diff --git a/.env.example b/.env.example index 5631f01..74ab654 100644 --- a/.env.example +++ b/.env.example @@ -21,10 +21,6 @@ SEND_UPDATE_TO_SQS= SQS_QUEUE_URL= MAX_SET_CONTENT_SIZE= -# Python configuration (used for survival endpoint) -SURVIVAL_PY_FILE= -PYTHON_PATH= - # Riff RIFF_URL= diff --git a/.github/workflows/check_pull_request.yml b/.github/workflows/check_pull_request.yml new file mode 100644 index 0000000..a235617 --- /dev/null +++ b/.github/workflows/check_pull_request.yml @@ -0,0 +1,25 @@ +name: Check Pull Request Quality + +on: + pull_request: + +jobs: + tests: + name: Run Tests + runs-on: ubuntu-latest + steps: + - name: Checkout Source Code + uses: actions/checkout@v3 + - name: Setup node + uses: actions/setup-node@v3 + with: + node-version: 20 + - name: Use Dependencies Cache + uses: actions/cache@v3 + with: + path: '**/node_modules' + key: ${{ runner.os }}-modules-${{ hashFiles('**/package-lock.json') }} + - name: Install Dependencies + run: npm ci + - name: Run tests + run: npm run test \ No newline at end of file diff --git a/.github/workflows/scan.yaml b/.github/workflows/scan.yaml new file mode 100644 index 0000000..fc9f6ed --- /dev/null +++ b/.github/workflows/scan.yaml @@ -0,0 +1,21 @@ +name: build +on: + pull_request: + +jobs: + build: + name: Build + runs-on: ubuntu-latest + steps: + - name: Checkout code + uses: actions/checkout@v3 + - name: Build an image from Dockerfile + run: | + docker build -t ${{ github.sha }} . + - name: Run Trivy vulnerability scanner + uses: aquasecurity/trivy-action@master + with: + image-ref: '${{ github.sha }}' + format: 'table' + exit-code: '1' + severity: 'CRITICAL,HIGH' \ No newline at end of file diff --git a/.gitignore b/.gitignore index e6206fe..fa1fa97 100644 --- a/.gitignore +++ b/.gitignore @@ -7,4 +7,5 @@ node_modules /docker/esdata/ /.idea/ dev/es_data/* -*.env-dev \ No newline at end of file +*.env-dev +venv \ No newline at end of file diff --git a/Dockerfile b/Dockerfile index de2cfb3..4cc1b49 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,18 +1,11 @@ -# First image to compile typescript to javascript -FROM node:16.13-alpine AS build-image +FROM node:20-alpine3.18 AS build WORKDIR /app COPY . . -RUN npm ci -RUN npm run clean -RUN npm run build +RUN npm ci && npm run cleanAndBuild -# Second image, that creates an image for production -FROM nikolaik/python-nodejs:python3.9-nodejs16-alpine AS prod-image +FROM node:20-alpine3.18 AS prod-image WORKDIR /app -COPY --from=build-image ./app/dist ./dist +COPY --from=build ./app/dist ./dist COPY package* ./ -COPY ./resource ./resource -RUN npm ci --production -RUN pip3 install -r resource/py/requirements.txt - +RUN apk update && apk upgrade --no-cache libcrypto3 libssl3 && npm ci --production CMD [ "node", "./dist/src/index.js" ] \ No newline at end of file diff --git a/README.md b/README.md index c65b43f..3fa89f0 100644 --- a/README.md +++ b/README.md @@ -12,7 +12,9 @@ Arranger server is an application that wraps Elasticsearch and provides a GraphQ ## Development -* Execute: `npm run build` then `npm run start` +* Execute: `npm run cbs` + +Note: You can execute this project in a docker container if you prefer: `docker run -u node -it --rm --network host -v ${PWD}:/app --workdir /app node:20-alpine3.18 sh` ### General diff --git a/admin/README.md b/admin/README.md index 71cc458..3c8b7cc 100644 --- a/admin/README.md +++ b/admin/README.md @@ -18,8 +18,8 @@ The Law of the Land is: 1 arranger project per environment (qa, staging, prod). npm run admin-project or # run the script with docker (PWD = root of the project) -docker run -it --network host --rm -v ${PWD}:/code --workdir /code node:16.13-alpine sh -c "npm install && npm run build && npm run admin-project" +docker run -it --network host --rm -v ${PWD}:/code --workdir /code node:20-alpine3.18 sh -c "npm install && npm run build && npm run admin-project" # run the script with docker (PWD = root of the project) and local elastic search (from /dev) -docker run -it --rm --network es-net -v ${PWD}:/code --workdir /code node:16.13-alpine sh -c "npm install && npm run build && npm run admin-project" +docker run -it --rm --network es-net -v ${PWD}:/code --workdir /code node:20-alpine3.18 sh -c "npm install && npm run build && npm run admin-project" ``` diff --git a/admin/addFieldsToStudies.mjs b/admin/addFieldsToStudies.mjs new file mode 100644 index 0000000..49066a7 --- /dev/null +++ b/admin/addFieldsToStudies.mjs @@ -0,0 +1,150 @@ +// You must be connected to the correct ES HOST +// You can do: +// docker run --rm -it -v ${PWD}:/app -u node --network=host --workdir /app node:20-alpine3.18 sh +// node admin/addFieldsToStudies.mjs +import assert from 'node:assert/strict'; +import EsInstance from '../dist/src/ElasticSearchClientInstance.js'; +import readline from 'readline'; + +import { mockStudies, validateStudies } from './mockStudies.mjs'; +const userReadline = readline.createInterface({ + input: process.stdin, + output: process.stdout, +}); + +const yesOrNo = await new Promise(resolve => { + userReadline.question(`This script is intend to be for INCLUDE. Do you want to proceed y/n? > `, answer => + resolve(answer === 'y'), + ); +}); +userReadline.close(); +if (!yesOrNo) { + console.info('Terminating Script'); + process.exit(0); +} + +const { keys, values } = Object; + +const ms = [...mockStudies]; + +const vr = validateStudies(ms); +const invalidStudies = vr.filter(v => !v[1]); +if (invalidStudies.length > 0) { + invalidStudies.forEach(v => { + const [code, , errors] = v; + console.log(`study=${code} is invalid`); + console.log(errors); + }); + process.exit(0); +} + +const sCodes = [...new Set(ms.map(x => x.study_code))]; +const nOfStudiesToEnhance = ms.length; +assert(sCodes.length === nOfStudiesToEnhance, 'Duplicated study_codes in mocks'); + +const client = await EsInstance.default.getInstance(); + +//Quick validation +const rM = await client.indices.getMapping({ index: 'study_centric' }); +assert(rM.statusCode === 200); +const m = values(rM.body)[0]?.mappings?.properties; +assert(!!m); +// !Notice Warning: mappings are multivalued (one for each study). Only the first found is used. So validation may, in certain instances, be incomplete, +const mappedKeys = ms.map(s => { + const sTopLevelKeys = keys(s); + const allKeysExistInMapping = sTopLevelKeys.every(sk => !!m[sk]); + return [allKeysExistInMapping, sTopLevelKeys.filter(sk => !m[sk])]; +}); + +const firstLevelNestedOK = ['dataset', 'data_types', 'contacts', 'experimental_strategies'].every(k => m[k]?.type === 'nested'); +const mappingSeemsValid = firstLevelNestedOK && mappedKeys.every(x => !!x[0]); +if (!mappingSeemsValid) { + console.error('It seems like not all values are mapped correctly.'); + if (m.dataset.type === 'nested') { + console.error('Problematic keys: ', [ + ...new Set( + mappedKeys + .filter(x => !x[0]) + .map(x => x[1]) + .flat(), + ), + ]); + } + process.exit(0); +} + +// Processing +const r = await client.search({ + index: 'study_centric', + size: sCodes.length, + body: { + query: { + bool: { + must: [ + { + terms: { + study_code: sCodes, + }, + }, + ], + }, + }, + }, +}); +assert(r.statusCode === 200); +const hits = r.body.hits; +assert( + hits.total.value <= nOfStudiesToEnhance && + hits?.hits && + hits.hits.every(h => sCodes.includes(h._source.study_code)), +); + +const operations = ms + .flatMap(doc => { + const oDoc = hits.hits.find(h => h._source.study_code === doc.study_code); + if (!oDoc) { + return undefined; + } + return [ + { update: { _index: oDoc._index, _id: oDoc._id } }, + { + doc: { + ...oDoc._source, + ...doc, + }, + }, + ]; + }) + .filter(x => !!x); + +assert(operations.length >= 1); +const br = await client.bulk({ refresh: true, body: operations }); +assert(br.statusCode === 200 || !br.body?.errors, br); + +// Post-validation +const uItems = br.body.items; +// Not a perfect check theoretically, but it should be largely sufficient. +// Besides, identity ( f(x)=x ) transform is considered as an update +const allUpdated = uItems.length === ms.length; +const updatedDocsIds = uItems.map(x => x.update._id) +const updatedCodes = updatedDocsIds.reduce((xs, x) => { + const code = hits.hits.find(h => h._id === x)?._source.study_code; + return code ? [...xs, code] : xs +}, []) +console.log('Codes updated'); +console.log(updatedCodes); +const notUpdatedCodes = sCodes.filter(c => !updatedCodes.includes(c)) +if (notUpdatedCodes.length > 0) { + console.log('Codes NOT updated (no studies found with these codes in study_centric)'); + console.log(notUpdatedCodes); +} +console.log( + allUpdated + ? 'All items were updated' + : `Updated ${br.body.items.length} docs (ids=${uItems + .map(item => item.update._id) + .sort() + .join(',')})`, +); + +process.exit(0); diff --git a/admin/arrangerApi.mjs b/admin/arrangerApi.mjs index 68e4a78..be3124c 100644 --- a/admin/arrangerApi.mjs +++ b/admin/arrangerApi.mjs @@ -1,7 +1,7 @@ -import { updateFieldExtendedMapping } from '@arranger/admin/dist/schemas/ExtendedMapping/utils'; -import { createNewIndex, getProjectMetadataEsLocation } from '@arranger/admin/dist/schemas/IndexSchema/utils'; -import { addArrangerProject } from '@arranger/admin/dist/schemas/ProjectSchema/utils'; -import { constants } from '@arranger/admin/dist/services/constants'; +import { updateFieldExtendedMapping } from '@arranger/admin/dist/schemas/ExtendedMapping/utils.js'; +import { createNewIndex, getProjectMetadataEsLocation } from '@arranger/admin/dist/schemas/IndexSchema/utils.js'; +import { addArrangerProject } from '@arranger/admin/dist/schemas/ProjectSchema/utils.js'; +import { constants } from '@arranger/admin/dist/services/constants.js'; const createNewIndices = async (esClient, confIndices) => { const createNewIndexWithClient = createNewIndex(esClient); @@ -10,11 +10,12 @@ const createNewIndices = async (esClient, confIndices) => { } }; -const fixExtendedMapping = async (esClient, confExtendedMappingMutations) => { +const fixExtendedMapping = async (esClient, mutations) => { const updateFieldExtendedMappingWithClient = updateFieldExtendedMapping(esClient); - for (const confExtendedMappingMutation of confExtendedMappingMutations) { + for (const [index, mutation] of mutations.entries()) { + console.debug('updating field = ', mutation?.field, ` ${index + 1} of ${mutations.length}`); await updateFieldExtendedMappingWithClient({ - ...confExtendedMappingMutation, + ...mutation, }); } }; diff --git a/admin/checkAliasWithRelease.mjs b/admin/checkAliasWithRelease.mjs new file mode 100644 index 0000000..da190a0 --- /dev/null +++ b/admin/checkAliasWithRelease.mjs @@ -0,0 +1,42 @@ +import { Client } from '@elastic/elasticsearch'; +import { esHost } from '../dist/src/env.js'; +import assert from 'node:assert/strict'; + +const cbKeepClinicalIndicesOnly = x => + ['file', 'biospecimen', 'participant', 'study'].some(stem => x.index.includes(stem)); + +const client = new Client({ node: esHost }); + +const rAllAliases = await client.cat.aliases({ + h: 'alias,index', + format: 'json', +}); + +assert(rAllAliases.statusCode === 200); + +const allAliases = rAllAliases.body; +const hasNext = allAliases.some(x => x.alias.includes('next_')); +const clinicalAliases = allAliases + .filter(cbKeepClinicalIndicesOnly) + .filter(x => (hasNext ? x.alias.includes('next_') : x)); + +const aliasToReleases = clinicalAliases.reduce((xs, x) => { + const r = 're' + x.index.split('_re_')[1]; + const v = [...new Set(xs[x.alias] ? [...xs[x.alias], r] : [r])]; + return { + ...xs, + [x.alias]: v, + all: v, + }; +}, {}); + +const { all, ...entities } = aliasToReleases; +console.log(`\n`); + +//not the best test but it should suffice +const ok = hasNext ? all.length === 1 : all.length <= 2 +if (!ok) { + console.warn('Check if the clinical aliases are ok - There might be a problem') +} +console.log(`Release(s) found: ${all}`); +console.log(entities); diff --git a/admin/checkConf.mjs b/admin/checkConf.mjs new file mode 100644 index 0000000..5e8dbc0 --- /dev/null +++ b/admin/checkConf.mjs @@ -0,0 +1,13 @@ +import includeConf from './confInclude.json' assert { type: "json" }; +import kfConf from './confKfNext.json' assert { type: "json" }; + +const kfs = kfConf.extendedMappingMutations.map(m => [m.field, m.graphqlField]); +const incs = includeConf.extendedMappingMutations.map(m => [m.field, m.graphqlField]); + +console.info('mutation in Kf only'); +const diffKfOnly = kfs.filter(kf => !incs.some(ins => kf[0] === ins[0] && kf[1] === ins[1])).map(x => ({ field: x[0], entity: x[1] })) +diffKfOnly.length === 0 ? console.log('No diff') : console.table(diffKfOnly) + +console.info('mutation in Include only'); +const diffIncOnly = incs.filter(ins => !kfs.some(kf => kf[0] === ins[0] && kf[1] === ins[1])).map(x => ({ field: x[0], entity: x[1] })) +diffIncOnly.length === 0 ? console.log('No diff') : console.table(diffIncOnly) diff --git a/admin/checkReleaseStats.mjs b/admin/checkReleaseStats.mjs new file mode 100644 index 0000000..0912483 --- /dev/null +++ b/admin/checkReleaseStats.mjs @@ -0,0 +1,113 @@ +import { Client } from '@elastic/elasticsearch'; +import { esHost } from '../dist/src/env.js'; +import assert from 'node:assert/strict'; +import { ENTITIES, getGlobalClinicalStats, getAllCountsPerStudy, studyIdToStudyCode } from './releaseStatsUtils.mjs'; + +const args = process.argv.slice(2); +const releaseArgument = args.find(a => a.startsWith('release:')) ?? ''; +const release = releaseArgument.split('release:')[1]; +assert(!!release, 'Missing release value'); + +const projectArgument = args.find(a => a.startsWith('project:')) ?? ''; +const project = projectArgument.split('project:')[1]?.toLocaleLowerCase() || ``; + +const isInclude = project.includes(`inc`); + +const client = new Client({ node: esHost }); + +console.log(`===== Project inferred is ${isInclude ? 