@rivm-loculus-tools/common-frontend 0.1.0 → 0.1.4

package/dist/theme/theme.d.ts

@@ -0,0 +1 @@
+export declare const theme: import('@mui/material').Theme;

package/dist/utils/DownloadUtil/DownloadUtil.d.ts

@@ -0,0 +1,3 @@
+export declare class DownloadUtil {
+    static datasetFilename(label: string): string;
+}

package/dist/utils/DownloadUtil/index.js

@@ -0,0 +1,10 @@
+//#region src/utils/DownloadUtil/DownloadUtil.ts
+var e = class {
+	static datasetFilename(e) {
+		return `${e.trim().replace(/\.[^.]+$/, "").replace(/[^a-zA-Z0-9._-]+/g, "_").replace(/^\.+|\.+$/g, "").slice(0, 80) || "alignment"}.fasta`;
+	}
+};
+//#endregion
+export { e as DownloadUtil };
+
+//# sourceMappingURL=index.js.map

package/dist/utils/DownloadUtil/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","names":[],"sources":["../../../src/utils/DownloadUtil/DownloadUtil.ts"],"sourcesContent":["export class DownloadUtil {\n  public static datasetFilename(label: string): string {\n    const withoutExtension = label.trim().replace(/\\.[^.]+$/, '');\n    const safeLabel = withoutExtension\n      .replace(/[^a-zA-Z0-9._-]+/g, '_')\n      .replace(/^\\.+|\\.+$/g, '')\n      .slice(0, 80);\n    return `${safeLabel || 'alignment'}.fasta`;\n  }\n}\n"],"mappings":";AAAA,IAAa,IAAb,MAA0B;CACxB,OAAc,gBAAgB,GAAuB;EAMnD,OAAO,GALkB,EAAM,KAAK,CAAC,CAAC,QAAQ,YAAY,EACxC,CAAA,CACf,QAAQ,qBAAqB,GAAG,CAAC,CACjC,QAAQ,cAAc,EAAE,CAAC,CACzB,MAAM,GAAG,EACF,KAAa,YAAY;CACrC;AACF"}

package/dist/utils/ErrorUtil/ErrorUtil.d.ts

@@ -0,0 +1,3 @@
+export declare class ErrorUtil {
+    static getErrorMessage(error: unknown, fallback: string): string;
+}

package/dist/utils/ErrorUtil/index.js

@@ -0,0 +1,10 @@
+//#region src/utils/ErrorUtil/ErrorUtil.ts
+var e = class {
+	static getErrorMessage(e, t) {
+		return e instanceof Error ? e.message : t;
+	}
+};
+//#endregion
+export { e as ErrorUtil };
+
+//# sourceMappingURL=index.js.map

package/dist/utils/ErrorUtil/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","names":[],"sources":["../../../src/utils/ErrorUtil/ErrorUtil.ts"],"sourcesContent":["export class ErrorUtil {\n  public static getErrorMessage(error: unknown, fallback: string): string {\n    return error instanceof Error ? error.message : fallback;\n  }\n}\n"],"mappings":";AAAA,IAAa,IAAb,MAAuB;CACrB,OAAc,gBAAgB,GAAgB,GAA0B;EACtE,OAAO,aAAiB,QAAQ,EAAM,UAAU;CAClD;AACF"}

package/dist/utils/FastaUtil/FastaUtil.d.ts

@@ -0,0 +1,6 @@
+import { FastaParseResult } from '../../models/fasta';
+export declare class FastaUtil {
+    static parseFasta(content: string): FastaParseResult;
+    static stripFastaHeaders(fastaContent: string): string;
+    private static createErrorResult;
+}

