@opencloning/utils 1.7.3 → 1.9.0

package/CHANGELOG.md

@@ -1,5 +1,80 @@
 # @opencloning/utils
 
+## 1.9.0
+
+### Minor Changes
+
+- [#711](https://github.com/OpenCloning/OpenCloning_frontend/pull/711) [`6813620`](https://github.com/OpenCloning/OpenCloning_frontend/commit/6813620f4a47c44857045866d667474efbf9a64c) Thanks [@manulera](https://github.com/manulera)! - Use authentication for cloning endpoints in opencloning-db
+
+### Patch Changes
+
+- Updated dependencies []:
+  - @opencloning/store@1.9.0
+
+## 1.8.2
+
+### Patch Changes
+
+- Updated dependencies []:
+  - @opencloning/store@1.8.2
+
+## 1.8.1
+
+### Patch Changes
+
+- Updated dependencies []:
+  - @opencloning/store@1.8.1
+
+## 1.8.0
+
+### Minor Changes
+
+- [#694](https://github.com/OpenCloning/OpenCloning_frontend/pull/694) [`2ff9010`](https://github.com/OpenCloning/OpenCloning_frontend/commit/2ff90103c1d9e8e984533e51ecf4dc7978756a57) Thanks [@manulera](https://github.com/manulera)! - \* Add alignment functionality functions.
+
+### Patch Changes
+
+- Updated dependencies [[`2ff9010`](https://github.com/OpenCloning/OpenCloning_frontend/commit/2ff90103c1d9e8e984533e51ecf4dc7978756a57)]:
+  - @opencloning/store@1.8.0
+
+## 1.7.8
+
+### Patch Changes
+
+- Updated dependencies []:
+  - @opencloning/store@1.7.8
+
+## 1.7.7
+
+### Patch Changes
+
+- [#689](https://github.com/manulera/OpenCloning_frontend/pull/689) [`c5d9309`](https://github.com/manulera/OpenCloning_frontend/commit/c5d93099583fdfafafd40e9924d2216b596e0cec) Thanks [@manulera](https://github.com/manulera)! - Added experimental feature for domestication that relies on API calls to goldenbraidpro
+
+- Updated dependencies []:
+  - @opencloning/store@1.7.7
+
+## 1.7.6
+
+### Patch Changes
+
+- Updated dependencies []:
+  - @opencloning/store@1.7.6
+
+## 1.7.5
+
+### Patch Changes
+
+- Updated dependencies [[`034c738`](https://github.com/manulera/OpenCloning_frontend/commit/034c73840dc183b6b3584365c1db899d2f0c548b)]:
+  - @opencloning/store@1.7.5
+
+## 1.7.4
+
+### Patch Changes
+
+- [#682](https://github.com/manulera/OpenCloning_frontend/pull/682) [`04703a9`](https://github.com/manulera/OpenCloning_frontend/commit/04703a9269a5d4cc4bdde478c1ec61e5c73b0d2a) Thanks [@manulera](https://github.com/manulera)! - Fix bug when copying pcr products
+
+- Updated dependencies []:
+  - @opencloning/store@1.7.4
+
 ## 1.7.3
 
 ### Patch Changes

package/package.json

@@ -1,7 +1,7 @@
 {
   "license": "MIT",
   "name": "@opencloning/utils",
-  "version": "1.7.3",
+  "version": "1.9.0",
   "type": "module",
   "main": "./src/utils/index.js",
   "exports": {
@@ -9,6 +9,7 @@
     "./readNwrite": "./src/utils/readNwrite.js",
     "./network": "./src/utils/network.js",
     "./getHttpClient": "./src/utils/getHttpClient.js",
+    "./httpClientAuth": "./src/utils/httpClientAuth.js",
     "./sourceFunctions": "./src/utils/sourceFunctions.js",
     "./error2String": "./src/utils/error2String.js",
     "./enzyme_utils": "./src/utils/enzyme_utils.js",
@@ -21,20 +22,21 @@
     "./other": "./src/utils/other.js",
     "./transformCoords": "./src/utils/transformCoords.js",
     "./selectedRegionUtils": "./src/utils/selectedRegionUtils.js",
-    "./normalizeSyntax": "./src/utils/normalizeSyntax.js"
+    "./normalizeSyntax": "./src/utils/normalizeSyntax.js",
+    "./alignmentUtils": "./src/utils/alignmentUtils.js"
   },
   "repository": {
     "type": "git",
-    "url": "https://github.com/manulera/OpenCloning_frontend.git",
+    "url": "https://github.com/OpenCloning/OpenCloning_frontend.git",
     "directory": "packages/utils"
   },
   "dependencies": {
-    "@opencloning/store": "1.7.3",
-    "@teselagen/bio-parsers": "^0.4.34",
+    "@opencloning/store": "1.9.0",
+    "@teselagen/bio-parsers": "^0.4.38",
     "@teselagen/sequence-utils": "^0.3.42",
-    "@zip.js/zip.js": "^2.7.62",
+    "@zip.js/zip.js": "^2.8.26",
     "dom-to-svg": "^0.12.2",
-    "lodash-es": "^4.17.23"
+    "lodash-es": "^4.18.1"
   },
   "peerDependencies": {
     "react": "^18.3.1",

