQueryKeyDependencies([s.CASES], !0)), n(), r;
+			}), i(100, m("Upload complete.")), await S.getInstance().invalidateQueryKeys(S.getInstance().getQueryKeyDependencies([s.CASES], !0)), n(), r;
 		} catch (e) {
 			throw r(e instanceof Error ? e : /* @__PURE__ */ Error("Unknown error occurred during upload")), e;
 		}
@@ -2805,16 +2805,16 @@ var di = /* @__PURE__ */ e(l(), 1), fi = /* @__PURE__ */ e(o(), 1), pi = class e
 	static getColumnMappingSchema(t, n) {
 		let r = {}, i = t[0].map((e, t) => t.toString());
 		return e.getSampleIdColIds(n).forEach((e) => {
-			r[e] = f(() => m().nullable().when(i, (t, n) => n.test("needs-identifier-issuer", h("An identifier issuer must be selected."), (n) => ![...t, n].includes(e) || !!n)));
+			r[e] = d(() => p().nullable().when(i, (t, n) => n.test("needs-identifier-issuer", m("An identifier issuer must be selected."), (n) => ![...t, n].includes(e) || !!n)));
 		}), i.forEach((e, n) => {
 			let a = i.filter((t) => t !== e);
-			r[e] = f(() => m().nullable().when(a, (e, r) => r.test("unique", h("This column has already been mapped to another field."), (t) => !t || !e.includes(t)).test("valid-case-id-values", h("The column mapped to the case id field must contain valid UUID's."), (e) => e !== "case_id" || t.slice(1).map((e) => e[n]).every((e) => !e || C.validate("UUID4", e)))));
-		}), p().shape(r);
+			r[e] = d(() => p().nullable().when(a, (e, r) => r.test("unique", m("This column has already been mapped to another field."), (t) => !t || !e.includes(t)).test("valid-case-id-values", m("The column mapped to the case id field must contain valid UUID's."), (e) => e !== "case_id" || t.slice(1).map((e) => e[n]).every((e) => !e || C.validate("UUID4", e)))));
+		}), f().shape(r);
 	}
 	static getCompleteCaseTypeColStats(e) {
-		let t = a.getColsByType(e, [_.ID_SAMPLE]), n = a.getColsByType(e, [_.GENETIC_SEQUENCE]);
+		let t = a.getColsByType(e, [g.ID_SAMPLE]), n = a.getColsByType(e, [g.GENETIC_SEQUENCE]);
 		return {
-			readsColumns: a.getColsByType(e, [_.GENETIC_READS]),
+			readsColumns: a.getColsByType(e, [g.GENETIC_READS]),
 			sampleIdColumns: t,
 			sequenceColumns: n,
 			writableColumns: Object.values(e.cols).filter((t) => a.getWritableColIds(e).includes(t.id))
@@ -2895,7 +2895,7 @@ var di = /* @__PURE__ */ e(l(), 1), fi = /* @__PURE__ */ e(o(), 1), pi = class e
 		let t = [];
 		return Object.values(Object.keys(e.cols)).forEach((n) => {
 			let r = e.cols[n];
-			e.ref_cols[r.ref_col_id]?.col_type === _.ID_SAMPLE && t.push(r.id);
+			e.ref_cols[r.ref_col_id]?.col_type === g.ID_SAMPLE && t.push(r.id);
 		}), t;
 	}
 	static getSequenceMappingStats(t, n) {
@@ -3004,7 +3004,7 @@ var di = /* @__PURE__ */ e(l(), 1), fi = /* @__PURE__ */ e(o(), 1), pi = class e
 		i(a + s * c + n * c, r);
 	}
 	static async uploadFilesForCases(t) {
-		let { caseBatchUploadResult: n, endPercentage: r, onProgress: i, sequenceFilesDataTransfer: a, sequenceMapping: o, signal: s, startPercentage: c } = t, l = [], d = [], f = 0;
+		let { caseBatchUploadResult: n, endPercentage: r, onProgress: i, sequenceFilesDataTransfer: a, sequenceMapping: o, signal: s, startPercentage: c } = t, l = [], u = [], d = 0;
 		for (let [e, r] of n.cases.entries()) {
 			let { id: n } = t.selectedValidatedCases[e];
 			if (o[n]) {
@@ -3015,80 +3015,84 @@ var di = /* @__PURE__ */ e(l(), 1), fi = /* @__PURE__ */ e(o(), 1), pi = class e