package/dist/utils/FastaUtil/index.js

@@ -0,0 +1,63 @@
+//#region src/utils/FastaUtil/FastaUtil.ts
+var e = class e {
+	static parseFasta(t) {
+		if (!t?.trim()) return e.createErrorResult("The FASTA input is empty.");
+		let n = t.split(/\r?\n/), r = [], i = "", a = [], o = () => {
+			if (i) {
+				let t = a.join("").replace(/\s/g, "").toUpperCase();
+				if (!t.length) return e.createErrorResult(`FASTA record "${i}" has no sequence.`);
+				let n = i.split(/[|\t]/)[0].trim().replace(/[():;,']/g, "_");
+				r.push({
+					accessionVersion: n,
+					header: i,
+					id: n,
+					length: t.length,
+					sequence: t
+				});
+			}
+			return null;
+		};
+		for (let t of n) {
+			let n = t.trim();
+			if (n) {
+				if (n.startsWith(">")) {
+					let t = o();
+					if (t) return t;
+					if (i = n.slice(1).trim(), !i) return e.createErrorResult("Every FASTA record needs a non-empty header.");
+					a = [];
+				} else {
+					if (!i) return e.createErrorResult("FASTA sequence data appeared before its first header.");
+					a.push(n);
+				}
+			}
+		}
+		let s = o();
+		if (s) return s;
+		if (r.length === 0) return e.createErrorResult("No FASTA records were found.");
+		let c = r[0].length, l = r.filter((e) => e.length !== c).map((e) => ({
+			id: e.id,
+			length: e.length
+		})), u = l.length === 0;
+		return {
+			expectedLength: c,
+			invalidSequences: u ? void 0 : l,
+			isAligned: u,
+			sequences: r
+		};
+	}
+	static stripFastaHeaders(e) {
+		return e.split("\n").map((e) => e.startsWith(">") ? `>${e.substring(1).trim().split(/[|\t]/)[0].trim().replace(/[():;,']/g, "_")}` : e).join("\n");
+	}
+	static createErrorResult(e) {
+		return {
+			error: e,
+			expectedLength: 0,
+			isAligned: !1,
+			sequences: []
+		};
+	}
+};
+//#endregion
+export { e as FastaUtil };
+
+//# sourceMappingURL=index.js.map

