@opencloning/opencloningdb 1.8.1 → 1.8.3

package/CHANGELOG.md

@@ -1,5 +1,29 @@
 # @opencloning/opencloningdb
 
+## 1.8.3
+
+### Patch Changes
+
+- [#732](https://github.com/OpenCloning/OpenCloning_frontend/pull/732) [`cb5ddf4`](https://github.com/OpenCloning/OpenCloning_frontend/commit/cb5ddf4502a288357f8f853242fb35e5ad2a2207) Thanks [@manulera](https://github.com/manulera)! - Create lines from button in list, enables reference strain + transformation + mating
+
+- [#732](https://github.com/OpenCloning/OpenCloning_frontend/pull/732) [`cb5ddf4`](https://github.com/OpenCloning/OpenCloning_frontend/commit/cb5ddf4502a288357f8f853242fb35e5ad2a2207) Thanks [@manulera](https://github.com/manulera)! - Auto-select new tag when creating it
+
+- [#737](https://github.com/OpenCloning/OpenCloning_frontend/pull/737) [`b40f86f`](https://github.com/OpenCloning/OpenCloning_frontend/commit/b40f86fc3219d6016d8d5c8390b171affc8987f8) Thanks [@manulera](https://github.com/manulera)! - Add button for bulk-download to text files
+
+- Updated dependencies [[`06bb1a5`](https://github.com/OpenCloning/OpenCloning_frontend/commit/06bb1a513519f598e9ec3b5eec73544e2ed3958e), [`bc045f9`](https://github.com/OpenCloning/OpenCloning_frontend/commit/bc045f9e74b4d5b84250dcb5a77b93de99e4d684)]:
+  - @opencloning/ui@1.9.2
+  - @opencloning/utils@1.9.2
+
+## 1.8.2
+
+### Patch Changes
+
+- [#725](https://github.com/OpenCloning/OpenCloning_frontend/pull/725) [`093feb9`](https://github.com/OpenCloning/OpenCloning_frontend/commit/093feb9f9fc2aef437dc56cc70e64b26c656d6dd) Thanks [@manulera](https://github.com/manulera)! - Add support for bulk submission of cloning strategies
+
+- [#724](https://github.com/OpenCloning/OpenCloning_frontend/pull/724) [`77771ac`](https://github.com/OpenCloning/OpenCloning_frontend/commit/77771ac74d72fbd43146490efeb60798773e4734) Thanks [@manulera](https://github.com/manulera)! - Bulk submit lines
+
+- [#722](https://github.com/OpenCloning/OpenCloning_frontend/pull/722) [`871688a`](https://github.com/OpenCloning/OpenCloning_frontend/commit/871688a3576b4f2aa7ffbd8ca919b95daf01e9e4) Thanks [@manulera](https://github.com/manulera)! - Allow submitting template sequences in bulk
+
 ## 1.8.1
 
 ### Patch Changes

package/package.json

@@ -1,7 +1,7 @@
 {
   "license": "MIT",
   "name": "@opencloning/opencloningdb",
-  "version": "1.8.1",
+  "version": "1.8.3",
   "type": "module",
   "main": "./src/index.js",
   "exports": {
@@ -15,8 +15,8 @@
   "dependencies": {
     "@mui/icons-material": "^5.18.0",
     "@mui/material": "^5.18.0",
-    "@opencloning/ui": "1.9.1",
-    "@opencloning/utils": "1.9.1",
+    "@opencloning/ui": "1.9.2",
+    "@opencloning/utils": "1.9.2",
     "axios": "^1.16.0"
   },
   "peerDependencies": {

package/src/GetSequenceFileAndDatabaseIdComponent.cy.jsx

@@ -29,6 +29,7 @@ describe('<GetSequenceFileAndDatabaseIdComponent />', () => {
     cy.setupOpenCloningDBTestAuth();
 
     cy.interceptOpenCloningDBStub('get_sequences_search_by_name', { alias: 'getSequences' });
+    cy.interceptOpenCloningDBStub('get_sequences_search_by_name_uid_query', { alias: 'getSequencesByNameUidQuery' });
     cy.interceptOpenCloningDBStub('get_text_file_sequence', { alias: 'getSequenceFile' });
 