package/src/utils/alignmentUtils.js

@@ -0,0 +1,120 @@
+import { getReverseComplementSequenceAndAnnotations, getReverseComplementSequenceString, rotateSequenceDataToPosition } from '@teselagen/sequence-utils';
+import { findRotation, syncChromatogramDataWithAlignment } from './sequenceManipulation.js';
+
+/**
+ * Process alignment sequence data by handling rotation and reverse complement.
+ * If fileContent has features, it aligns the sequence data to match the alignment
+ * by computing rotation and optionally reverse-complementing.
+ */
+export function processAlignmentSequenceData(fileContent, alignmentSequence) {
+  if (!(fileContent.features && fileContent.features.length > 0)) {
+    return {
+      name: fileContent.name || '',
+      sequence: alignmentSequence,
+    };
+  }
+
+  let alignmentSequenceData = fileContent;
+  let rotation = findRotation(fileContent.sequence, alignmentSequence);
+  const reverseComplemented = rotation === -1;
+  if (reverseComplemented) {
+    rotation = findRotation(fileContent.sequence, getReverseComplementSequenceString(alignmentSequence));
+    alignmentSequenceData = getReverseComplementSequenceAndAnnotations(fileContent);
+  }
+  if (rotation !== -1 && rotation !== 0) {
+    rotation = reverseComplemented ? fileContent.sequence.length - rotation : rotation;
+    alignmentSequenceData = rotateSequenceDataToPosition(alignmentSequenceData, rotation);
+  }
+  return alignmentSequenceData;
+}
+
+/**
+ * Build a single alignment track from parsed file content and an alignment file object.
+ * @param {Object} fileContent - Parsed sequence data (output of getTeselaJsonFromBase64)
+ * @param {Object} alignmentFile - Alignment file object with { file_name, alignment }
+ * @returns {{ sequenceData: Object, alignmentData: Object, chromatogramData: Object|undefined }}
+ */
+export function buildAlignmentTrack(fileContent, alignmentFile) {
+  const alignmentSequence = alignmentFile.alignment[1].replaceAll('-', '');
+  let chromatogramData = fileContent.chromatogramData;
+
+  if (chromatogramData) {
+    chromatogramData = syncChromatogramDataWithAlignment(chromatogramData, alignmentFile.alignment[1]);
+  }
+
+  const alignmentSequenceData = processAlignmentSequenceData(fileContent, alignmentSequence);
+
+  return {
+    sequenceData: { ...alignmentSequenceData, name: alignmentFile.file_name },
+    alignmentData: {
+      sequence: alignmentFile.alignment[1],
+      name: alignmentFile.file_name,
+    },
+    chromatogramData,
+  };
+}
+
+/**
+ * Build the reference (first) alignment track.
+ * @param {Object} sequenceData - The reference sequence data
+ * @param {string} firstAlignmentSequence - The alignment string for the reference
+ * @returns {{ sequenceData: Object, alignmentData: Object }}
+ */
+export function buildReferenceTrack(sequenceData, firstAlignmentSequence) {
+  return {
+    sequenceData,
+    alignmentData: {
+      sequence: firstAlignmentSequence,
+      name: sequenceData.name,
+    },
+  };
+}
+
+/**
+ * Build the full alignment configuration object for addAlignment.
+ * @param {number} id - Sequence id
+ * @param {Object} sequenceData - Reference sequence data
+ * @param {Array} alignmentTracks - Array of alignment track objects (reference + others)
+ * @returns {Object} Alignment config for addAlignment
+ */
+export function buildAlignmentConfig(id, sequenceData, alignmentTracks) {
+  return {
+    id: 'simpleAlignment',
+    alignmentType: 'Sequencing alignment',
+    name: `Seq. ${id}`,
+    alignmentAnnotationVisibility: {
+      features: true,
+      parts: true,
+      translations: true,
+    },
+    alignmentTracks,
+  };
+}
+
+/**
+ * Remove a panel from panelsShown by id.
+ * @param {Array} panelsShown - Current panelsShown array (array of arrays)
+ * @param {string} panelId - The panel id to remove
+ * @returns {Array} New panelsShown with the panel filtered out
+ */
+export function removePanelFromShown(panelsShown, panelId) {
+  return [[...panelsShown[0].filter((p) => p.id !== panelId)]];
+}
+
+/**
+ * Return new panelsShown with the simpleAlignment panel appended.
+ * @param {Array} panelsShown - Current panelsShown (already with simpleAlignment removed)
+ * @returns {Array} New panelsShown with simpleAlignment panel added
+ */
+export function updatePanelsShownWithAlignment(panelsShown) {
+  return [[
+    ...panelsShown[0].filter((p) => p.id !== 'simpleAlignment'),
+    {
+      id: 'simpleAlignment',
+      type: 'alignment',
+      name: 'Alignments',
+      active: true,
+      isFullscreen: false,
+    },
+  ]];
+}