package/dist/utils/FastaUtil/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","names":[],"sources":["../../../src/utils/FastaUtil/FastaUtil.ts"],"sourcesContent":["import type {\n  FastaParseResult,\n  FastaSequence,\n} from '../../models/fasta';\n\nexport class FastaUtil {\n  public static parseFasta(content: string): FastaParseResult {\n    if (!content?.trim()) {\n      return FastaUtil.createErrorResult('The FASTA input is empty.');\n    }\n\n    const lines = content.split(/\\r?\\n/);\n    const sequences: FastaSequence[] = [];\n    let currentHeader = '';\n    let currentSeqParts: string[] = [];\n\n    const commitSequence = (): FastaParseResult | null => {\n      if (currentHeader) {\n        const fullSeq = currentSeqParts.join('').replace(/\\s/g, '').toUpperCase();\n        if (!fullSeq.length) {\n          return FastaUtil.createErrorResult(`FASTA record \"${currentHeader}\" has no sequence.`);\n        }\n\n        // Extract ID: part before pipe or tab, sanitized for Newick compatibility\n        const firstPart = currentHeader.split(/[|\\t]/)[0].trim();\n        const safeId = firstPart.replace(/[():;,']/g, '_');\n\n        sequences.push({\n          accessionVersion: safeId,\n          header: currentHeader,\n          id: safeId,\n          length: fullSeq.length,\n          sequence: fullSeq,\n        });\n      }\n      return null;\n    };\n\n    for (const sourceLine of lines) {\n      const line = sourceLine.trim();\n      if (!line) {\n        continue;\n      }\n\n      if (line.startsWith('>')) {\n        const error = commitSequence();\n        if (error) {\n          return error;\n        }\n        currentHeader = line.slice(1).trim();\n        if (!currentHeader) {\n          return FastaUtil.createErrorResult('Every FASTA record needs a non-empty header.');\n        }\n        currentSeqParts = [];\n      } else {\n        if (!currentHeader) {\n          return FastaUtil.createErrorResult('FASTA sequence data appeared before its first header.');\n        }\n        currentSeqParts.push(line);\n      }\n    }\n    const error = commitSequence();\n    if (error) {\n      return error;\n    }\n\n    if (sequences.length === 0) {\n      return FastaUtil.createErrorResult('No FASTA records were found.');\n    }\n\n    // Pre-alignment validation: verify all sequence lengths are equal\n    const firstLength = sequences[0].length;\n    const invalidSequences = sequences.filter((s) => s.length !== firstLength).map((s) => ({ id: s.id, length: s.length }));\n\n    const isAligned = invalidSequences.length === 0;\n\n    return {\n      expectedLength: firstLength,\n      invalidSequences: isAligned ? undefined : invalidSequences,\n      isAligned,\n      sequences,\n    };\n  }\n\n  public static stripFastaHeaders(fastaContent: string): string {\n    const lines = fastaContent.split('\\n');\n    const strippedLines = lines.map((line) => {\n      if (line.startsWith('>')) {\n        const cleanHeader = line.substring(1).trim();\n        const firstPart = cleanHeader.split(/[|\\t]/)[0].trim();\n        const safeId = firstPart.replace(/[():;,']/g, '_');\n        return `>${safeId}`;\n      }\n      return line;\n    });\n    return strippedLines.join('\\n');\n  }\n\n\n  private static createErrorResult(error: string): FastaParseResult {\n    return {\n      error,\n      expectedLength: 0,\n      isAligned: false,\n      sequences: [],\n    };\n  }\n\n}\n"],"mappings":";AAKA,IAAa,IAAb,MAAa,EAAU;CACrB,OAAc,WAAW,GAAmC;EAC1D,IAAI,CAAC,GAAS,KAAK,GACjB,OAAO,EAAU,kBAAkB,2BAA2B;EAGhE,IAAM,IAAQ,EAAQ,MAAM,OAAO,GAC7B,IAA6B,CAAC,GAChC,IAAgB,IAChB,IAA4B,CAAC,GAE3B,UAAgD;GACpD,IAAI,GAAe;IACjB,IAAM,IAAU,EAAgB,KAAK,EAAE,CAAC,CAAC,QAAQ,OAAO,EAAE,CAAC,CAAC,YAAY;IACxE,IAAI,CAAC,EAAQ,QACX,OAAO,EAAU,kBAAkB,iBAAiB,EAAc,mBAAmB;IAKvF,IAAM,IADY,EAAc,MAAM,OAAO,CAAC,CAAC,EAAE,CAAC,KACnC,CAAA,CAAU,QAAQ,aAAa,GAAG;IAEjD,EAAU,KAAK;KACb,kBAAkB;KAClB,QAAQ;KACR,IAAI;KACJ,QAAQ,EAAQ;KAChB,UAAU;IACZ,CAAC;GACH;GACA,OAAO;EACT;EAEA,KAAK,IAAM,KAAc,GAAO;GAC9B,IAAM,IAAO,EAAW,KAAK;GACxB,OAIL;QAAI,EAAK,WAAW,GAAG,GAAG;KACxB,IAAM,IAAQ,EAAe;KAC7B,IAAI,GACF,OAAO;KAGT,IADA,IAAgB,EAAK,MAAM,CAAC,CAAC,CAAC,KAAK,GAC/B,CAAC,GACH,OAAO,EAAU,kBAAkB,8CAA8C;KAEnF,IAAkB,CAAC;IACrB,OAAO;KACL,IAAI,CAAC,GACH,OAAO,EAAU,kBAAkB,uDAAuD;KAE5F,EAAgB,KAAK,CAAI;IAC3B;;EACF;EACA,IAAM,IAAQ,EAAe;EAC7B,IAAI,GACF,OAAO;EAGT,IAAI,EAAU,WAAW,GACvB,OAAO,EAAU,kBAAkB,8BAA8B;EAInE,IAAM,IAAc,EAAU,EAAE,CAAC,QAC3B,IAAmB,EAAU,QAAQ,MAAM,EAAE,WAAW,CAAW,CAAC,CAAC,KAAK,OAAO;GAAE,IAAI,EAAE;GAAI,QAAQ,EAAE;EAAO,EAAE,GAEhH,IAAY,EAAiB,WAAW;EAE9C,OAAO;GACL,gBAAgB;GAChB,kBAAkB,IAAY,KAAA,IAAY;GAC1C;GACA;EACF;CACF;CAEA,OAAc,kBAAkB,GAA8B;EAW5D,OAVc,EAAa,MAAM,IACX,CAAA,CAAM,KAAK,MAC3B,EAAK,WAAW,GAAG,IAId,IAHa,EAAK,UAAU,CAAC,CAAC,CAAC,KACpB,CAAA,CAAY,MAAM,OAAO,CAAC,CAAC,EAAE,CAAC,KACjC,CAAA,CAAU,QAAQ,aAAa,GACnC,MAEN,CAEF,CAAA,CAAc,KAAK,IAAI;CAChC;CAGA,OAAe,kBAAkB,GAAiC;EAChE,OAAO;GACL;GACA,gBAAgB;GAChB,WAAW;GACX,WAAW,CAAC;EACd;CACF;AAEF"}