     cy.mount(
@@ -57,6 +58,7 @@ describe('<GetSequenceFileAndDatabaseIdComponent />', () => {
 
     cy.setupOpenCloningDBTestAuth();
     cy.interceptOpenCloningDBStub('get_sequences_search_by_name', { alias: 'getSequences' });
+    cy.interceptOpenCloningDBStub('get_sequences_search_by_name_uid_query', { alias: 'getSequencesByNameUidQuery' });
 
     cy.getStub('get_text_file_sequence').then((textFileSequenceStub) => {
       let callCount = 0;

package/src/SequenceSelect.cy.jsx

@@ -1,15 +1,18 @@
 import React from 'react';
+import endpoints from './endpoints';
 import SequenceSelect from './SequenceSelect';
 import { clickMultiSelectOption } from '../../../cypress/e2e/common_functions';
 
 const SEQUENCE_NAME = 'ase1_CDS_PCR';
+const SEQUENCE_UID = 'example_sequencing-sample';
 
 describe('<SequenceSelect />', () => {
-  it('searches for a sequence and shows results', () => {
+  it('searches for a sequence by name and shows results', () => {
     cy.setupOpenCloningDBTestAuth();
     const onChangeSpy = cy.spy().as('onChangeSpy');
 
     cy.interceptOpenCloningDBStub('get_sequences_search_by_name', { alias: 'getSequences' });
+    cy.interceptOpenCloningDBStub('get_sequences_search_by_name_uid_query', { alias: 'getSequencesByUid' });
 
     cy.mount(
       <SequenceSelect label="Sequence" onChange={onChangeSpy} multiple={false} />
@@ -29,4 +32,31 @@ describe('<SequenceSelect />', () => {
 
     cy.get('input').should('have.value', SEQUENCE_NAME);
   });
+  it('searches for a sequence by uid and shows results', () => {
+    cy.setupOpenCloningDBTestAuth();
+    const onChangeSpy = cy.spy().as('onChangeSpy');
+
+    cy.interceptOpenCloningDBStub('get_sequences_search_by_uid', { alias: 'getSequencesByUid' });
+    cy.interceptOpenCloningDBStub('get_sequences_search_by_uid_name_query', { alias: 'getSequencesByName' });
+
+
+    cy.mount(
+      <SequenceSelect label="Sequence" onChange={onChangeSpy} multiple={false} />
+    );
+    cy.get('input').click();
+    cy.contains('Type at least').should('exist');
+    cy.get('input').type(SEQUENCE_UID);
+    cy.get('.MuiAutocomplete-listbox li', { timeout: 10000 }).should('have.length.greaterThan', 0);
+
+    // We need to incercept, because it will submit the value of combined name + uid which is not in a stub
+    cy.intercept('GET', Cypress.getDbURL(endpoints.sequences, '*'), { statusCode: 200, body: { items: [] } }).as('getSequences2');
+    clickMultiSelectOption('Sequence', SEQUENCE_UID, 'div');
+
+    cy.getStub('get_sequences_search_by_uid').then((stub) => {
+      const stubSequence = stub.response.body.items.find((sequence) => sequence.sample_uids.includes(SEQUENCE_UID));
+      expect(stubSequence).to.exist;
+      cy.get('@onChangeSpy').should('have.been.calledWith', stubSequence);
+      cy.get('input').should('have.value', `${stubSequence.name} (${SEQUENCE_UID})`);
+    });
+  });
 });

package/src/SequenceSelect.jsx

@@ -1,6 +1,6 @@
 import React from 'react';
 import { QuerySelect, useDebouncedSearchQuery } from '@opencloning/ui';
-import { openCloningDBHttpClient } from './common';
+import { formatSequenceName, openCloningDBHttpClient } from './common';
 import endpoints from './endpoints';
 
 const messages = {
@@ -8,19 +8,25 @@ const messages = {
   errorMessage: 'Could not retrieve sequences from OpenCloningDB',
 };
 