package/src/utils/dnaUtils.js

@@ -0,0 +1,22 @@
+
+export function featureToGenbankLocationString(feat) {
+  const [ inclusive1BasedStart, inclusive1BasedEnd ] = [false, false];
+  let locStr = "";
+
+  if (feat.locations && feat.locations.length > 1) {
+    feat.locations.forEach((loc, i) => {
+      locStr +=`${parseInt(loc.start, 10) + (inclusive1BasedStart ? 0 : 1)}..${parseInt(loc.end, 10) + (inclusive1BasedEnd ? 0 : 1)}`;
+      if (i !== feat.locations.length - 1) {
+        locStr += ",";
+      }
+    });
+    locStr = "join(" + locStr + ")";
+  } else {
+    locStr +=`${parseInt(feat.start, 10) + (inclusive1BasedStart ? 0 : 1)}..${parseInt(feat.end, 10) + (inclusive1BasedEnd ? 0 : 1)}`;
+  }
+
+  if (feat.strand === -1) {
+    locStr = "complement(" + locStr + ")";
+  }
+  return locStr;
+}

package/src/utils/getHttpClient.js

@@ -1,4 +1,5 @@
 import axios from 'axios';
+import { attachAuthInterceptors } from './httpClientAuth';
 import urlWhitelist from '../config/urlWhitelist';
 
 export default function getHttpClient(extraUrls = []) {
@@ -22,3 +23,9 @@ export default function getHttpClient(extraUrls = []) {
 
   return client;
 }
+
+export function getAuthenticatedHttpClient(extraUrls = []) {
+  const client = getHttpClient(extraUrls);
+  attachAuthInterceptors(client);
+  return client;
+}

package/src/utils/getHttpClient.test.js

@@ -0,0 +1,19 @@
+import { describe, expect, it } from 'vitest';
+
+import getHttpClient, { getAuthenticatedHttpClient } from './getHttpClient';
+
+describe('getHttpClient', () => {
+  it('creates a generic client without auth interceptors', () => {
+    const client = getHttpClient();
+
+    expect(client.interceptors.request.handlers.filter(Boolean)).toHaveLength(1);
+    expect(client.interceptors.response.handlers.filter(Boolean)).toHaveLength(0);
+  });
+
+  it('creates an authenticated client with auth interceptors', () => {
+    const client = getAuthenticatedHttpClient();
+
+    expect(client.interceptors.request.handlers.filter(Boolean)).toHaveLength(2);
+    expect(client.interceptors.response.handlers.filter(Boolean)).toHaveLength(1);
+  });
+});