'INCLUDE' : 'KF'} =====`); +const globalStats = await getGlobalClinicalStats(client, release); +assert(!globalStats[0], globalStats[0]); +console.table(globalStats[1]); + +const rStudyDict = await studyIdToStudyCode(client, release); +assert(!rStudyDict[0], rStudyDict[0]); +const studyDict = rStudyDict[1]; + +const rAllCounts = await getAllCountsPerStudy(client, release, studyDict); +assert(!rAllCounts[0], rAllCounts[0]); +const allCounts = rAllCounts[1]; +console.table(allCounts); + +const FIELD_DUPLICATE_SPECIMEN = isInclude ? `container_id` : 'fhir_id'; +const BUCKET_SIZE_FOR_DUPES = 1; +const mSearchDuplicatesResponse = await client.msearch({ + body: [ + { index: `${ENTITIES.study_centric}*${release}*` }, + { + size: 0, + aggs: { + duplicates: { + terms: { + field: 'study_id', + size: BUCKET_SIZE_FOR_DUPES, + min_doc_count: 2, + }, + }, + }, + }, + { index: `${ENTITIES.participant_centric}*${release}*` }, + { + size: 0, + aggs: { + duplicates: { + terms: { + field: 'participant_id', + size: BUCKET_SIZE_FOR_DUPES, + min_doc_count: 2, + }, + }, + }, + }, + { index: `${ENTITIES.file_centric}*${release}*` }, + { + size: 0, + aggs: { + duplicates: { + terms: { + field: 'file_id', + size: 1, + min_doc_count: 2, + }, + }, + }, + }, + { index: `${ENTITIES.biospecimen_centric}*${release}*` }, + { + size: 0, + aggs: { + duplicates: { + terms: { + field: FIELD_DUPLICATE_SPECIMEN, + size: BUCKET_SIZE_FOR_DUPES, + min_doc_count: 2, + }, + }, + }, + }, + ], +}); +const mResponsesForDuplicates = mSearchDuplicatesResponse?.body?.responses || []; +const duplicates = Object.fromEntries( + [ + [ENTITIES.study_centric, undefined], + [ENTITIES.participant_centric, undefined], + [ENTITIES.file_centric, undefined], + [ENTITIES.biospecimen_centric, undefined], + ] + .map((x, index) => { + const key = x[0]; + const buckets = mResponsesForDuplicates[index].aggregations?.duplicates?.buckets || []; + const hasDuplicates = buckets.length > 0; + return [key, { duplicates: hasDuplicates }]; + }) + .sort((x, y) => { + //ref: https://stackoverflow.com/questions/17387435/javascript-sort-array-of-objects-by-a-boolean-property + // true values first + if (x[1].duplicates === y[1].duplicates) { + return 0; + } + return x[1].duplicates ? -1 : 1; + }), +); +console.table(duplicates); diff --git a/admin/compareReleases.mjs b/admin/compareReleases.mjs new file mode 100644 index 0000000..ecd7a18 --- /dev/null +++ b/admin/compareReleases.mjs @@ -0,0 +1,93 @@ +//ex: node admin/compareReleases --a:relA --b:relB --verbose:true +import assert from 'node:assert/strict'; +import { Client } from '@elastic/elasticsearch'; +import { esHost } from '../dist/src/env.js'; +import { getAllCountsPerStudy, studyIdToStudyCode } from './releaseStatsUtils.mjs'; + +const args = process.argv.slice(2); +const aArgument = args.find(x => x.startsWith('--a:')) ?? ''; +const a = aArgument.split('--a:')[1]; +const bArgument = args.find(x => x.startsWith('--b:')) ?? ''; +const b = bArgument.split('--b:')[1]; +assert(!!a && !!b, 'Missing releases'); + +const verboseArgument = args.find(a => a.startsWith('verbose:')) ?? ''; +const verbose = ['true', 'yes', 'y'].includes(verboseArgument.split('verbose:')[1]?.toLocaleLowerCase() || ``); + +const client = new Client({ node: esHost }); + +const xs = []; +for (const x of [a, b]) { + const rStudyDict = await studyIdToStudyCode(client, x); + assert(!rStudyDict[0], rStudyDict[0]); + const studyDict = rStudyDict[1]; + const rAllCounts = await getAllCountsPerStudy(client, x, studyDict); + assert(!rAllCounts[0], rAllCounts[0]); + xs.push(rAllCounts[1]); +} + +assert(xs.length === 2); + +const showOperator = (n, m) => { + // both strings or both numbers is ok + if (n === m) { + return '='; + } + + if ([n, m].some(x => !Number.isInteger(x))) { + return '?'; + } + + if (n > m) { + return '>'; + } else if (n < m) { + return '<'; + } + // should be dead code, but better safe than sorry + return '?'; +}; + +const [aCounts, bCounts] = xs; +const res = Object.entries(aCounts).reduce( + (xs, x) => { + const [messages, table] = xs; + const [id, v] = x; + + const next = bCounts[id]; + if (!next) { + return [[...messages, id], table]; + } + return [ + messages, + { + ...table, + [id]: { + code: v.code, + participant_centric: [ + v.participant_centric, + next.participant_centric, + showOperator(v.participant_centric, next.participant_centric), + ], + file_centric: [v.file_centric, next.file_centric, showOperator(v.file_centric, next.file_centric)], + biospecimen_centric: [ + v.biospecimen_centric, + next.biospecimen_centric, + showOperator(v.biospecimen_centric, next.biospecimen_centric), + ], + releases: `${v.release} vs ${next.release}`, + }, + }, + ]; + }, + [[], {}], +); + +const messages = res[0]; +if (messages.length > 0) { + console.warn(`${messages.length} studies skipped (exist only in 1 release, not both)`); + if (verbose) { + console.log(messages); + } +} + +console.table(res[1]); diff --git a/admin/conf.json b/admin/conf.json deleted file mode 100644 index a23d805..0000000 --- a/admin/conf.json +++ /dev/null @@ -1,260 +0,0 @@ -{ - "migration_test_qa": { - "indices": [ - { - "graphqlField": "members", - "esIndex": "members-public" - }, - { - "graphqlField": "studies", - "esIndex": "migration_test_study_centric" - }, - { - "graphqlField": "participant", - "esIndex": "migration_test_participant_centric" - }, - { - "graphqlField": "variants", - "esIndex": "variant_centric" - }, - { - "graphqlField": "genes", - "esIndex": "gene_centric" - }, - { - "graphqlField": "biospecimens", - "esIndex": "migration_test_biospecimen_centric" - }, - { - "graphqlField": "files", - "esIndex": "migration_test_file_centric" - } - ], - "extendedMappingMutations": [ - { - "field": "experimental_strategy", - "graphqlField": "studies", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "controlled_access", - "graphqlField": "studies", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "data_category", - "graphqlField": "studies", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "acls", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "gene_external_reference", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "genes.cosmic.tumour_types_germline", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "external_study_ids", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "variant_external_reference", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "vep_impacts", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "zygosity", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "transmissions", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "studies.acls", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "studies.external_study_ids", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "studies.transmissions", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "studies.participant_ids", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "genes.alias", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "genes.omim.inheritance", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "genes.omim.inheritance_code", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "genes.orphanet.inheritance", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "consequences", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "consequences.consequences", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "clinvar.clin_sig", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "clinvar.conditions", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "clinvar.inheritance", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "clinvar.interpretations", - "graphqlField": "variants", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "alias", - "graphqlField": "genes", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "acl", - "graphqlField": "files", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "observed_phenotype.parents", - "graphqlField": "participant", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "observed_phenotype.age_at_event_days", - "graphqlField": "participant", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "roles", - "graphqlField": "members", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "searchableInterests", - "graphqlField": "members", - "extendedFieldMappingInput": { - "isArray": true - } - }, - { - "field": "interests", - "graphqlField": "members", - "extendedFieldMappingInput": { - "isArray": true - } - } - ] - } -} diff --git a/admin/confInclude.json b/admin/confInclude.json new file mode 100644 index 0000000..bc6d8ee --- /dev/null +++ b/admin/confInclude.json @@ -0,0 +1,424 @@ +{ + "indices": [ + { + "graphqlField": "biospecimen", + "esIndex": "biospecimen_centric" + }, + { + "graphqlField": "file", + "esIndex": "file_centric" + }, + { + "graphqlField": "genes", + "esIndex": "gene_centric" + }, + { + "graphqlField": "participant", + "esIndex": "participant_centric" + }, + { + "graphqlField": "study", + "esIndex": "study_centric" + }, + { + "graphqlField": "variants", + "esIndex": "variant_centric" + } + ], + "extendedMappingMutations": [ + { + "field": "diagnoses", + "graphqlField": "biospecimen", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "diagnoses.source_text_tumor_location", + "graphqlField": "biospecimen", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "acl", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "files", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "participants", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "participants.biospecimens", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "participants.biospecimens.diagnoses", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "participants.biospecimens.diagnoses.source_text_tumor_location", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "participants.down_syndrome_diagnosis", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "sequencing_experiment", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true, + "type": "nested" + } + }, + { + "field": "alias", + "graphqlField": "genes", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "down_syndrome_diagnosis", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "files.biospecimens.diagnoses", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "files.biospecimens.diagnoses.source_text_tumor_location", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "files.sequencing_experiment", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true, + "type": "nested" + } + }, + { + "field": "mondo.parents", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "observed_phenotype.age_at_event_days", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "observed_phenotype.parents", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "contacts", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "controlled_access", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "data_category", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "data_sources", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "data_types", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset.access_limitations", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset.access_requirements", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset.data_types", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset.expected_data_categories", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset.publications", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "domains", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "expected_data_categories", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "experimental_strategies", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "external_ids", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "institutions", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "investigator_names", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "part_lifespan_stages", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "publications", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "selection_criteria", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "study_designs", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "clinvar.clin_sig", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "clinvar.conditions", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "clinvar.inheritance", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "clinvar.interpretations", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "gene_external_reference", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.alias", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.consequences.consequence", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.consequences.refseq_mrna_id", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.cosmic.tumour_types_germline", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.omim.inheritance", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.omim.inheritance_code", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.orphanet.inheritance", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.spliceai.type", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "studies.participant_ids", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "studies.transmission", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "studies.zygosity", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + } + ] +} \ No newline at end of file diff --git a/admin/confKfNext.json b/admin/confKfNext.json new file mode 100644 index 0000000..b4e3f28 --- /dev/null +++ b/admin/confKfNext.json @@ -0,0 +1,449 @@ +{ + "indices": [ + { + "graphqlField": "biospecimen", + "esIndex": "next_biospecimen_centric" + }, + { + "graphqlField": "file", + "esIndex": "next_file_centric" + }, + { + "graphqlField": "genes", + "esIndex": "next_gene_centric" + }, + { + "graphqlField": "members", + "esIndex": "members-public" + }, + { + "graphqlField": "participant", + "esIndex": "next_participant_centric" + }, + { + "graphqlField": "study", + "esIndex": "next_study_centric" + }, + { + "graphqlField": "variants", + "esIndex": "next_variant_centric" + } + ], + "extendedMappingMutations": [ + { + "field": "diagnoses", + "graphqlField": "biospecimen", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "diagnoses.source_text_tumor_location", + "graphqlField": "biospecimen", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "acl", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "files", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "participants", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "participants.biospecimens", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "participants.biospecimens.diagnoses", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "participants.biospecimens.diagnoses.source_text_tumor_location", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "participants.down_syndrome_diagnosis", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "sequencing_experiment", + "graphqlField": "file", + "extendedFieldMappingInput": { + "isArray": true, + "type": "nested" + } + }, + { + "field": "alias", + "graphqlField": "genes", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "interests", + "graphqlField": "members", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "roles", + "graphqlField": "members", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "searchableInterests", + "graphqlField": "members", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "down_syndrome_diagnosis", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "files.biospecimens.diagnoses", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "files.biospecimens.diagnoses.source_text_tumor_location", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "files.sequencing_experiment", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true, + "type": "nested" + } + }, + { + "field": "mondo.parents", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "observed_phenotype.age_at_event_days", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "observed_phenotype.parents", + "graphqlField": "participant", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "contacts", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "controlled_access", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "data_category", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "data_sources", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "data_types", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset.access_limitations", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset.access_requirements", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset.data_types", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset.expected_data_categories", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "dataset.publications", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "domains", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "expected_data_categories", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "experimental_strategies", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "external_ids", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "institutions", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "investigator_names", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "part_lifespan_stages", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "publications", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "selection_criteria", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "study_designs", + "graphqlField": "study", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "clinvar.clin_sig", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "clinvar.conditions", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "clinvar.inheritance", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "clinvar.interpretations", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "gene_external_reference", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.alias", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.consequences.consequence", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.consequences.refseq_mrna_id", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.cosmic.tumour_types_germline", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.omim.inheritance", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.omim.inheritance_code", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.orphanet.inheritance", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "genes.spliceai.type", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "studies.participant_ids", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "studies.transmission", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + }, + { + "field": "studies.zygosity", + "graphqlField": "variants", + "extendedFieldMappingInput": { + "isArray": true + } + } + ] +} \ No newline at end of file diff --git a/admin/delClinicalIndicesBySuffix.mjs b/admin/delClinicalIndicesBySuffix.mjs new file mode 100644 index 0000000..6d85a65 --- /dev/null +++ b/admin/delClinicalIndicesBySuffix.mjs @@ -0,0 +1,83 @@ +//FIX: DUPLICATED CODE +/** + * node ... delClinicalIndicesBySuffix.mjs -- suffix:xyz + * + * */ +import assert from 'node:assert/strict'; +import readline from 'readline'; +import { Client } from '@elastic/elasticsearch'; +import { esHost } from '../dist/src/env.js'; +import { cbKeepClinicalIndicesOnly } from './utils.mjs'; + +const args = process.argv.slice(2); +const rawSuffix = args.find(a => a.startsWith('suffix:')) ?? ''; +const suffix = (rawSuffix.split(':')[1] || '').trim(); +assert(!!suffix, 'You must instruct the suffix of an index name. For instance, "suffix:sd_bhjxbdqk_20240611_1"'); + +const userReadline = readline.createInterface({ + input: process.stdin, + output: process.stdout, +}); + +const displayDoYouWantToProceed = () => + new Promise(resolve => { + userReadline.question(`You are about to delete indices. Do you want to proceed y/n? > `, answer => + resolve(answer === 'y'), + ); + }); + +const wannaProceed = await displayDoYouWantToProceed(); + +if (!wannaProceed) { + userReadline.close(); + process.exit(0); +} + +const client = new Client({ node: esHost }); + +const catIndicesResponse = await client.cat.indices({ + index: `*${suffix}`, + h: 'index', + format: 'json', +}); + +if (catIndicesResponse.statusCode !== 200) { + console.error('Received bad response', catIndicesResponse, ' Terminating.'); + process.exit(1); +} + +const clinicalIndices = catIndicesResponse.body.filter(cbKeepClinicalIndicesOnly).map(x => x.index); +assert(Array.isArray(clinicalIndices) && clinicalIndices.length > 0, 'No index found. Terminating'); + +const rAllAliases = await client.cat.aliases({ + h: 'alias,index', + format: 'json', +}); +assert(rAllAliases.statusCode === 200); + +const allAliases = rAllAliases.body; +const clinicalAliases = allAliases.filter(cbKeepClinicalIndicesOnly); + +const displayDoYouWantToDeleteIndices = () => + new Promise(resolve => { + console.log('found', clinicalIndices.length, 'indices.'); + console.log( + JSON.stringify( + clinicalIndices.sort().map(x => { + return clinicalAliases.some(a => a.index === x) ? ['Aliased', x] : x; + }), + null, + 2, + ), + ); + userReadline.question(`Do you want to delete those indices y/n? > `, answer => resolve(answer === 'y')); + }); + +const okDelete = await displayDoYouWantToDeleteIndices(); +if (okDelete) { + const deleteResponse = await client.indices.delete({ + index: clinicalIndices, + }); + console.log(deleteResponse.body); +} +userReadline.close(); diff --git a/admin/deleteClinicalIndicesFromRelease.mjs b/admin/deleteClinicalIndicesFromRelease.mjs new file mode 100644 index 0000000..dac34c8 --- /dev/null +++ b/admin/deleteClinicalIndicesFromRelease.mjs @@ -0,0 +1,124 @@ +//FIX: DUPLICATED CODE +/** + * npm run delete-clinical-indices-helper -- release:re_20231030_1 + * + * */ +import assert from 'node:assert/strict'; +import readline from 'readline'; +import { Client } from '@elastic/elasticsearch'; +import { esHost } from '../dist/src/env.js'; +import { cbKeepClinicalIndicesOnly } from './utils.mjs'; + +const args = process.argv.slice(2); +const releaseArgument = args.find(a => a.startsWith('release:')) ?? ''; +const releaseTag = releaseArgument.split(':')[1]; +assert(!!releaseTag, 'You must instruct a release tag. For instance, "-- release:re_xyz --interactive"'); +const isInteractive = args.some(a => a === '--interactive'); + +const userReadline = readline.createInterface({ + input: process.stdin, + output: process.stdout, +}); + +const displayDoYouWantToProceed = () => + new Promise(resolve => { + userReadline.question(`You are about to delete indices. Do you want to proceed y/n? > `, answer => + resolve(answer === 'y'), + ); + }); + +const wannaProceed = await displayDoYouWantToProceed(); + +if (!wannaProceed) { + process.exit(0); +} + +const client = new Client({ node: esHost }); + +const catIndicesResponse = await client.cat.indices({ + index: `*_${releaseTag}`, + h: 'index', + format: 'json', +}); + +if (catIndicesResponse.statusCode !