+
 const getGetQuery = (sequenceTypes) => {
-  return (name) => ({
-    queryKey: ['sequences', { sequence_types: sequenceTypes, name }],
+  return (query) => ({
+    queryKey: ['sequences', { sequence_types: sequenceTypes, query }],
     queryFn: async () => {
-      const { data } = await openCloningDBHttpClient.get(endpoints.sequences, {
-        params: { sequence_types: sequenceTypes, name },
-      });
-      return data.items;
+      const results = await Promise.all([
+        openCloningDBHttpClient.get(endpoints.sequences, {
+          params: { sequence_types: sequenceTypes, uid: query },
+        }),
+        openCloningDBHttpClient.get(endpoints.sequences, {
+          params: { sequence_types: sequenceTypes, name: query },
+        }),
+      ]);
+      return [...results[0].data.items, ...results[1].data.items];
     },
   })};
 
 function SequenceSelect({ value, onChange, label, multiple = true, sequenceTypes = undefined, ...rest }) {
-  const { query, autocompleteProps, clearInput } = useDebouncedSearchQuery(getGetQuery(sequenceTypes));
+  const { query, autocompleteProps, clearInput } = useDebouncedSearchQuery(getGetQuery(sequenceTypes), {minChars: 1});
 
   return (
     <QuerySelect
@@ -29,7 +35,7 @@ function SequenceSelect({ value, onChange, label, multiple = true, sequenceTypes
       loadingMessage={messages.loadingMessage}
       errorMessage={messages.errorMessage}
       multiple={multiple}
-      getOptionLabel={(seq) => seq.name ?? `Sequence ${seq.id}`}
+      getOptionLabel={formatSequenceName}
       getOptionKey={(seq) => seq.id}
       value={value}
       onChange={onChange}

package/src/common.js

@@ -40,3 +40,12 @@ export const openCloningDBHttpClient = axios.create({
 });
 
 attachAuthInterceptors(openCloningDBHttpClient);
+
+export function formatSequenceName({ id, name, sample_uids: sampleUids }) {
+  if (!name) return `Sequence ${id}`;
+  let out = name;
+  if (sampleUids && sampleUids.length > 0) {
+    out += ` (${sampleUids.join(', ')})`;
+  }
+  return out;
+}

package/src/endpoints.js

@@ -12,6 +12,8 @@ const endpoints = {
   sequenceSearch: '/sequences/search',
   sequencesValidateUpload: '/sequences/validate-upload',
   sequencesBulk: '/sequences/bulk',
+  sequencesCloningStrategyBulkValidate: '/sequences/cloning_strategy/bulk/validate',
+  sequencesCloningStrategyBulk: '/sequences/cloning_strategy/bulk',
   sequencingFileDownload: (id) => `/sequencing_files/${id}/download`,
   sequenceSequencingFileDelete: (sequenceId, fileId) => `/sequences/${sequenceId}/sequencing_files/${fileId}`,
   postSequence: '/sequences',
@@ -27,6 +29,8 @@ const endpoints = {
   lineTags: (id) => `/lines/${id}/tags`,
   inputEntityTags: (id) => `/input_entities/${id}/tags`,
   postLine: '/lines',
+  linesValidateUpload: '/lines/validate-upload',
+  linesBulk: '/lines/bulk',
   tags: '/tags',
   tagPost: '/tags',
   tagUnlinkLine: (lineId, tagId) => `/lines/${lineId}/tags/${tagId}`,
@@ -41,6 +45,9 @@ const endpoints = {
   postWorkspace: '/workspaces',
   workspace: (id) => `/workspaces/${id}`,
   templateSequences: '/template_sequences',
+  templateSequencesValidateUpload: '/template_sequences/validate-upload',
+  templateSequencesBulk: '/template_sequences/bulk',
+  export: '/export',
 };
 
 export default endpoints;

package/src/index.js

@@ -1,4 +1,4 @@
 export { default as OpenCloningDBInterface } from './OpenCloningDBInterface.js';
-export { openCloningDBHttpClient, setUnauthorizedHandler, setWorkspaceHeader, clearWorkspaceHeader, baseUrl } from './common.js';
+export { openCloningDBHttpClient, setUnauthorizedHandler, setWorkspaceHeader, clearWorkspaceHeader, baseUrl, formatSequenceName } from './common.js';
 export { default as endpoints } from './endpoints.js';
 export { default as SequenceSelect } from './SequenceSelect.jsx';