package/dist/utils/MetaDataUtil/MetaDataUtil.d.ts

@@ -0,0 +1,20 @@
+import { MetadataParseResult, MetadataRecord } from '../../models/metadata';
+export declare class MetaDataUtil {
+    /**
+     * Compute the best matching metadata column for the given FASTA sequence IDs.
+     */
+    static findBestMatchingColumn: (columns: string[], recordsByColumn: Record<string, Record<string, MetadataRecord>>, fastaIds: string[]) => {
+        bestColumn: null | string;
+        matchCounts: Record<string, number>;
+    };
+    static getHighlightedIds(query: string, allAccessions: string[], metadataRecords: MetadataRecord[], matchKeyField?: null | string): string[];
+    /**
+     * Count FASTA sequence ID matches for each metadata column.
+     */
+    static getMatchCounts: (columns: string[], recordsByColumn: Record<string, Record<string, MetadataRecord>>, fastaIds: string[]) => Record<string, number>;
+    /**
+     * Retrieve metadata record for a given sample/node name with fallback strategies.
+     */
+    static readonly getRecordForSample: (metadata: MetadataParseResult | null | undefined, sampleId: string, matchKeyField?: null | string) => MetadataRecord | undefined;
+    static parseTsv: (content: string) => MetadataParseResult;
+}