package/src/utils/httpClientAuth.js

@@ -0,0 +1,36 @@
+const AUTH_INTERCEPTORS_ATTACHED = '__opencloningHttpClientAuthAttached';
+
+let unauthorizedHandler = null;
+
+export function setHttpClientUnauthorizedHandler(fn) {
+  unauthorizedHandler = fn;
+}
+
+export function attachAuthInterceptors(client, { tokenStorageKey = 'token' } = {}) {
+  if (client[AUTH_INTERCEPTORS_ATTACHED]) {
+    return client;
+  }
+
+  client[AUTH_INTERCEPTORS_ATTACHED] = true;
+
+  client.interceptors.request.use((config) => {
+    const token = localStorage.getItem(tokenStorageKey);
+    if (token) {
+      config.headers = config.headers ?? {};
+      config.headers.Authorization = `Bearer ${token}`;
+    }
+    return config;
+  });
+
+  client.interceptors.response.use(
+    (response) => response,
+    (error) => {
+      if (error.response?.status === 401 && unauthorizedHandler) {
+        unauthorizedHandler();
+      }
+      return Promise.reject(error);
+    },
+  );
+
+  return client;
+}

package/src/utils/httpClientAuth.test.js

@@ -0,0 +1,52 @@
+import axios from 'axios';
+import { afterEach, beforeEach, describe, expect, it, vi } from 'vitest';
+
+import { attachAuthInterceptors, setHttpClientUnauthorizedHandler } from './httpClientAuth';
+
+describe('httpClientAuth', () => {
+  beforeEach(() => {
+    localStorage.clear();
+    setHttpClientUnauthorizedHandler(null);
+  });
+
+  afterEach(() => {
+    localStorage.clear();
+    setHttpClientUnauthorizedHandler(null);
+  });
+
+  it('adds the bearer token to authenticated requests', () => {
+    const client = attachAuthInterceptors(axios.create());
+    const requestFulfilled = client.interceptors.request.handlers[0].fulfilled;
+    const config = { headers: {} };
+
+    localStorage.setItem('token', '__TEST_TOKEN__');
+
+    const result = requestFulfilled(config);
+
+    expect(result).toBe(config);
+    expect(config.headers.Authorization).toBe('Bearer __TEST_TOKEN__');
+  });
+
+  it('calls the shared unauthorized handler for 401 responses', async () => {
+    const client = attachAuthInterceptors(axios.create());
+    const responseRejected = client.interceptors.response.handlers[0].rejected;
+    const handler = vi.fn();
+    const error = { response: { status: 401 } };
+
+    setHttpClientUnauthorizedHandler(handler);
+
+    await expect(responseRejected(error)).rejects.toBe(error);
+
+    expect(handler).toHaveBeenCalledTimes(1);
+  });
+
+  it('does not attach duplicate interceptors to the same client', () => {
+    const client = axios.create();
+
+    attachAuthInterceptors(client);
+    attachAuthInterceptors(client);
+
+    expect(client.interceptors.request.handlers.filter(Boolean)).toHaveLength(1);
+    expect(client.interceptors.response.handlers.filter(Boolean)).toHaveLength(1);
+  });
+});

package/src/utils/index.js

@@ -4,6 +4,7 @@
 export * from './readNwrite.js';
 export * from './network.js';
 export * from './getHttpClient.js';
+export * from './httpClientAuth.js';
 export * from './sourceFunctions.js';
 export { default as error2String } from './error2String.js';
 export * from './enzyme_utils.js';
@@ -17,3 +18,4 @@ export * from './other.js';
 export { default as getTransformCoords } from './transformCoords.js';
 export * from './selectedRegionUtils.js';
 export * from './normalizeSyntax.js';
+export * from './dnaUtils.js';

package/src/utils/network.js

@@ -100,11 +100,19 @@ export const shiftState = (newState, oldState, skipPrimers = false) => {
   return shiftStateIds(newState, oldState, skipPrimers);
 };
 