== 200) { + console.error('Received bad response', catIndicesResponse, ' Terminating.'); + process.exit(1); +} + +const INDEX_CLINICAL_CATEGORIES = ['file', 'participant', 'study', 'biospecimen']; +const releaseClinicalIndices = catIndicesResponse.body + .map(x => x.index) + .filter(x => INDEX_CLINICAL_CATEGORIES.some(c => x.includes(c))) + .sort(); +assert(Array.isArray(releaseClinicalIndices) && releaseClinicalIndices.length > 0, 'No index found. Terminating'); + +// Extra check. Might not be needed, but cheap to test. +const hasOnlyClinicalIndices = releaseClinicalIndices.every(r => { + const indexPrefix = r.split('_')[0]; + return ( + ['gene', 'variant', 'member'].some(prefix => !r.startsWith(prefix)) && + INDEX_CLINICAL_CATEGORIES.includes(indexPrefix) + ); +}); +assert( + hasOnlyClinicalIndices, + `Oops it seems like non-clinical indices are included. Requires: ${INDEX_CLINICAL_CATEGORIES.join( + ', ', + )} only. Terminating`, +); + +const rAllAliases = await client.cat.aliases({ + h: 'alias,index', + format: 'json', +}); + +assert(rAllAliases.statusCode === 200); + +const allAliases = rAllAliases.body; +const clinicalAliases = allAliases.filter(cbKeepClinicalIndicesOnly); + +const isAliased = clinicalAliases.some(x => x.index.includes(releaseTag)); +assert(!isAliased, `${releaseTag} is aliased`); + +const displayIndicesQuestion = () => + new Promise(resolve => { + userReadline.question( + `${releaseClinicalIndices.length} were found. Do you want to display them y/n? > `, + answer => { + const yes = answer === 'y'; + if (yes) { + console.log(releaseClinicalIndices); + } + resolve(); + }, + ); + }); + +isInteractive && (await displayIndicesQuestion()); + +const displayIndicesQuestionAfterShowThem = () => + new Promise(resolve => { + userReadline.question(`Do you want to delete them y/n? > `, answer => { + const isYes = answer === 'y'; + resolve(isYes); + }); + }); +const proceedToDeletion = isInteractive ? await displayIndicesQuestionAfterShowThem() : true; +if (proceedToDeletion) { + if (!isInteractive) { + const maxDisplay = 5; + console.log( + `Deleting ${releaseClinicalIndices.length} indices: ${releaseClinicalIndices + .slice(0, maxDisplay) + .join(', ')} ${releaseClinicalIndices.length > maxDisplay ? '...' : ''}`, + ); + } + const deleteResponse = await client.indices.delete({ + index: releaseClinicalIndices, + }); + console.log(deleteResponse.body); +} + +userReadline.close(); +process.exit(0); diff --git a/admin/findClinicalIndicesUsage.mjs b/admin/findClinicalIndicesUsage.mjs new file mode 100644 index 0000000..063ac2f --- /dev/null +++ b/admin/findClinicalIndicesUsage.mjs @@ -0,0 +1,75 @@ +/** +(WIP) Helper script to find unused indices + * */ +import assert from 'node:assert/strict'; +import { Client } from '@elastic/elasticsearch'; +import { esHost } from '../dist/src/env.js'; +import { cbKeepClinicalIndicesOnly } from './utils.mjs'; + +const client = new Client({ node: esHost }); + +const catIndicesResponse = await client.cat.indices({ + index: `*centric*`, + h: 'index,creation.date,creation.date.string', + format: 'json', +}); + +if (catIndicesResponse.statusCode !== 200) { + console.error('Received bad response', catIndicesResponse, ' Terminating.'); + process.exit(1); +} + +const clinicalIndices = catIndicesResponse.body.filter(cbKeepClinicalIndicesOnly); +assert(Array.isArray(clinicalIndices) && clinicalIndices.length > 0, 'No index found. Terminating'); + +const allAliases = await client.cat.aliases({ + h: 'alias,index', + format: 'json', +}); + +const clinicalAliases = allAliases.body.filter(cbKeepClinicalIndicesOnly); + +const makeReleaseToCreationDate = l => + l + .filter(x => x.index.includes('_re_')) + .sort((a, b) => b['creation.date'] - a['creation.date']) + .map(x => ['re_' + x.index.split('re_')[1], x['creation.date.string']]) + .reduce((xs, x) => (xs.some(y => y[0] === x[0]) ? xs : [...xs, x]), []) + .map(x => ({ release: x[0], creation_date: x[1] })); + +const clinicalIndicesNotAliased = clinicalIndices.filter(x => clinicalAliases.every(a => a.index !== x.index)); +const unaliasedClinicalIndicesWithCreationDate = makeReleaseToCreationDate(clinicalIndicesNotAliased); + +// Make sure that no aliased index contains previously found unaliased releases. +const unaliasedReleases = unaliasedClinicalIndicesWithCreationDate.map(x => x.release); +assert(clinicalAliases.every(x => !unaliasedReleases.includes(`re_${x.index.split('re_')[1]}`))); + +console.log(`===== Not Aliased (pattern:re_*)`); + +unaliasedClinicalIndicesWithCreationDate.length + ? console.table(unaliasedClinicalIndicesWithCreationDate) + : console.log('None'); + +console.log(`===== Aliased (pattern:re_*)`); +const clinicalIndicesAliased = clinicalIndices.filter(x => clinicalAliases.some(a => a.index === x.index)); +const aliasedClinicalIndicesWithCreationDate = makeReleaseToCreationDate(clinicalIndicesAliased); +aliasedClinicalIndicesWithCreationDate.length + ? console.table(aliasedClinicalIndicesWithCreationDate) + : console.log('None'); + +console.log(`===== Others (Clinical)`); +const othersClinical = clinicalIndices + .filter(x => !x.index.includes('_re_')) + .sort((a, b) => b['creation.date'] - a['creation.date']) + .map(x => { + const release = x.index + .split('sd_')[1] + .split('_') + .slice(1) + .join('_'); + return [release, x['creation.date.string']]; + }) + .reduce((xs, x) => (xs.some(y => y[0] === x[0]) ? xs : [...xs, x]), []) + .map(x => ({ release: x[0], creation_date: x[1] })); + +othersClinical.length ? console.table(othersClinical) : console.log('None'); diff --git a/admin/mockStudies.mjs b/admin/mockStudies.mjs new file mode 100644 index 0000000..5868857 --- /dev/null +++ b/admin/mockStudies.mjs @@ -0,0 +1,869 @@ +import Ajv from 'ajv'; + +export const mockStudies = [ + { + controlled_access: ['Registered', 'Controlled'], + data_category: [ + 'Genomics', + 'Transcriptomics', + 'Proteomics', + 'Metabolomics', + 'Cognitive', + 'Immune maps', + 'Microbiome', + 'Imaging', + 'Clinical', + ], + dataset: [ + { + dataset_id: 'HTP-TR', + external_dataset_id: '', + dataset_name: 'HTP Whole Blood RNAseq (v1)', + date_collection_start_year: '2016', + date_collection_end_year: '2020', + data_category: 'Transcriptomics', + data_types: ['Normalized relative expression (FPKM)'], + expected_number_participants: 400, + experimental_strategy: 'Bulk polyA+ RNAseq', + experimental_platform: 'Illumina Novaseq', + is_harmonized: true, + publications: ['PMID: 37379383'], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: [], + dbgap: '', + repository: 'Gene Expression Omnibus', + repository_url: 'https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190125', + participant_count: 402, + biospecimen_count: 402, + file_count: 3200, + }, + { + dataset_id: 'HTP-MET', + external_dataset_id: '', + dataset_name: 'HTP Plasma Metabolomics (v1)', + date_collection_start_year: '2016', + date_collection_end_year: '2020', + data_category: 'Metabolomics', + data_types: ['Preprocessed metabolite relative abundance'], + expected_number_participants: 418, + experimental_strategy: 'LCMS Metabolomics', + experimental_platform: 'Ultra high-performance liquid chromatography-mass spectrometry (UHPLC-MS)', + is_harmonized: false, + publications: ['PMID: 37379383'], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: [], + dbgap: 'phs002981', + repository: 'Metabolomics Workbench', + repository_url: + 'http://dev.metabolomicsworkbench.org:22222/data/DRCCMetadata.php?Mode=Study&StudyID=ST002200&Access=UrlT3545', + participant_count: 418, + biospecimen_count: 3743, + file_count: 477, + }, + { + dataset_id: 'HTP-UNHAR', + external_dataset_id: '', + dataset_name: 'HTP Unharmonized Demographic/Clinical Data', + date_collection_start_year: '2016', + date_collection_end_year: '', + data_category: 'Unharmonized Demographic/Clinical Data', + data_types: [], + expected_number_participants: 1055, + experimental_strategy: '', + experimental_platform: '', + is_harmonized: false, + publications: ['PMID: 37379383'], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: [], + dbgap: '', + repository: '', + repository_url: '', + participant_count: 1055, + biospecimen_count: 0, + file_count: 1, + }, + { + dataset_id: 'HTP-PRO', + external_dataset_id: '', + dataset_name: 'HTP Plasma Inflammatory Markers (MSD v1)', + date_collection_start_year: '2016', + date_collection_end_year: '2020', + data_category: 'Proteomics', + data_types: ['Protein abundance (absolute protein concentration)'], + expected_number_participants: 477, + experimental_strategy: 'Multiplex immunoassay', + experimental_platform: 'Meso Scale Discovery Assays (MSD)', + is_harmonized: false, + publications: ['PMID: 37379383'], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: [], + dbgap: '', + repository: 'Synapse', + repository_url: 'https://www.synapse.org/#!Synapse:syn31475487', + participant_count: 479, + biospecimen_count: 4371, + file_count: 477, + }, + ], + date_collection_end_year: '', + date_collection_start_year: '2016', + experimental_strategies: [ + { + file_count: 3200, + experimental_strategy: 'RNA-Seq', + }, + { + file_count: 880, + experimental_strategy: 'Whole Genome Sequencing', + }, + { + file_count: 447, + experimental_strategy: 'Multiplex Immunoassay', + }, + { + file_count: 418, + experimental_strategy: 'LCMS Metabolomics', + }, + ], + external_ids: ['phs002330', 'phs002981'], + institutions: ['Linda Crnic Institute for Down Syndrome'], + investigator_names: ['Joaquin M. Espinosa'], + is_harmonized: true, + study_code: 'HTP', + }, + { + controlled_access: ['Registered', 'Controlled'], + data_category: ['Genomics', 'Clinical'], + dataset: [ + { + dataset_id: 'DS-COG-ALL-GEN', + external_dataset_id: '', + dataset_name: 'DS-COG-ALL Whole Genome Sequencing', + date_collection_start_year: '', + date_collection_end_year: '', + data_category: 'Genomics', + data_types: [], + expected_data_categories: [], + expected_number_participants: 530, + experimental_strategy: 'Whole Genome Sequencing', + experimental_platform: 'Illumina', + is_harmonized: true, + publications: [], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: [], + dbgap: 'phs002330', + repository: '', + repository_url: '', + participant_count: 530, + biospecimen_count: 834, + file_count: 7211, + }, + { + dataset_id: 'DS-COG-ALL-UNHAR', + external_dataset_id: '', + dataset_name: 'DS-COG-ALL Unharmonized Demographic/Clinical Data', + date_collection_start_year: '', + date_collection_end_year: '', + data_category: 'Unharmonized Demographic/Clinical Data', + data_types: [], + expected_data_categories: [], + expected_number_participants: 530, + experimental_strategy: '', + experimental_platform: '', + is_harmonized: false, + publications: [], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: [], + dbgap: 'phs002330', + repository: '', + repository_url: '', + participant_count: 530, + biospecimen_count: 0, + file_count: 1, + }, + ], + date_collection_end_year: '', + date_collection_start_year: '', + experimental_strategies: [ + { + file_count: 0, + experimental_strategy: 'RNA-Seq', + }, + { + file_count: 7211, + experimental_strategy: 'Whole Genome Sequencing', + }, + { + file_count: 0, + experimental_strategy: 'Multiplex Immunoassay', + }, + { + file_count: 0, + experimental_strategy: 'LCMS Metabolomics', + }, + ], + external_ids: ['phs002330'], + institutions: ['Baylor College Of Medicine'], + investigator_names: ['Phillip J. Lupo'], + is_harmonized: true, + study_code: 'DS-COG-ALL', + }, + { + controlled_access: ['Controlled'], + data_category: ['Genomics', 'Clinical'], + dataset: [ + { + dataset_id: 'DS360-CHD-GEN', + external_dataset_id: '', + dataset_name: 'DS360-CHD Whole Genome Sequencing', + date_collection_start_year: '', + date_collection_end_year: '', + data_category: 'Genomics', + data_types: [], + expected_data_categories: [], + expected_number_participants: 1327, + experimental_strategy: 'Whole Genome Sequencing', + experimental_platform: 'Illumina', + is_harmonized: true, + publications: [], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: ['not for profit organisation use only (DUO:0000045)'], + dbgap: 'phs002330', + repository: '', + repository_url: '', + participant_count: 1327, + biospecimen_count: 1344, + file_count: 4922, + }, + { + dataset_id: 'DS360-CHD-UNHAR', + external_dataset_id: '', + dataset_name: 'DS360-CHD Unharmonized Demographic/Clinical Data', + date_collection_start_year: '', + date_collection_end_year: '', + data_category: 'Unharmonized Demographic/Clinical Data', + data_types: [], + expected_data_categories: [], + expected_number_participants: 1327, + experimental_strategy: '', + experimental_platform: '', + is_harmonized: false, + publications: [], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: ['not for profit organisation use only (DUO:0000045)'], + dbgap: 'phs002330', + repository: '', + repository_url: '', + participant_count: 1327, + biospecimen_count: 0, + file_count: 1, + }, + ], + date_collection_end_year: '', + date_collection_start_year: '', + experimental_strategies: [ + { + file_count: 0, + experimental_strategy: 'RNA-Seq', + }, + { + file_count: 3769, + experimental_strategy: 'Whole Genome Sequencing', + }, + { + file_count: 0, + experimental_strategy: 'Multiplex Immunoassay', + }, + { + file_count: 0, + experimental_strategy: 'LCMS Metabolomics', + }, + ], + external_ids: ['phs002330'], + institutions: ['Emory University School of Medicine'], + investigator_names: ['Stephanie Sherman'], + is_harmonized: true, + study_code: 