package/dist/utils/MetaDataUtil/index.js

@@ -0,0 +1,133 @@
+//#region src/utils/MetaDataUtil/MetaDataUtil.ts
+var e = class e {
+	static findBestMatchingColumn = (t, n, r) => {
+		let i = e.getMatchCounts(t, n, r), a = null, o = -1;
+		if (!t || !n || !r || r.length === 0) return {
+			bestColumn: null,
+			matchCounts: {}
+		};
+		let s = [
+			"displayname",
+			"accessionversion",
+			"accession",
+			"sampleid",
+			"sample_id",
+			"id",
+			"strain",
+			"isolate",
+			"submissionid",
+			"name"
+		];
+		for (let e of t) {
+			if (!n[e]) continue;
+			let t = i[e];
+			if (t > o) o = t, a = e;
+			else if (t === o && t > 0 && a) {
+				let t = s.indexOf(a.toLowerCase()), n = s.indexOf(e.toLowerCase());
+				n !== -1 && (t === -1 || n < t) && (a = e);
+			}
+		}
+		if (o <= 0) {
+			for (let e of s) {
+				let n = t.find((t) => t.toLowerCase() === e);
+				if (n) {
+					a = n;
+					break;
+				}
+			}
+			!a && t.length > 0 && (a = t[0]);
+		}
+		return {
+			bestColumn: a,
+			matchCounts: i
+		};
+	};
+	static getHighlightedIds(e, t, n, r = null) {
+		let i = e.trim().toLowerCase();
+		if (!i) return [];
+		let a = /* @__PURE__ */ new Set();
+		return t.forEach((e) => {
+			e.toLowerCase().includes(i) && a.add(e);
+		}), n.forEach((e) => {
+			let t = r && e[r] || e.displayName || e.accessionVersion || e.accession || e.id || e.submissionId || e.SampleID;
+			t && Object.values(e).some((e) => typeof e == "string" && e.toLowerCase().includes(i)) && a.add(t);
+		}), Array.from(a);
+	}
+	static getMatchCounts = (e, t, n) => {
+		let r = {};
+		if (!e || !t || !n || n.length === 0) return r;
+		for (let i of e) {
+			let e = t[i];
+			if (!e) continue;
+			let a = 0;
+			for (let t of n) e[t] && a++;
+			r[i] = a;
+		}
+		return r;
+	};
+	static getRecordForSample = (e, t, n) => {
+		if (e && t) {
+			if (n && e.recordsByColumn?.[n]) {
+				let r = e.recordsByColumn[n][t];
+				if (r) return r;
+			}
+			if (e.recordsByColumn?.displayName?.[t]) return e.recordsByColumn.displayName[t];
+			if (e.recordsByColumn?.accessionVersion?.[t]) return e.recordsByColumn.accessionVersion[t];
+			if (e.recordsByAccession[t]) return e.recordsByAccession[t];
+			if (e.recordsBySampleId[t]) return e.recordsBySampleId[t];
+			if (e.recordsByColumn) for (let n of Object.keys(e.recordsByColumn)) {
+				let r = e.recordsByColumn[n][t];
+				if (r) return r;
+			}
+		}
+	};
+	static parseTsv = (e) => {
+		if (!e?.trim()) return {
+			columns: [],
+			error: "Empty metadata content provided.",
+			records: [],
+			recordsByAccession: {},
+			recordsByColumn: {},
+			recordsBySampleId: {}
+		};
+		let t = e.trim().split("\n");
+		if (t.length < 2) return {
+			columns: [],
+			error: "Metadata file must contain at least a header row and one data row.",
+			records: [],
+			recordsByAccession: {},
+			recordsByColumn: {},
+			recordsBySampleId: {}
+		};
+		let n = t[0].trim(), r = "	";
+		!n.includes("	") && n.includes(",") && (r = ",");
+		let i = n.split(r).map((e) => e.trim().replace(/^["']|["']$/g, "")).filter((e) => e.length > 0), a = [], o = {}, s = {}, c = {};
+		i.forEach((e) => {
+			c[e] = {};
+		});
+		for (let e = 1; e < t.length; e++) {
+			let n = t[e].trim();
+			if (!n) continue;
+			let l = n.split(r).map((e) => e.trim().replace(/^["']|["']$/g, "")), u = {};
+			i.forEach((e, t) => {
+				let n = l[t] ?? "";
+				u[e] = n, n && (c[e][n] = u);
+			}), a.push(u);
+			let d = u.displayName || u.accessionVersion || u.accession || u.id || u.submissionId || u.strain || u.isolate || u.name;
+			d && (o[d] = u);
+			let f = u.SampleID || u.sampleId || u.sample_id || u.specimenCollectorSampleId || u.id;
+			f && (s[f] = u);
+		}
+		return {
+			columns: i,
+			records: a,
+			recordsByAccession: o,
+			recordsByColumn: c,
+			recordsBySampleId: s
+		};
+	};
+};
+//#endregion
+export { e as MetaDataUtil };
+
+//# sourceMappingURL=index.js.map