+export function getSequenceIdsThatAreInput(sources) {
+  return sources.reduce((result, source) => result.concat(source.input.map(({sequence}) => sequence)), []);
+}
+
+export function getSequenceIdsThatAreNotInput(sequences, sources) {
+  const sequenceIdsThatAreInput = getSequenceIdsThatAreInput(sources);
+  return sequences.filter((sequence) => !sequenceIdsThatAreInput.includes(sequence.id)).map((sequence) => sequence.id);
+}
+
 export function getGraftSequenceId({ sources, sequences }) {
-  const sequenceIdsThatAreInput = sources.reduce((result, source) => result.concat(source.input.map(({sequence}) => sequence)), []);
-  const allSequenceIds = sequences.map((seq) => seq.id);
-  const sequenceIdsThatAreNotInput = allSequenceIds.filter((sequenceId) => !sequenceIdsThatAreInput.includes(sequenceId));
-  const sourcesWithoutOutput = sources.filter((source) => !allSequenceIds.includes(source.id));
+  const allSequenceIds = new Set(sequences.map((seq) => seq.id));
+  const sequenceIdsThatAreNotInput = getSequenceIdsThatAreNotInput(sequences, sources);
+  const sourcesWithoutOutput = sources.filter((source) => !allSequenceIds.has(source.id));
   if (sourcesWithoutOutput.length === 0 && sequenceIdsThatAreNotInput.length === 1) {
     return sequenceIdsThatAreNotInput[0];
   }
@@ -182,3 +190,18 @@ export const mergeStates = (newState, oldState, skipPrimers = false) => {
   }
   return { mergedState, idShift };
 };
+
+export function getParentSequencesFromSource(source, sequences) {
+  const parentSequenceIds = source.input.map(({sequence}) => sequence);
+  return sequences.filter((sequence) => parentSequenceIds.includes(sequence.id));
+}
+
+export function getParentSourcesFromSource(source, sources) {
+  const parentSourceIds = source.input.map(({sequence}) => sequence);
+  return sources.filter((source) => parentSourceIds.includes(source.id));
+}
+
+export function getSequencesNotInDatabase(sources, sequences) {
+  const sequenceIds = sources.filter((s) => !s.database_id).map((s) => s.id);
+  return sequences.filter((sequence) => sequenceIds.includes(sequence.id));
+}

package/src/utils/readNwrite.js

@@ -43,6 +43,14 @@ export const file2base64 = (file) => new Promise((resolve) => {
   reader.readAsDataURL(file);
 });
 
+export const file2string = (file) => new Promise((resolve) => {
+  const reader = new FileReader();
+  reader.onload = () => {
+    resolve(reader.result);
+  };
+  reader.readAsText(file);
+});
+
 export const downloadTextFile = (text, fileName, type = 'text/plain') => {
   const blob = new Blob([text], { type });
   downloadBlob(blob, fileName);

package/src/utils/thunks.js

@@ -3,6 +3,7 @@ import { base64ToBlob, downloadStateAsJson, downloadStateAsZip, loadFilesToSessi
 import { cloningActions } from '@opencloning/store/cloning';
 import { collectParentSequencesAndSources, getSubState, mergeStates } from './network';
 import { getVerificationFileName } from './readNwrite';
+import { getUsedPrimerIds } from '@opencloning/store/cloning_utils';
 
 const { setState: setCloningState } = cloningActions;
 
@@ -27,12 +28,14 @@ export const CopySequenceThunk = (sequenceId) => async (dispatch, getState) => {
   const { parentSequences, parentSources } = collectParentSequencesAndSources(sourcesToCopy[0], sources, sequences);
   sequencesToCopy.push(...parentSequences);
   sourcesToCopy.push(...parentSources);
+  const primerIdsToCopy = getUsedPrimerIds(sourcesToCopy);
+  const primersToCopy = state.cloning.primers.filter((p) => primerIdsToCopy.includes(p.id));
   const sequenceIds = sequencesToCopy.map((e) => e.id);
   const filesToCopy = state.cloning.files.filter((f) => sequenceIds.includes(f.sequence_id));
   const newState = cloneDeep({
     sequences: sequencesToCopy,
     sources: sourcesToCopy,
-    primers: [],
+    primers: primersToCopy,
     files: filesToCopy,
   });
   const files = filesToCopy.map((f) => new File(
@@ -40,7 +43,7 @@ export const CopySequenceThunk = (sequenceId) => async (dispatch, getState) => {
     getVerificationFileName(f),
     { type: 'application/octet-stream' },
   ));
-  const { mergedState, idShift } = mergeStates(newState, state.cloning, true);
+  const { mergedState, idShift } = mergeStates(newState, state.cloning, false);
   dispatch(setCloningState(mergedState));
   await loadFilesToSessionStorage(files, idShift);
 };