 						caseId: e,
 						colId: t,
 						fileName: r
-					}), f += n?.size || 0);
+					}), d += n?.size || 0);
 				}
 				for (let [t, r] of Object.entries(o[n].readsFileNames)) {
 					if (r.fwd) {
 						let n = Array.from(a.files).find((e) => e.name === r.fwd);
-						n && (d.push({
+						n && (u.push({
 							caseId: e,
 							colId: t,
 							fileName: r.fwd,
 							is_fwd: !0
-						}), f += n?.size || 0);
+						}), d += n?.size || 0);
 					}
 					if (r.rev) {
 						let n = Array.from(a.files).find((e) => e.name === r.rev);
-						n && (d.push({
+						n && (u.push({
 							caseId: e,
 							colId: t,
 							fileName: r.rev,
 							is_fwd: !1
-						}), f += n?.size || 0);
+						}), d += n?.size || 0);
 					}
 				}
 			}
 		}
-		let p = 0;
+		let f = 0;
 		for (let t of n.cases) {
-			let n = l.find((e) => e.caseId === t.id), o = d.filter((e) => e.caseId === t.id);
+			let n = l.find((e) => e.caseId === t.id), o = u.filter((e) => e.caseId === t.id);
 			if (n) {
 				let t = Array.from(a.files).find((e) => e.name === n.fileName);
 				if (t) {
 					let a = t.size, o = await e.readFileAsBase64(t);
-					await g.getInstance().createFileForSeq(n.caseId, n.colId, {
-						file_compression: u.getFileCompressionFromFileName(n.fileName),
+					await h.getInstance().createFileForSeq(n.caseId, n.colId, {
+						file_compression: e.getFileCompressionFromFileName(n.fileName),
 						file_content: o,
 						file_format: b.FASTA
 					}, { signal: s }), e.reportFileUploadProgress({
 						endPercentage: r,
 						fileSize: a,
-						message: h("Uploading sequence file \"{{fileName}}\" for case ID \"{{caseId}}\"...", {
+						message: m("Uploading sequence file \"{{fileName}}\" for case ID \"{{caseId}}\"...", {
 							caseId: n.caseId,
 							fileName: n.fileName
 						}),
 						onProgress: i,
 						startPercentage: c,
-						totalFileSizeToUpload: f,
-						uploadedFileSize: p
-					}), p += a;
+						totalFileSizeToUpload: d,
+						uploadedFileSize: f
+					}), f += a;
 				}
 			}
 			for (let t of o) {
 				let n = Array.from(a.files).find((e) => e.name === t.fileName);
 				if (n) {
 					let a = n.size, o = await e.readFileAsBase64(n);
-					await g.getInstance().createFileForReadSet(t.caseId, t.colId, {
-						file_compression: u.getFileCompressionFromFileName(t.fileName),
+					await h.getInstance().createFileForReadSet(t.caseId, t.colId, {
+						file_compression: e.getFileCompressionFromFileName(t.fileName),
 						file_content: o,
 						file_format: y.FASTQ,
 						is_fwd: t.is_fwd
 					}, { signal: s }), e.reportFileUploadProgress({
 						endPercentage: r,
 						fileSize: a,
-						message: h("Uploading read set file \"{{fileName}}\" for case ID \"{{caseId}}\"...", {
+						message: m("Uploading read set file \"{{fileName}}\" for case ID \"{{caseId}}\"...", {
 							caseId: t.caseId,
 							fileName: t.fileName
 						}),
 						onProgress: i,
 						startPercentage: c,
-						totalFileSizeToUpload: f,
-						uploadedFileSize: p
-					}), p += a;
+						totalFileSizeToUpload: d,
+						uploadedFileSize: f
+					}), f += a;
 				}
 			}
 		}
 	}
+	static getFileCompressionFromFileName(e) {
+		let t = e.toLowerCase();
+		return t.endsWith(".gz") || t.endsWith(".gzip") ? v.GZIP : v.NONE;
+	}
 	static idToRegex(e) {
 		return new RegExp(e.replace(/[-/\\^$*+?.()|[\]{}]/g, "\\$&"));
 	}