package/dist/utils/MetaDataUtil/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","names":[],"sources":["../../../src/utils/MetaDataUtil/MetaDataUtil.ts"],"sourcesContent":["import type {\n  MetadataParseResult,\n  MetadataRecord,\n} from '../../models/metadata';\n\nexport class MetaDataUtil {\n  /**\n   * Compute the best matching metadata column for the given FASTA sequence IDs.\n   */\n  public static findBestMatchingColumn = (\n    columns: string[],\n    recordsByColumn: Record<string, Record<string, MetadataRecord>>,\n    fastaIds: string[],\n  ): { bestColumn: null | string; matchCounts: Record<string, number> } => {\n    const matchCounts = MetaDataUtil.getMatchCounts(columns, recordsByColumn, fastaIds);\n    let bestColumn: null | string = null;\n    let maxMatches = -1;\n\n    if (!columns || !recordsByColumn || !fastaIds || fastaIds.length === 0) {\n      return { bestColumn: null, matchCounts: {} };\n    }\n\n    const prioritizedKeys = [\n      'displayname',\n      'accessionversion',\n      'accession',\n      'sampleid',\n      'sample_id',\n      'id',\n      'strain',\n      'isolate',\n      'submissionid',\n      'name',\n    ];\n\n    for (const col of columns) {\n      const colDict = recordsByColumn[col];\n      if (!colDict) {\n        continue;\n      }\n\n      const count = matchCounts[col];\n\n      if (count > maxMatches) {\n        maxMatches = count;\n        bestColumn = col;\n      } else if (count === maxMatches && count > 0 && bestColumn) {\n        // Tie-breaker: prioritize standard ID column names\n        const currentPriority = prioritizedKeys.indexOf(bestColumn.toLowerCase());\n        const newPriority = prioritizedKeys.indexOf(col.toLowerCase());\n        if (newPriority !== -1 && (currentPriority === -1 || newPriority < currentPriority)) {\n          bestColumn = col;\n        }\n      }\n    }\n\n    if (maxMatches <= 0) {\n      // If no matches, default to highest priority known ID column if available\n      for (const pKey of prioritizedKeys) {\n        const found = columns.find((c) => c.toLowerCase() === pKey);\n        if (found) {\n          bestColumn = found;\n          break;\n        }\n      }\n      if (!bestColumn && columns.length > 0) {\n        bestColumn = columns[0];\n      }\n    }\n\n    return { bestColumn, matchCounts };\n  };\n\n  public static getHighlightedIds(query: string, allAccessions: string[], metadataRecords: MetadataRecord[], matchKeyField: null | string = null): string[] {\n    const trimmed = query.trim().toLowerCase();\n    if (!trimmed) {\n      return [];\n    }\n\n    const matched = new Set<string>();\n\n    // Check accession names / fasta IDs\n    allAccessions.forEach((acc) => {\n      if (acc.toLowerCase().includes(trimmed)) {\n        matched.add(acc);\n      }\n    });\n\n    // Check metadata records\n    metadataRecords.forEach((rec) => {\n      const acc =\n        (matchKeyField && rec[matchKeyField]) ||\n        rec.displayName ||\n        rec.accessionVersion ||\n        rec.accession ||\n        rec.id ||\n        rec.submissionId ||\n        rec.SampleID;\n      if (acc) {\n        const matchesAnyField = Object.values(rec).some(\n          (val) => typeof val === 'string' && val.toLowerCase().includes(trimmed),\n        );\n        if (matchesAnyField) {\n          matched.add(acc);\n        }\n      }\n    });\n\n    return Array.from(matched);\n  }\n  /**\n   * Count FASTA sequence ID matches for each metadata column.\n   */\n  public static getMatchCounts = (\n    columns: string[],\n    recordsByColumn: Record<string, Record<string, MetadataRecord>>,\n    fastaIds: string[],\n  ): Record<string, number> => {\n    const matchCounts: Record<string, number> = {};\n\n    if (!columns || !recordsByColumn || !fastaIds || fastaIds.length === 0) {\n      return matchCounts;\n    }\n\n    for (const col of columns) {\n      const colDict = recordsByColumn[col];\n      if (!colDict) {\n        continue;\n      }\n\n      let count = 0;\n      for (const id of fastaIds) {\n        if (colDict[id]) {\n          count++;\n        }\n      }\n      matchCounts[col] = count;\n    }\n\n    return matchCounts;\n  };\n\n  /**\n   * Retrieve metadata record for a given sample/node name with fallback strategies.\n   */\n  public static readonly getRecordForSample = (\n    metadata: MetadataParseResult | null | undefined,\n    sampleId: string,\n    matchKeyField?: null | string,\n  ): MetadataRecord | undefined => {\n    if (!metadata || !sampleId) {\n      return undefined;\n    }\n\n    // 1. If matchKeyField is specified and exists, check it first\n    if (matchKeyField && metadata.recordsByColumn?.[matchKeyField]) {\n      const rec = metadata.recordsByColumn[matchKeyField][sampleId];\n      if (rec) {\n        return rec;\n      }\n    }\n\n    // 2. Check displayName\n    if (metadata.recordsByColumn?.['displayName']?.[sampleId]) {\n      return metadata.recordsByColumn['displayName'][sampleId];\n    }\n\n    // 3. Check accessionVersion\n    if (metadata.recordsByColumn?.['accessionVersion']?.[sampleId]) {\n      return metadata.recordsByColumn['accessionVersion'][sampleId];\n    }\n\n    // 4. Check accession maps\n    if (metadata.recordsByAccession[sampleId]) {\n      return metadata.recordsByAccession[sampleId];\n    }\n    if (metadata.recordsBySampleId[sampleId]) {\n      return metadata.recordsBySampleId[sampleId];\n    }\n\n    // 5. 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package/dist/utils/UrlUtil/UrlUtil.d.ts