'DS360-CHD', + }, + { + controlled_access: ['Controlled'], + data_category: ['Genomics', 'Clinical'], + dataset: [ + { + dataset_id: 'DS-PCGC-GEN', + external_dataset_id: '', + dataset_name: 'DS-PCGC Whole Genome Sequencing', + date_collection_start_year: '', + date_collection_end_year: '', + data_category: 'Genomics', + data_types: [], + expected_data_categories: [], + expected_number_participants: 369, + experimental_strategy: 'Whole Genome Sequencing', + experimental_platform: 'Illumina', + is_harmonized: true, + publications: [], + access_limitations: ['health or medical or biomedical research (DUO:0000006)'], + access_requirements: ['not for profit organisation use only (DUO:0000045)'], + dbgap: 'phs001138', + repository: '', + repository_url: '', + participant_count: 369, + biospecimen_count: 369, + file_count: 818, + }, + { + dataset_id: 'DS-PCGC-UNHAR', + external_dataset_id: '', + dataset_name: 'DS-PCGC Unharmonized Demographic/Clinical Data', + date_collection_start_year: '', + date_collection_end_year: '', + data_category: 'Unharmonized Demographic/Clinical Data', + data_types: [], + expected_data_categories: [], + expected_number_participants: 369, + experimental_strategy: '', + experimental_platform: '', + is_harmonized: false, + publications: [], + access_limitations: ['health or medical or biomedical research (DUO:0000006)'], + access_requirements: ['not for profit organisation use only (DUO:0000045)'], + dbgap: 'phs001138', + repository: '', + repository_url: '', + participant_count: 369, + biospecimen_count: 0, + file_count: 1, + }, + ], + date_collection_end_year: '', + date_collection_start_year: '', + experimental_strategies: [ + { + file_count: 0, + experimental_strategy: 'RNA-Seq', + }, + { + file_count: 818, + experimental_strategy: 'Whole Genome Sequencing', + }, + { + file_count: 0, + experimental_strategy: 'Multiplex Immunoassay', + }, + { + file_count: 0, + experimental_strategy: 'LCMS Metabolomics', + }, + ], + external_ids: ['phs001138', 'phs002330'], + institutions: ["Cincinnati Children's Hospital Medical Center"], + investigator_names: ['Eileen C. King'], + is_harmonized: true, + study_code: 'DS-PCGC', + }, + { + controlled_access: ['Registered'], + data_category: ['Genomics', 'Transcriptomics', 'Imaging', 'Clinical'], + dataset: [ + { + dataset_id: 'X01-Hakon-GEN', + external_dataset_id: '', + dataset_name: 'X01-Hakonarson Whole Genome Sequencing', + date_collection_start_year: '', + date_collection_end_year: '', + data_category: 'Genomics', + data_types: [], + expected_data_categories: [], + expected_number_participants: 1134, + experimental_strategy: 'Whole Genome Sequencing', + experimental_platform: 'Illumina', + is_harmonized: true, + publications: [], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: [], + dbgap: 'phs002983', + repository: '', + repository_url: '', + participant_count: 1152, + biospecimen_count: 1908, + file_count: 2565, + }, + { + dataset_id: 'X01-Hakon-RNASeq', + external_dataset_id: '', + dataset_name: 'X01-Hakonarson RNASeq', + date_collection_start_year: '', + date_collection_end_year: '', + data_category: 'Transcriptomics', + data_types: [], + expected_data_categories: [], + expected_number_participants: 1152, + experimental_strategy: 'Bulk RNA-Seq', + experimental_platform: 'Illumina', + is_harmonized: true, + publications: [], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: [], + dbgap: 'phs002983', + repository: '', + repository_url: '', + participant_count: 1152, + biospecimen_count: 1908, + file_count: 2565, + }, + { + dataset_id: 'X01-Hakon-UNHAR', + external_dataset_id: '', + dataset_name: 'X01-Hakonarson Unharmonized Demographic/Clinical Data', + date_collection_start_year: '', + date_collection_end_year: '', + data_category: 'Unharmonized Demographic/Clinical Data', + data_types: [], + expected_data_categories: [], + expected_number_participants: 1152, + experimental_strategy: '', + experimental_platform: '', + is_harmonized: false, + publications: [], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: [], + dbgap: 'phs002983', + repository: '', + repository_url: '', + participant_count: 369, + biospecimen_count: 0, + file_count: 1, + }, + ], + date_collection_end_year: '', + date_collection_start_year: '', + experimental_strategies: [ + { + file_count: 2565, + experimental_strategy: 'RNA-Seq', + }, + { + file_count: 0, + experimental_strategy: 'Whole Genome Sequencing', + }, + { + file_count: 0, + experimental_strategy: 'Multiplex Immunoassay', + }, + { + file_count: 0, + experimental_strategy: 'LCMS Metabolomics', + }, + ], + external_ids: ['phs002983'], + institutions: ["Children's Hospital of Philadelphia"], + investigator_names: ['Hakon Hakonarson'], + is_harmonized: true, + study_code: 'X01-Hakonarson', + }, + { + controlled_access: ['Registered'], + data_category: ['Clinical'], + dataset: [ + { + dataset_id: 'X01-deSmith-GEN', + external_dataset_id: '', + dataset_name: 'X01-deSmith Whole Genome Sequencing', + date_collection_start_year: '', + date_collection_end_year: '', + data_category: 'Genomics', + data_types: [], + expected_data_categories: [], + expected_number_participants: 436, + experimental_strategy: 'Whole Genome Sequencing', + experimental_platform: 'Illumina', + is_harmonized: true, + publications: [], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: [], + dbgap: 'phs002982', + repository: '', + repository_url: '', + participant_count: 436, + biospecimen_count: 436, + file_count: 0, + }, + { + dataset_id: 'X01-deSmith-UNHAR', + external_dataset_id: '', + dataset_name: 'X01-deSmith Unharmonized Demographic/Clinical Data', + date_collection_start_year: '', + date_collection_end_year: '', + data_category: 'Unharmonized Demographic/Clinical Data', + data_types: [], + expected_data_categories: [], + expected_number_participants: 436, + experimental_strategy: '', + experimental_platform: '', + is_harmonized: false, + publications: [], + access_limitations: ['general research use (DUO:0000042)'], + access_requirements: [], + dbgap: 'phs002982', + repository: '', + repository_url: '', + participant_count: 436, + biospecimen_count: 436, + file_count: 1, + }, + ], + date_collection_end_year: '', + date_collection_start_year: '', + experimental_strategies: [ + { + file_count: 0, + experimental_strategy: 'RNA-Seq', + }, + { + file_count: 0, + experimental_strategy: 'Whole Genome Sequencing', + }, + { + file_count: 0, + experimental_strategy: 'Multiplex Immunoassay', + }, + { + file_count: 0, + experimental_strategy: 'LCMS Metabolomics', + }, + ], + external_ids: ['phs002982'], + institutions: ['University of Oxford'], + investigator_names: ['Adam de Smith'], + is_harmonized: true, + study_code: 'X01-deSmith', + }, + { + controlled_access: ['Registered'], + data_category: ['Transcriptomics', 'Clinical'], + dataset: [], + date_collection_end_year: '', + date_collection_start_year: '2018', + experimental_strategies: [ + { + file_count: 253, + experimental_strategy: 'RNA-Seq', + }, + { + file_count: 0, + experimental_strategy: 'Whole Genome Sequencing', + }, + { + file_count: 0, + experimental_strategy: 'Multiplex Immunoassay', + }, + { + file_count: 0, + experimental_strategy: 'LCMS Metabolomics', + }, + ], + external_ids: [], + institutions: ['Benaroya Research Institute'], + investigator_names: ['Jane Buckner'], + is_harmonized: true, + study_code: 'BRI-DSR', + }, + { + controlled_access: ['Controlled'], + data_category: ['Genomics', 'Clinical'], + dataset: [], + date_collection_end_year: '', + date_collection_start_year: '', + experimental_strategies: [ + { + file_count: 0, + experimental_strategy: 'RNA-Seq', + }, + { + file_count: 123, + experimental_strategy: 'Whole Genome Sequencing', + }, + { + file_count: 0, + experimental_strategy: 'Multiplex Immunoassay', + }, + { + file_count: 0, + experimental_strategy: 'LCMS Metabolomics', + }, + ], + external_ids: [], + institutions: ['Linda Crnic Institute for Down Syndrome'], + investigator_names: ['Joaquin Espinosa'], + is_harmonized: true, + study_code: 'DS-NEXUS', + }, + { + controlled_access: [], + data_category: ['Clinical'], + dataset: [], + date_collection_end_year: '', + date_collection_start_year: '', + experimental_strategies: [ + { + file_count: 0, + experimental_strategy: 'RNA-Seq', + }, + { + file_count: 0, + experimental_strategy: 'Whole Genome Sequencing', + }, + { + file_count: 0, + experimental_strategy: 'Multiplex Immunoassay', + }, + { + file_count: 0, + experimental_strategy: 'LCMS Metabolomics', + }, + ], + external_ids: [], + institutions: ['Geisinger Health System'], + investigator_names: ['Christa Martin'], + is_harmonized: true, + study_code: 'DS-Sleep', + }, + { + controlled_access: [], + data_category: ['Clinical'], + dataset: [ + { + dataset_id: 'DS-Connect-UNHAR', + external_dataset_id: '', + dataset_name: 'DS-Connect Unharmonized Demographic/Clinical Data', + date_collection_start_year: '2013', + date_collection_end_year: '', + data_category: 'Unharmonized Demographic/Clinical Data', + data_types: ['Social Determinants of Health', 'Demographics', 'Co-occurring Conditions'], + expected_data_categories: ['Unharmonized Demographic/Clinical Data'], + expected_number_participants: 3634, + experimental_strategy: '', + experimental_platform: '', + is_harmonized: false, + publications: [], + access_limitations: [], + access_requirements: [], + dbgap: '', + repository: '', + repository_url: '', + participant_count: 3484, + biospecimen_count: 0, + file_count: 1, + }, + ], + date_collection_end_year: '', + date_collection_start_year: '2013', + experimental_strategies: [ + { + file_count: 0, + experimental_strategy: 'RNA-Seq', + }, + { + file_count: 0, + experimental_strategy: 'Whole Genome Sequencing', + }, + { + file_count: 0, + experimental_strategy: 'Multiplex Immunoassay', + }, + { + file_count: 0, + experimental_strategy: 'LCMS Metabolomics', + }, + ], + external_ids: [], + institutions: ['Eunice Kennedy Shriver National Institute of Child Health and Human Development'], + investigator_names: ['Sujata Bardhan'], + is_harmonized: true, + study_code: 'DSC', + }, + { + controlled_access: [], + data_category: ['Clinical'], + dataset: [], + date_collection_end_year: '', + date_collection_start_year: '', + experimental_strategies: [ + { + file_count: 0, + experimental_strategy: 'RNA-Seq', + }, + { + file_count: 0, + experimental_strategy: 'Whole Genome Sequencing', + }, + { + file_count: 0, + experimental_strategy: 'Multiplex Immunoassay', + }, + { + file_count: 0, + experimental_strategy: 'LCMS Metabolomics', + }, + ], + external_ids: [], + institutions: ['University of Pittsburgh'], + investigator_names: ['Bradley T. Christian', 'Benjamin L. Handen', 'Elizabeth Head', 'Mark Mapstone'], + is_harmonized: true, + study_code: 'ABC-DS', + }, +]; + +const sSchema = { + title: 'Study', + type: 'object', + properties: { + controlled_access: { + type: 'array', + items: { + type: 'string', + }, + }, + data_category: { + type: 'array', + items: { + type: 'string', + }, + }, + dataset: { + type: 'array', + items: { + type: 'object', + properties: { + dbgap: { + type: 'string', + }, + dataset_id: { + type: 'string', + }, + external_dataset_id: { + type: 'string', + }, + dataset_name: { + type: 'string', + }, + date_collection_start_year: { + type: 'string', + }, + date_collection_end_year: { + type: 'string', + }, + data_category: { + type: 'string', + }, + data_types: { + type: 'array', + items: { + type: 'string', + }, + }, + expected_number_participants: { + type: 'integer', + }, + experimental_strategy: { + type: 'string', + }, + experimental_platform: { + type: 'string', + }, + publications: { + type: 'array', + items: { + type: 'string', + }, + }, + access_limitations: { + type: 'array', + items: { + type: 'string', + }, + }, + access_requirements: { + type: 'array', + items: { + type: 'string', + }, + }, + repository: { + type: 'string', + }, + repository_url: { + type: 'string', + }, + participant_count: { + type: 'integer', + }, + biospecimen_count: { + type: 'integer', + }, + file_count: { + type: 'integer', + }, + is_harmonized: { + type: 'boolean', + }, + }, + }, + }, + date_collection_end_year: { + type: 'string', + }, + date_collection_start_year: { + type: 'string', + }, + experimental_strategies: { + type: 'array', + items: { + type: 'object', + properties: { + file_count: { + type: 'integer', + }, + experimental_strategy: { + type: 'string', + }, + }, + }, + }, + external_ids: { + type: 'array', + items: { + type: 'string', + }, + }, + institutions: { + type: 'array', + items: { + type: 'string', + }, + }, + is_harmonized: { + type: 