@@ -0,0 +1,5 @@
+export declare class UrlUtil {
+    static clearSearchParams(): void;
+    static fastaLabelFromUrl(url: string): string;
+    static validateFastaUrl(url: string): string;
+}

package/dist/utils/UrlUtil/index.js

@@ -0,0 +1,30 @@
+import { WindowService as e } from "@gen-epix/ui-core/classes/services/WindowService";
+//#region src/utils/UrlUtil/UrlUtil.ts
+var t = class {
+	static clearSearchParams() {
+		let t = new URL(e.getInstance().window.location.href);
+		t.search = "", e.getInstance().window.history.replaceState(null, "", t.toString());
+	}
+	static fastaLabelFromUrl(e) {
+		try {
+			let t = new URL(e), n = t.pathname.split("/").filter(Boolean).pop();
+			return n ? decodeURIComponent(n) : `${t.hostname}.fasta`;
+		} catch {
+			return "remote-alignment.fasta";
+		}
+	}
+	static validateFastaUrl(e) {
+		let t;
+		try {
+			t = new URL(e.trim());
+		} catch {
+			throw Error("Enter a valid FASTA URL.");
+		}
+		if (t.protocol !== "http:" && t.protocol !== "https:") throw Error("FASTA URLs must use HTTP or HTTPS.");
+		return t.href;
+	}
+};
+//#endregion
+export { t as UrlUtil };
+
+//# sourceMappingURL=index.js.map

package/dist/utils/UrlUtil/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","names":[],"sources":["../../../src/utils/UrlUtil/UrlUtil.ts"],"sourcesContent":["import { WindowService } from '@gen-epix/ui-core/classes/services/WindowService';\n\nexport class UrlUtil {\n  public static clearSearchParams(): void {\n    const url = new URL(WindowService.getInstance().window.location.href);\n    url.search = '';\n    WindowService.getInstance().window.history.replaceState(null, '', url.toString());\n  }\n\n  public static fastaLabelFromUrl(url: string): string {\n    try {\n      const urlObject = new URL(url);\n      const segment = urlObject.pathname.split('/').filter(Boolean).pop();\n      if (segment) {\n        return decodeURIComponent(segment);\n      }\n      return `${urlObject.hostname}.fasta`;\n    } catch {\n      return 'remote-alignment.fasta';\n    }\n  }\n\n  public static validateFastaUrl(url: string): string {\n    let urlObject: URL;\n    try {\n      urlObject = new URL(url.trim());\n    } catch {\n      throw new Error('Enter a valid FASTA URL.');\n    }\n    if (urlObject.protocol !== 'http:' && urlObject.protocol !== 'https:') {\n      throw new Error('FASTA URLs must use HTTP or HTTPS.');\n    }\n    return urlObject.href;\n  }\n}\n"],"mappings":";;AAEA,IAAa,IAAb,MAAqB;CACnB,OAAc,oBAA0B;EACtC,IAAM,IAAM,IAAI,IAAI,EAAc,YAAY,CAAC,CAAC,OAAO,SAAS,IAAI;EAEpE,AADA,EAAI,SAAS,IACb,EAAc,YAAY,CAAC,CAAC,OAAO,QAAQ,aAAa,MAAM,IAAI,EAAI,SAAS,CAAC;CAClF;CAEA,OAAc,kBAAkB,GAAqB;EACnD,IAAI;GACF,IAAM,IAAY,IAAI,IAAI,CAAG,GACvB,IAAU,EAAU,SAAS,MAAM,GAAG,CAAC,CAAC,OAAO,OAAO,CAAC,CAAC,IAAI;GAIlE,OAHI,IACK,mBAAmB,CAAO,IAE5B,GAAG,EAAU,SAAS;EAC/B,QAAQ;GACN,OAAO;EACT;CACF;CAEA,OAAc,iBAAiB,GAAqB;EAClD,IAAI;EACJ,IAAI;GACF,IAAY,IAAI,IAAI,EAAI,KAAK,CAAC;EAChC,QAAQ;GACN,MAAU,MAAM,0BAA0B;EAC5C;EACA,IAAI,EAAU,aAAa,WAAW,EAAU,aAAa,UAC3D,MAAU,MAAM,oCAAoC;EAEtD,OAAO,EAAU;CACnB;AACF"}