'boolean', + }, + investigator_names: { + type: 'array', + items: { + type: 'string', + }, + }, + study_code: { + type: 'string', + }, + }, + required: ['study_code'], +}; + +export const validateStudies = sData => { + const ajv = new Ajv(); + const validate = ajv.compile(sSchema); + return sData.map(s => { + const valid = validate(s); + return [s.study_code, valid, validate.errors]; + }); +}; diff --git a/admin/poorsManEsMappingsInpector.mjs b/admin/poorsManEsMappingsInpector.mjs new file mode 100644 index 0000000..d45ebcd --- /dev/null +++ b/admin/poorsManEsMappingsInpector.mjs @@ -0,0 +1,31 @@ +import assert from 'node:assert/strict'; +import { Client } from '@elastic/elasticsearch'; +import { esHost } from '../dist/src/env.js'; + +const client = new Client({ node: esHost }); + +const r = await client.indices.getMapping({ index: '*_centric_*' }); +assert(r.statusCode === 200 && !!r.body); + +const indicesWithMappingContainingIgnoreAbove = Object.entries(r.body) + .map(([k, v]) => [k, v.mappings.properties]) + .reduce((xs, x) => { + const [indexName, m] = x; + const sm = JSON.stringify(m); + const matchesStartPos = [...sm.matchAll(/ignore_above/g)].map(x => x.index); + if (matchesStartPos.length === 0) { + return xs; + } + const radiusInChars = 75; + return [ + ...xs, + { index: indexName, loci: matchesStartPos.map(n => sm.slice(n - radiusInChars, n + radiusInChars)) }, + ]; + }, []); + +console.log(`==> Inspection for all centric mappings from: ${esHost}`); +if (indicesWithMappingContainingIgnoreAbove.length === 0) { + console.log('No ignore_above found in any mappings for entity'); +} else { + console.table(indicesWithMappingContainingIgnoreAbove); +} diff --git a/admin/postReleaseIndicesToAliasesHelper.mjs b/admin/postReleaseIndicesToAliasesHelper.mjs new file mode 100644 index 0000000..d0280ae --- /dev/null +++ b/admin/postReleaseIndicesToAliasesHelper.mjs @@ -0,0 +1,171 @@ +/** + * This script is a helper that can be used to create + * aliases for indices of a given release. + * + * npm run post-re-alias-helper -- release:re_test_023 action:remove + * + * npm run post-re-alias-helper -- release:re_test_023 action:remove test + * + * */ +import assert from 'node:assert/strict'; +import readline from 'readline'; +import { Client } from '@elastic/elasticsearch'; +import { esHost } from '../dist/src/env.js'; +import { cbKeepClinicalIndicesOnly } from './utils.mjs'; + +const args = process.argv.slice(2); +const releaseArgument = args.find(a => a.startsWith('release:')) ?? ''; +const releaseTag = releaseArgument.split(':')[1]; +assert(!!releaseTag, 'You must instruct a release tag. For instance, "-- release:re_xyz"'); + +const aliasActionArgument = args.find(a => a.startsWith('action:')) ?? ''; +const ALIAS_ACTIONS = { + add: 'add', + remove: 'remove', +}; +const aliasAction = aliasActionArgument.split(':')?.[1]?.toLocaleLowerCase() ?? ALIAS_ACTIONS.add; +assert( + Object.values(ALIAS_ACTIONS).includes(aliasAction), + `Alias actions must be one of: "${Object.values(ALIAS_ACTIONS).join(', ')}". For instance, "-- action:${ + ALIAS_ACTIONS.remove + }"`, +); + +const testArgument = args.find(a => a.startsWith('test')) ?? ''; +const isTest = !!testArgument; + +const userReadline = readline.createInterface({ + input: process.stdin, + output: process.stdout, +}); + +const client = new Client({ node: esHost }); + +const catIndicesResponse = await client.cat.indices({ + index: `*_${releaseTag}`, + h: 'index', + format: 'json', +}); + +if (catIndicesResponse.statusCode !== 200) { + console.error('Received bad response', catIndicesResponse, ' Terminating.'); + process.exit(1); +} + +const releaseIndices = catIndicesResponse.body + .filter(cbKeepClinicalIndicesOnly) + .map(x => x.index) + .sort(); +assert(Array.isArray(releaseIndices) && releaseIndices.length > 0, 'No index found. Terminating'); + +const displayIndicesQuestion = () => + new Promise(resolve => { + userReadline.question( + `${releaseIndices.length} were found. Do you want to display its counts per entity y/n? > `, + answer => { + if (answer === 'y') { + const entityToStudies = releaseIndices.reduce((xs, x) => { + const [entity, studyIdWithRelease] = x.split('_centric_'); + const studyId = studyIdWithRelease.split('_re')[0]; + return { + ...xs, + [entity]: xs[entity] ? [...xs[entity], studyId] : [studyId], + }; + }, {}); + const entityCounts = Object.entries(entityToStudies).map(([k, v]) => ({ + entity: k, + study_counts: v.length, + })); + console.table(entityCounts); + } + resolve(); + }, + ); + }); +await displayIndicesQuestion(); + +const INDICES_PREFIXES = ['biospecimen_centric', 'participant_centric', 'study_centric', 'file_centric']; + +const allAliases = await client.cat.aliases({ + h: 'alias', + format: 'json', +}); + +//At this point, KF next uses the prefix next. +const isNextFormat = allAliases.body + .map(x => x.alias) + .some( + x => + x.startsWith('next_study_centric') || + x.startsWith('next_participant_centric') || + x.startsWith('next_biospecimen_centric') || + x.startsWith('next_variant_centric') || + x.startsWith('next_gene_centric') || + x.startsWith('next_file_centric'), + ); + +const actions = releaseIndices.reduce((xs, x) => { + const prefix = INDICES_PREFIXES.find(p => x.startsWith(p)); + if (!prefix) { + // Must never happen + return xs; + } + const alias = isNextFormat ? `next_${prefix}` : prefix; + return [ + ...xs, + { + [aliasAction]: { + index: x, + alias: isTest ? `${alias}_test` : alias, + }, + }, + ]; +}, []); +assert(actions.length === releaseIndices.length); + +const allIndexTargetsCorrectAlias = actions.every(a => { + const index = a[aliasAction].index; + const alias = a[aliasAction].alias; + return index.startsWith(alias.replace('next_', '')); +}); +assert(allIndexTargetsCorrectAlias); + +const displayActionQuestion = () => + new Promise(resolve => { + userReadline.question('Do want to see an actions sample that are about to be sent to ES y/n? > ', answer => { + console.log(answer); + if (answer === 'y') { + INDICES_PREFIXES.forEach(x => { + console.log( + x, + '=> ', + [...actions].find(a => a[aliasAction].index.includes(x)), + ); + }); + } + + resolve(); + }); + }); +await displayActionQuestion(); + +const displayProceedQuestion = () => + new Promise(resolve => { + userReadline.question('Execute actions y/n? > ', answer => resolve(answer === 'y')); + }); + +const mustExecuteActions = await displayProceedQuestion(); +if (!mustExecuteActions) { + userReadline.close(); + console.log('Terminating. No actions executed'); + process.exit(0); +} + +userReadline.close(); + +const updateAliasesResponse = await client.indices.updateAliases({ + body: { + actions, + }, +}); +console.log(updateAliasesResponse.body); diff --git a/admin/projectsConfig.mjs b/admin/projectsConfig.mjs index f48bae4..b1ad26a 100644 --- a/admin/projectsConfig.mjs +++ b/admin/projectsConfig.mjs @@ -1,11 +1,17 @@ -import config from './conf.json'; +import includeConf from './confInclude.json' assert { type: "json" }; +import kfConf from './confKfNext.json' assert { type: "json" }; -export const projectsConfig = () => - Object.entries(config).map(([key, value]) => { - const lambda = x => ({ ...x, projectId: key }); - return { - name: key, - indices: [...value.indices].map(lambda), - extendedMappingMutations: [...value.extendedMappingMutations].map(lambda), - }; - }); +export const projectsConfig = (projectName, env) => { + const envToConf = { + kf: kfConf, + include: includeConf, + }; + const lambda = x => ({ ...x, projectId: projectName }); + return [ + { + name: projectName, + indices: [...envToConf[env].indices].map(lambda), + extendedMappingMutations: [...envToConf[env].extendedMappingMutations].map(lambda), + } + ] +}; diff --git a/admin/releaseStatsUtils.mjs b/admin/releaseStatsUtils.mjs new file mode 100644 index 0000000..ed901f3 --- /dev/null +++ b/admin/releaseStatsUtils.mjs @@ -0,0 +1,131 @@ +export const ENTITIES = { + study_centric: 'study_centric', + participant_centric: 'participant_centric', + file_centric: 'file_centric', + biospecimen_centric: 'biospecimen_centric', +}; + +export const getGlobalClinicalStats = async (client, re) => { + const entitiesOrder = [ + ENTITIES.study_centric, + ENTITIES.participant_centric, + ENTITIES.file_centric, + ENTITIES.biospecimen_centric, + ]; + const mSearchesGlobalResponse = await client.msearch({ + body: [ + { index: `${entitiesOrder[0]}*${re}*` }, + { query: { match_all: {} }, size: 0, track_total_hits: true }, + { index: `${entitiesOrder[1]}*${re}*` }, + { query: { match_all: {} }, size: 0, track_total_hits: true }, + { index: `${entitiesOrder[2]}*${re}*` }, + { query: { match_all: {} }, size: 0, track_total_hits: true }, + { index: `${entitiesOrder[3]}*${re}*` }, + { query: { match_all: {} }, size: 0, track_total_hits: true }, + ], + }); + + const responses = mSearchesGlobalResponse?.body?.responses || []; + if (!responses.every(r => r.status === 200)) { + return ['got problematic statuses while doing a multiple search', undefined]; + } + return [ + undefined, + (responses || []).reduce( + (xs, x, index) => ({ + ...xs, + [entitiesOrder[index]]: { total: x.hits.total.value, release: re }, + }), + {}, + ), + ]; +}; + +export const studiesStats = async (client, re, indices, studyToId) => { + const studies = [...new Set(indices.map(x => x.index.split('centric_')[1]))]; + + const rAllCounts = await client.msearch({ + body: studies + .sort() + .map(x => [ + { index: `${ENTITIES.study_centric}_${x}` }, + { _source: '', query: { match_all: {} }, size: 1, track_total_hits: true }, + { index: `${ENTITIES.participant_centric}_${x}` }, + { _source: '', query: { match_all: {} }, size: 1, track_total_hits: true }, + { index: `${ENTITIES.file_centric}_${x}` }, + { _source: '', query: { match_all: {} }, size: 1, track_total_hits: true }, + { index: `${ENTITIES.biospecimen_centric}_${x}` }, + { _source: '', query: { match_all: {} }, size: 1, track_total_hits: true }, + ]) + .flat(), + }); + + // 404: an index that does not exist. For instance, a given study with no files. + const responses = rAllCounts?.body?.responses || []; + if (responses.some(r => ![200, 404].includes(r.status))) { + return ['got unsupported status(es) while doing a multiple search for stats', undefined]; + } + + const allCounts = responses.reduce((xs, x) => { + const is404 = x.status === 404; + const indexName = is404 ? x.error.index : x.hits.hits[0]._index; + const entity = `${indexName.split('centric_')[0]}centric`; + const studyId = indexName.replace(`_${re}`, '').split('centric_')[1]; + return { + ...xs, + [studyId]: { + ...(xs[studyId] || {}), + [entity]: x?.hits?.total?.value || 'N/A', + release: re, + code: studyToId[studyId], + }, + }; + }, {}); + return [undefined, allCounts]; +}; + +export const clinicalIndexStems = ['file', 'participant', 'study', 'biospecimen']; +export const isClinicalIndex = index => !!index && clinicalIndexStems.some(x => index.startsWith(x)); + +export const studyIdToStudyCode = async (client, re) => { + const allStudiesSearchResponse = await client.search({ + index: `${ENTITIES.study_centric}*${re}*`, + body: { + _source: ['study_id', 'study_code'], + size: 1000, + }, + }); + + const allStudiesHits = allStudiesSearchResponse?.body?.hits?.hits || []; + if (allStudiesSearchResponse.statusCode !== 200 || allStudiesHits.length === 0) { + return ['Studies are expected but did not received any', undefined]; + } + return [ + undefined, + allStudiesHits.reduce((xs, x) => { + const id = x._source.study_id.toLowerCase(); + const code = x._source.study_code; + return { + ...xs, + [id]: code, + }; + }, {}), + ]; +}; + +export const getAllCountsPerStudy = async (client, re, studyDict) => { + const catIndicesResponse = await client.cat.indices({ + index: `*_${re}`, + h: 'index', + format: 'json', + }); + if (catIndicesResponse.statusCode !== 200) { + return ['Could not retrieve all indices correctly', undefined]; + } + const allIndices = catIndicesResponse.body.filter(x => isClinicalIndex(x.index)); + if (allIndices.length === 0) { + return [`No found data for release=${re}`, undefined]; + } + + return await studiesStats(client, re, allIndices, studyDict); +}; diff --git a/admin/run.mjs b/admin/run.mjs index 1ad2240..fbf0dd2 100644 --- a/admin/run.mjs +++ b/admin/run.mjs @@ -1,12 +1,16 @@ +// docker run -u node -it --rm --network host -v ${PWD}:/code --workdir /code node:20-alpine3.18 sh +// examples: npm run admin-project p:include e:include test OR npm run admin-project p:next_prd (will default to kf) +//kf-api-arranger/node_modules/@arranger/mapping-utils/dist/extendMapping.js change rangeStep: ['double', 'float', 'half_float', 'scaled_float'].includes(type) ? 