package/package.json

@@ -1,7 +1,11 @@
 {
   "name": "@rivm-loculus-tools/common-frontend",
-  "version": "0.1.0",
+  "version": "0.1.4",
   "license": "EUPL-1.2",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/RIVM-bioinformatics/loculus-tools"
+  },
   "type": "module",
   "peerDependencies": {
     "@emotion/cache": "*",
@@ -55,12 +59,10 @@
     "vite-plugin-static-copy": "4.1.1",
     "vite": "8.3.0"
   },
-  "types": "./dist/index.d.ts",
+  "files": [
+    "dist"
+  ],
   "exports": {
-    ".": {
-      "types": "./dist/index.d.ts",
-      "import": "./dist/index.js"
-    },
     "./classes/services/FastaDataEventBusService": {
       "types": "./dist/classes/services/FastaDataEventBusService/index.d.ts",
       "import": "./dist/classes/services/FastaDataEventBusService/index.js"
@@ -155,5 +157,6 @@
     "start": "vite",
     "build": "vite build",
     "preview": "vite preview"
-  }
+  },
+  "types": "./dist/index.d.ts"
 }

package/CHANGELOG.md

@@ -1,8 +0,0 @@
-# Changelog
-
-## 0.1.0 (2026-10-13)
-
-
-### Features
-
-* setup release please ([8cb6a5a](https://github.com/RIVM-bioinformatics/loculus-tools/commit/8cb6a5ad5325b37737d95bef2e6892892b7d4043))

package/eslint.config.js

@@ -1,16 +0,0 @@
-import baseEslintConfig from '@gen-epix/eslint-config';
-
-// Example of adding a custom rule
-// /** @type {import('@typescript-eslint/utils/ts-eslint').FlatConfig.ConfigArray} */
-// const rules = eslintConfig.find(c => c.files && c.files.includes('**/*.ts')).rules;
-// rules['@stylistic/jsx-sort-props'] = ['error', {
-//   ignoreCase: true,
-//   callbacksLast: true,
-//   shorthandFirst: true,
-//   reservedFirst: true,
-//   noSortAlphabetically: true,
-//   multiline: 'ignore',
-// }];
-
-
-export default baseEslintConfig;

package/scripts/update-exports.js

@@ -1,9 +0,0 @@
-#!/usr/bin/env node
-import { fileURLToPath } from 'url';
-import {
-  dirname,
-  join,
-} from 'path';
-
-// eslint-disable-next-line import-x/dynamic-import-chunkname
-await import(join(dirname(fileURLToPath(import.meta.url)), '../../../../scripts/update-exports.mjs'));

package/src/classes/services/FastaDataEventBusService/FastaDataEventBusService.ts

@@ -1,22 +0,0 @@
-import { EventBusAbstract } from '@gen-epix/ui-core/classes/abstracts/EventBusAbstract';
-import { HmrUtil } from '@gen-epix/ui-core/utils/HmrUtil';
-
-
-export type Event = {
-  onCloseImportDialog: undefined;
-  onShowImportDialog: string | undefined;
-};
-
-export class FastaDataEventBusService extends EventBusAbstract<Event> {
-  private static __instance: FastaDataEventBusService;
-
-
-  private constructor() {
-    super();
-  }
-
-  public static getInstance(): FastaDataEventBusService {
-    FastaDataEventBusService.__instance = HmrUtil.getHmrSingleton('fastaDataEventBusService', FastaDataEventBusService.__instance, () => new FastaDataEventBusService());
-    return FastaDataEventBusService.__instance;
-  }
-}