0.01 : 1 to rangeStep: 1.0 /* eslint-disable no-console */ -import 'regenerator-runtime/runtime'; +import 'regenerator-runtime/runtime.js'; -import EsInstance from '../dist/src/ElasticSearchClientInstance'; -import { countNOfDocs, createIndexIfNeeded } from '../dist/src/esUtils'; +import EsInstance from '../dist/src/ElasticSearchClientInstance.js'; +import { countNOfDocs, createIndexIfNeeded } from '../dist/src/esUtils.js'; import { ArrangerApi } from './arrangerApi.mjs'; import { projectsConfig } from './projectsConfig.mjs'; import { esHost } from '../dist/src/env.js'; +import { clinicalIndexStems, isClinicalIndex } from './releaseStatsUtils.mjs'; const hasProjectArrangerMetadataIndex = async (esClient, projectName) => { const r = await esClient.indices.exists({ @@ -28,22 +32,94 @@ const sameIndices = (xs, ys) => { return xs.length === ys.length && xs.every(x => s.has(x)); }; +const ENV = { + kf: 'kf', + include: 'include', +}; + +const args = process.argv.slice(2); + +//de-hardcode when possible +const SUPPORTED_PROJECT_NAMES = ['next_prd', 'next_qa', 'include', 'test']; +const projectArg = args.find(a => a.startsWith('p:'))?.split(':')[1]; +if (!projectArg || !SUPPORTED_PROJECT_NAMES.some(sp => sp === projectArg)) { + console.warn( + `admin-project-script - You must input a supported arranger project name. Got "${projectArg}" where supported values are: "${SUPPORTED_PROJECT_NAMES.join( + ', ', + )}"`, + ); + process.exit(1); +} + +const envArg = args.find(a => a.startsWith('e:')) ?? ''; +let envVal = ENV.kf; +if (envArg) { + const value = envArg.split(':')[1].toLocaleLowerCase(); + if (Object.values(ENV).includes(value)) { + envVal = ENV[value]; + } else { + console.warn( + `admin-project-script - Unsupported project "${value}". Supported projects are: "${Object.values(ENV).join( + ', ', + )}"`, + ); + } +} + //===== Start =====// console.info(`admin-project-script - Starting script`); +console.info(`admin-project-script - Project value is=${envVal}`); + +console.debug(`admin-project-script - Reaching to ElasticSearch at ${esHost}`); +const client = await EsInstance.default.getInstance(); +const isTest = args.some(a => a === 'test'); +const appendTestIfNeeded = x => (isTest && isClinicalIndex(x) ? `${x}_test` : x); +if (isTest) { + const allAliases = await client.cat.aliases({ + h: 'alias', + format: 'json', + }); + const clinicalTestAliases = allAliases.body + .filter(x => isClinicalIndex(x.alias) && x.alias.endsWith('_test')) + .map(x => x.alias); + if (!clinicalTestAliases || !clinicalIndexStems.every(s => clinicalTestAliases.some(x => x.includes(s)))) { + console.debug( + `admin-project-script - Terminating. When creating a test, all clinical entities must be aliased with _test suffix`, + ); + console.debug(`admin-project-script - received test aliases: `); + console.debug(clinicalTestAliases); + process.exit(1); + } +} //values are hardcoded for now, but as soon as possible, we should use env var from env.ts -const projectIndices = - [ - 'migration_test_participant_centric', - 'migration_test_study_centric', - 'migration_test_biospecimen_centric', - 'migration_test_file_centric', - 'variant_centric', - 'gene_centric', - 'members-public', - ] - ?.filter(p => !!p) - ?.map(p => p?.trim()) ?? []; +const kfNext = [ + 'next_participant_centric', + 'next_study_centric', + 'next_biospecimen_centric', + 'next_file_centric', + 'next_variant_centric', + 'next_gene_centric', + 'members-public', +].map(x => (isTest && isClinicalIndex(x) ? appendTestIfNeeded(x) : x)); + +const include = [ + 'participant_centric', + 'study_centric', + 'biospecimen_centric', + 'file_centric', + 'variant_centric', + 'gene_centric', +].map(x => (isTest && isClinicalIndex(x) ? appendTestIfNeeded(x) : x)); + +const envToIndicesPrefixes = { + kf: kfNext, + include: include, +}; + +const indicesPrefixes = envToIndicesPrefixes[envVal]; + +const projectIndices = indicesPrefixes?.filter(p => !!p)?.map(p => p?.trim()) ?? []; if (projectIndices.length === 0) { console.warn( @@ -52,13 +128,18 @@ if (projectIndices.length === 0) { process.exit(0); } -const allProjectsConf = projectsConfig(); +const projectName = projectArg; -const projectsConf = allProjectsConf.filter(p => { - const indicesInConf = p.indices.map(i => i.esIndex); - // indices in conf are the same as target indices from env vars? - return sameIndices(indicesInConf, projectIndices); -}); +//TODO: refactor to tolerate only 1 project per conf +const allProjectsConf = projectsConfig(projectName, envVal); + +const projectsConf = allProjectsConf + .map(x => ({ ...x, indices: x.indices.map(i => ({ ...i, esIndex: appendTestIfNeeded(i.esIndex) })) })) + .filter(p => { + const indicesInConf = p.indices.map(i => i.esIndex); + // indices in conf are the same as target indices from env vars? + return sameIndices(indicesInConf, projectIndices); + }); if (projectsConf.length === 0) { console.info( @@ -74,9 +155,6 @@ if (projectsConf.length === 0) { const projectConf = projectsConf[0]; -console.debug(`admin-project-script - Reaching to ElasticSearch at ${esHost}`); -const client = await EsInstance.default.getInstance(); - const addArrangerProjectWithClient = ArrangerApi.addArrangerProject(client); const hasCreatedIndex = await createIndexIfNeeded(client, ArrangerApi.constants.ARRANGER_PROJECT_INDEX); @@ -86,8 +164,6 @@ if (hasCreatedIndex) { ); } -const projectName = projectConf.name; - const resolveSanityConditions = async () => await Promise.all([ hasProjectArrangerMetadataIndex(client, projectName), @@ -102,9 +178,8 @@ if (creationConditions.every(b => !b)) { const addResp = await addArrangerProjectWithClient(projectName); console.debug(`admin-project-script - (Project addition) received this response from arranger api: `, addResp); console.debug( - `admin-project-script - Creating these new graphql fields: ${projectConf.indices - .map(i => `'${i.graphqlField}' from es index '${i.esIndex}'`) - .join(', ')}`, + `admin-project-script - Creating these new graphql fields: `, + projectConf.indices.map(i => `${i.graphqlField}' from es index '${i.esIndex}`), ); await ArrangerApi.createNewIndices(client, projectConf.indices); } else if (creationConditions.some(b => b !== creationConditions[0])) { @@ -125,7 +200,9 @@ if (updateConditions.every(b => b)) { ); if (nOfDocsInProjectMetadata === projectConf.indices.length) { console.debug(`admin-project-script - Applying extended mapping mutations.`); + console.time("fixExtendedMapping") await ArrangerApi.fixExtendedMapping(client, projectConf.extendedMappingMutations); + console.timeEnd("fixExtendedMapping") } } diff --git a/admin/sortConf.mjs b/admin/sortConf.mjs new file mode 100644 index 0000000..811db56 --- /dev/null +++ b/admin/sortConf.mjs @@ -0,0 +1,62 @@ +import fs from 'node:fs'; +import assert from 'node:assert/strict'; + +const sortConf = conf => { + const indices = conf.indices; + const sIndices = conf.indices + .map(x => x.graphqlField) + .sort() + .map(x => ({ ...indices.find(y => y.graphqlField === x) })); + + const mutations = conf.extendedMappingMutations; + const sGraphqlFields = [...new Set(mutations.map(x => x.graphqlField))].sort(); + const sMutations = sGraphqlFields.reduce((xs, x) => { + const elWithSameGqlField = mutations + .filter(m => m.graphqlField === x) + .map(x => x.field) + .sort() + .map(x => ({ ...mutations.find(m => m.field === x) })); + return [...xs, ...elWithSameGqlField]; + }, []); + + return { + indices: sIndices, + extendedMappingMutations: sMutations, + }; +}; + +const processConf = path => { + const guessProject = (() => { + if (path.toLocaleLowerCase().includes('include')) { + return 'Include'; + } + if (path.toLocaleLowerCase().includes('kfnext')) { + return 'Kids-First Next'; + } + return ''; + })(); + fs.readFile(path, 'utf8', (err, data) => { + if (err) { + console.error(err); + return; + } + console.info(`Reading ${guessProject} Conf...`); + const conf = { ...JSON.parse(data) }; + assert(Object.keys(conf).every(k => ['indices', 'extendedMappingMutations'].includes(k))); + const sConf = { ...sortConf(conf) }; + assert( + conf.indices.length === sConf.indices.length && + conf.extendedMappingMutations.length === sConf.extendedMappingMutations.length, + ); + fs.writeFile(path, JSON.stringify(sConf, null, 2), err => { + if (err) { + console.error(err); + } + console.info(`Writing Sorted ${guessProject} Conf...`); + }); + }); +}; + +processConf('admin/confKfNext.json'); +processConf('admin/confInclude.json'); + diff --git a/admin/suggestStepFnPayload.mjs b/admin/suggestStepFnPayload.mjs new file mode 100644 index 0000000..b9c966e --- /dev/null +++ b/admin/suggestStepFnPayload.mjs @@ -0,0 +1,107 @@ +import { Client } from '@elastic/elasticsearch'; +import { esHost } from '../dist/src/env.js'; +import { cbKeepClinicalIndicesOnly } from './utils.mjs'; +import assert from 'node:assert/strict'; + +const isInt = n => { + return !isNaN(parseInt(n, 10)) && isFinite(n); +}; + +const formatNow = () => { + //https://futurestud.io/tutorials/how-to-format-a-date-yyyy-mm-dd-in-javascript-or-node-js + const now = new Date(); + const year = now.getFullYear(); + const month = String(now.getMonth() + 1).padStart(2, '0'); + const day = String(now.getDate()).padStart(2, '0'); + return `${year}${month}${day}`; +}; + +const args = process.argv.slice(2); +const envArgument = args.find(x => x.startsWith('--env:')) ?? ''; +const env = (envArgument.split('--env:')[1] || 'qa').toLowerCase(); +assert(['qa', 'prd'].includes(env)); + +const client = new Client({ node: esHost }); + +const rArrProjects = await client.search({ + index: `arranger-projects`, +}); + +const allArrProjects = rArrProjects.body.hits.hits.map(x => x._id); + +const project = allArrProjects.includes('include') ? 'include' : 'kf'; +const isInclude = project === 'include'; + +const catIndicesResponse = await client.cat.indices({ + index: `*centric*`, + h: 'index,creation.date,creation.date.string', + format: 'json', +}); + +if (catIndicesResponse.statusCode !== 200) { + console.error('Received bad response', catIndicesResponse, ' Terminating.'); + process.exit(1); +} + +const clinicalIndices = catIndicesResponse.body.filter(cbKeepClinicalIndicesOnly); +assert(Array.isArray(clinicalIndices) && clinicalIndices.length > 0, 'No index found. Terminating'); + +const newReleaseWithoutAttempt = `re_${formatNow()}_`; + +const todayIndices = clinicalIndices.filter(x => x.index.includes(newReleaseWithoutAttempt)); + +const attemptGuessed = + todayIndices.length > 0 + ? Math.max( + ...todayIndices + .map(x => x.index.split(newReleaseWithoutAttempt)[1].replace('_kf', '')) + .filter(x => isInt(x)) + .map(x => parseInt(x, 10)), + ) + 1 + : 1; + +const rel = `${newReleaseWithoutAttempt}${attemptGuessed}`; + +const allStudiesSearchResponse = await client.search({ + index: isInclude ? `*study_centric` : 'next_study_centric', + body: { + _source: ['study_id', 'study_code'], + size: 1000, + }, +}); + +const allStudiesHits = (allStudiesSearchResponse?.body?.hits?.hits || []).sort(); + +const fhirUrls = { + ['kf-qa']: 'https://kf-api-fhir-service-upgrade-qa.kf-strides.org', + ['kf-prd']: 'https://kf-api-fhir-service-upgrade.kf-strides.org', + ['inc-qa']: 'https://include-api-fhir-service-upgrade-qa.includedcc.org', + ['inc-prd']: 'https://include-api-fhir-service-upgrade.includedcc.org', +}; + +if (project === 'include') { + const payloadInc = { + releaseId: rel, + studyIds: allStudiesHits.filter(x => !x._index.includes('kf')).map(x => x._source.study_id), + clusterSize: 'medium', + portalEtlName: `clin-${env}-inc-${rel}`, + fhirUrl: fhirUrls[`inc-${env}`], + runGenomicEtl: false, + verbose: 'false', + }; + console.log(JSON.stringify(payloadInc, null, 4)); + console.log('\n'); +} + +const addKfSuffixToRelIfInclude = () => `${rel}${isInclude ? '_kf' : ''}`; + +const payloadKf = { + releaseId: addKfSuffixToRelIfInclude(), + studyIds: allStudiesHits.filter(x => (isInclude ? x._index.includes('kf') : x)).map(x => x._source.study_id), + clusterSize: 'medium', + portalEtlName: `clin-${env}-${isInclude ? 'inc-kf' : 'kf'}-${addKfSuffixToRelIfInclude()}`, + fhirUrl: fhirUrls[`kf-${env}`], + runGenomicEtl: false, + verbose: 'false', +}; +console.log(JSON.stringify(payloadKf, null, 4)); diff --git a/admin/utils.mjs b/admin/utils.mjs new file mode 100644 index 0000000..08820c5 --- /dev/null +++ b/admin/utils.mjs @@ -0,0 +1,3 @@ +export const cbKeepClinicalIndicesOnly = x => + ['file', 'biospecimen', 'participant', 'study'].some(stem => x.index.includes(stem)); + diff --git a/docker-compose.yml b/docker-compose.yml index 1030fff..ad2b27a 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,21 +1,21 @@ version: "3.9" services: kf_arranger: - image: node:16.13-alpine - working_dir: /code + image: node:20-alpine3.18 + working_dir: /app volumes: - - .:/code - command: sh -c 'npm install && npm run build && npm start' + - .:/app + command: sh -c 'npm install && npm run cbs' profiles: - dev ports: - "5050:5050" kf_arranger_with_local_es: - image: node:16.13-alpine - working_dir: /code + image: node:20-alpine3.18 + working_dir: /app volumes: - - .:/code - command: sh -c 'npm install && npm run build && npm start' + - .:/app + command: sh -c 'npm install && npm run cbs' profiles: - dev_with_local_es ports: @@ -23,10 +23,10 @@ services: networks: - es-net kf_arranger_test: - image: node:16.13-alpine - working_dir: /code + image: node:20-alpine3.18 + working_dir: /app volumes: - - .:/code + - .:/app command: sh -c 'npm install && npm run test' profiles: - test diff --git a/include.next.deploy b/include.next.deploy new file mode 100644 index 0000000..5e571bf --- /dev/null +++ b/include.next.deploy @@ -0,0 +1,24 @@ +@Library(value="kids-first/aws-infra-jenkins-shared-libraries", changelog=false) _ +deploy { + architecture_type = "aws-ecs-service-type-1" + jenkinsfile_name = "include.next.deploy" + main_branch="2.0" + projectName = "arranger-next" + environments = "qa,prd" + docker_image_type = "alpine" + internal_app = "false" + create_default_iam_role = "0" + entrypoint_command = "node dist/src/index.js" + deploy_scripts_version = "master" + quick_deploy = "true" + external_config_repo = "false" + container_port = "443" + vcpu_container = "2048" + memory_container = "4096" + vcpu_task = "2048" + memory_task = "4096" + health_check_path = "/status" + dependencies = "ecr" + prd_cidr = "0.0.0.0/0" + add_cloudfront = "1" +} diff --git a/next.deploy b/next.deploy new file mode 100644 index 0000000..7c34bc6 --- /dev/null +++ b/next.deploy @@ -0,0 +1,24 @@ + +@Library(value="kids-first/aws-infra-jenkins-shared-libraries", changelog=false) _ +deploy { + architecture_type = "aws-ecs-service-type-1" + jenkinsfile_name = "next.deploy" + main_branch="2.0" + projectName = "kf-api-arranger-next" + environments = "qa,prd" + docker_image_type = "alpine" + internal_app = "false" + create_default_iam_role = "0" + entrypoint_command = "node dist/src/index.js" + deploy_scripts_version = "master" + quick_deploy = "true" + external_config_repo = "false" + container_port = "443" + vcpu_container = "2048" + memory_container = "4096" + vcpu_task = "2048" + memory_task = "4096" + health_check_path = "/status" + dependencies = "ecr" + prd_cidr = "0.0.0.0/0" +} diff --git a/package-lock.json b/package-lock.json index 746ea21..2f9302f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -13,19 +13,19 @@ "@arranger/middleware": "^2.16.0", "@arranger/server": "^2.16.1", "@awaitjs/express": "^0.8.0", + "@aws-sdk/client-sqs": "^3.438.0", "@elastic/elasticsearch": "^7.9.1", - "aws-sdk": "^2.1035.0", + "ajv": "^8.12.0", "cors": "2.8.5", "dotenv": "^10.0.0", "express": "^4.17.1", "filesize": "^3.6.1", "graphql-parse-resolve-info": "4.11.0", "http-status-codes": "^2.1.4", - "keycloak-connect": "^14.0.0", + "keycloak-connect": "^22.0.5", "lodash": "^4.17.21", "node-cache": "^5.1.2", "node-fetch": "^2.6.5", - "python-shell": "^3.0.0", "regenerator-runtime": "^0.13.9" }, "devDependencies": { @@ -47,7 +47,6 @@ "prettier": "^1.19.1", "supertest": 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See https://www.apollographql.com/docs/apollo-server/previous-versions/ for more details.", + "dependencies": { + "apollo-server-caching": "^0.7.0", + "apollo-server-env": "^3.2.0" + }, + "engines": { + "node": ">=6" + } + }, + "node_modules/apollo-graphql": { + "version": "0.9.5", "resolved": "https://registry.npmjs.org/apollo-graphql/-/apollo-graphql-0.9.5.tgz", "integrity": "sha512-RGt5k2JeBqrmnwRM0VOgWFiGKlGJMfmiif/4JvdaEqhMJ+xqe/9cfDYzXfn33ke2eWixsAbjEbRfy8XbaN9nTw==", "dependencies": { @@ -2555,12 +4018,13 @@ } }, "node_modules/apollo-server": { - "version": "2.25.3", - "resolved": "https://registry.npmjs.org/apollo-server/-/apollo-server-2.25.3.tgz", - "integrity": "sha512-+eUY2//DLkU7RkJLn6CTl1P89/ZMHuUQnWqv8La2iJ2hLT7Me+nMx+hgHl3LqlT/qDstQ8qA45T85FuCayplmQ==", + "version": "2.26.2", + "resolved": "https://registry.npmjs.org/apollo-server/-/apollo-server-2.26.2.tgz", + "integrity": "sha512-VgEvOSqcGgMofUVji97nsHnUCXPaMg9efBbM3xI/HbTn3baKQHoRjqfnR4xZeEd9DkhgxwrmSZHBjWCjGOYExg==", + "deprecated": "The `apollo-server` package is part of Apollo Server v2 and v3, which are now deprecated (end-of-life October 22nd 2023 and October 22nd 2024, respectively). This package's functionality is now found in the `@apollo/server` package. See https://www.apollographql.com/docs/apollo-server/previous-versions/ for more details.", "dependencies": { - "apollo-server-core": "^2.25.3", - "apollo-server-express": "^2.25.3", + "apollo-server-core": "^2.26.2", + "apollo-server-express": "^2.26.2", "express": "^4.0.0", "graphql-subscriptions": "^1.0.0", "graphql-tools": "^4.0.8", @@ -2582,28 +4046,29 @@ } }, "node_modules/apollo-server-core": { - "version": "2.25.3", - "resolved": "https://registry.npmjs.org/apollo-server-core/-/apollo-server-core-2.25.3.tgz", - "integrity": "sha512-Midow3uZoJ9TjFNeCNSiWElTVZlvmB7G7tG6PPoxIR9Px90/v16Q6EzunDIO0rTJHRC3+yCwZkwtf8w2AcP0sA==", + "version": "2.26.2", + "resolved": "https://registry.npmjs.org/apollo-server-core/-/apollo-server-core-2.26.2.tgz", + "integrity": "sha512-r8jOhf1jElaxsNsALFMy/MLiJCqSa1ZiwxkerVYbsEkyWrpD1Khy0extDkTBrfa6uK8CatX7xK9U413bYNhJFA==", + "deprecated": "The `apollo-server-core` package is part of Apollo Server v2 and v3, which are now deprecated (end-of-life October 22nd 2023 and October 22nd 2024, respectively). This package's functionality is now found in the `@apollo/server` package. See https://www.apollographql.com/docs/apollo-server/previous-versions/ for more details.", "dependencies": { "@apollographql/apollo-tools": "^0.5.0", "@apollographql/graphql-playground-html": "1.6.27", - "@apollographql/graphql-upload-8-fork": "^8.1.3", + "@apollographql/graphql-upload-8-fork": "^8.1.4", "@josephg/resolvable": "^1.0.0", "@types/ws": "^7.0.0", - "apollo-cache-control": "^0.14.0", - "apollo-datasource": "^0.9.0", + "apollo-cache-control": "^0.15.0", + "apollo-datasource": "^0.10.0", "apollo-graphql": "^0.9.0", "apollo-reporting-protobuf": "^0.8.0", "apollo-server-caching": "^0.7.0", - "apollo-server-env": "^3.1.0", + "apollo-server-env": "^3.2.0", "apollo-server-errors": "^2.5.0", - "apollo-server-plugin-base": "^0.13.0", - "apollo-server-types": "^0.9.0", - "apollo-tracing": "^0.15.0", + "apollo-server-plugin-base": "^0.14.0", + "apollo-server-types": "^0.10.0", + "apollo-tracing": "^0.16.0", "async-retry": "^1.2.1", "fast-json-stable-stringify": "^2.0.0", - "graphql-extensions": "^0.15.0", + "graphql-extensions": "^0.16.0", "graphql-tag": "^2.11.0", "graphql-tools": "^4.0.8", "loglevel": "^1.6.7", @@ -2628,9 +4093,10 @@ } }, "node_modules/apollo-server-env": { - "version": "3.1.0", - "resolved": "https://registry.npmjs.org/apollo-server-env/-/apollo-server-env-3.1.0.tgz", - "integrity": "sha512-iGdZgEOAuVop3vb0F2J3+kaBVi4caMoxefHosxmgzAbbSpvWehB8Y1QiSyyMeouYC38XNVk5wnZl+jdGSsWsIQ==", + "version": "3.2.0", + "resolved": "https://registry.npmjs.org/apollo-server-env/-/apollo-server-env-3.2.0.tgz", + "integrity": "sha512-V+kO5e6vUo2JwqV1/Ng71ZE3J6x1hCOC+nID2/++bCYl0/fPY9iLChbBNSgN/uoFcjhgmBchOv+m4o0Nie/TFQ==", + "deprecated": "The `apollo-server-env` package is part of Apollo Server v2 and v3, which are now deprecated (end-of-life October 22nd 2023 and October 22nd 2024, respectively). This package's functionality is now found in the `@apollo/utils.fetcher` package. See https://www.apollographql.com/docs/apollo-server/previous-versions/ for more details.", "dependencies": { "node-fetch": "^2.6.1", "util.promisify": "^1.0.0" @@ -2651,9 +4117,10 @@ } }, "node_modules/apollo-server-express": { - "version": "2.25.3", - "resolved": "https://registry.npmjs.org/apollo-server-express/-/apollo-server-express-2.25.3.tgz", - "integrity": "sha512-tTFYn0oKH2qqLwVj7Ez2+MiKleXACODiGh5IxsB7VuYCPMAi9Yl8iUSlwTjQUvgCWfReZjnf0vFL2k5YhDlrtQ==", + "version": "2.26.2", + "resolved": "https://registry.npmjs.org/apollo-server-express/-/apollo-server-express-2.26.2.tgz", + "integrity": "sha512-8KaDwc6/DMK6e5KmP4AGH/NNY7OhEOFxusz3JZ/Du08a+PN8c/JmaEAwQ0aTNpySb5PWpv6xeXRPPwNfaPK9IQ==", + "deprecated": "The `apollo-server-express` package is part of Apollo Server v2 and v3, which are now deprecated (end-of-life October 22nd 2023 and October 22nd 2024, respectively). This package's functionality is now found in the `@apollo/server` package. See https://www.apollographql.com/docs/apollo-server/previous-versions/ for more details.", "dependencies": { "@apollographql/graphql-playground-html": "1.6.27", "@types/accepts": "^1.3.5", @@ -2662,8 +4129,8 @@ "@types/express": "^4.17.12", "@types/express-serve-static-core": "^4.17.21", "accepts": "^1.3.5", - "apollo-server-core": "^2.25.3", - "apollo-server-types": "^0.9.0", + "apollo-server-core": "^2.26.2", + "apollo-server-types": "^0.10.0", "body-parser": "^1.18.3", "cors": "^2.8.5", "express": "^4.17.1", @@ -2686,11 +4153,12 @@ "integrity": "sha512-C7srjHiVG3Ey1nR6d511dtDkCEjxuN9W1HWAEjGq8kpcwmNM6JJkpC0xvabM7BXTG2wDq8Eu33iH9aQKa7IvLQ==" }, "node_modules/apollo-server-plugin-base": { - "version": "0.13.0", - "resolved": "https://registry.npmjs.org/apollo-server-plugin-base/-/apollo-server-plugin-base-0.13.0.tgz", - "integrity": "sha512-L3TMmq2YE6BU6I4Tmgygmd0W55L+6XfD9137k+cWEBFu50vRY4Re+d+fL5WuPkk5xSPKd/PIaqzidu5V/zz8Kg==", + "version": "0.14.0", + "resolved": "https://registry.npmjs.org/apollo-server-plugin-base/-/apollo-server-plugin-base-0.14.0.tgz", + "integrity": "sha512-nTNSFuBhZURGjtWptdVqwemYUOdsvABj/GSKzeNvepiEubiv4N0rt4Gvy1inHDiMbo98wQTdF/7XohNcB9A77g==", + "deprecated": "The `apollo-server-plugin-base` package is part of Apollo Server v2 and v3, which are now deprecated (end-of-life October 22nd 2023 and October 22nd 2024, respectively). This package's functionality is now found in the `@apollo/server` package. See https://www.apollographql.com/docs/apollo-server/previous-versions/ for more details.", "dependencies": { - "apollo-server-types": "^0.9.0" + "apollo-server-types": "^0.10.0" }, "engines": { "node": ">=6" @@ -2700,13 +4168,14 @@ } }, "node_modules/apollo-server-types": { - "version": "0.9.0", - "resolved": "https://registry.npmjs.org/apollo-server-types/-/apollo-server-types-0.9.0.tgz", - "integrity": "sha512-qk9tg4Imwpk732JJHBkhW0jzfG0nFsLqK2DY6UhvJf7jLnRePYsPxWfPiNkxni27pLE2tiNlCwoDFSeWqpZyBg==", + "version": "0.10.0", + "resolved": "https://registry.npmjs.org/apollo-server-types/-/apollo-server-types-0.10.0.tgz", + "integrity": "sha512-LsB3epw1X3Co/HGiKHCGtzWG35J59gG8Ypx0p22+wgdM9AVDm1ylsNGZy+osNIVJc1lUJf3nF5kZ90vA866K/w==", + "deprecated": "The `apollo-server-types` package is part of Apollo Server v2 and v3, which are now deprecated (end-of-life October 22nd 2023 and October 22nd 2024, respectively). This package's functionality is now found in the `@apollo/server` package. See https://www.apollographql.com/docs/apollo-server/previous-versions/ for more details.", "dependencies": { "apollo-reporting-protobuf": "^0.8.0", "apollo-server-caching": "^0.7.0", - "apollo-server-env": "^3.1.0" + "apollo-server-env": "^3.2.0" }, "engines": { "node": ">=6" @@ -2716,13 +4185,13 @@ } }, "node_modules/apollo-tracing": { - "version": "0.15.0", - "resolved": "https://registry.npmjs.org/apollo-tracing/-/apollo-tracing-0.15.0.tgz", - "integrity": "sha512-UP0fztFvaZPHDhIB/J+qGuy6hWO4If069MGC98qVs0I8FICIGu4/8ykpX3X3K6RtaQ56EDAWKykCxFv4ScxMeA==", + "version": "0.16.0", + "resolved": "https://registry.npmjs.org/apollo-tracing/-/apollo-tracing-0.16.0.tgz", + "integrity": "sha512-Oy8kTggB+fJ/hHXwHyMpuTl5KW7u1XetKFDErZVOobUKc2zjc/NgWiC/s7SGYZCgfLodBjvwfa6rMcvLkz7c0w==", "deprecated": "The `apollo-tracing` package is no longer part of Apollo Server 3. 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"has-symbols": "^1.0.1", - "object.getownpropertydescriptors": "^2.1.1" + "has-proto": "^1.0.1", + "has-symbols": "^1.0.3", + "object.getownpropertydescriptors": "^2.1.6", + "safe-array-concat": "^1.0.0" } }, "utils-merge": { @@ -18635,6 +22313,18 @@ "is-symbol": "^1.0.3" } }, + "which-typed-array": { + "version": "1.1.13", + "resolved": "https://registry.npmjs.org/which-typed-array/-/which-typed-array-1.1.13.tgz", + "integrity": "sha512-P5Nra0qjSncduVPEAr7xhoF5guty49ArDTwzJ/yNuPIbZppyRxFQsRCWrocxIY+CnMVG+qfbU2FmDKyvSGClow==", + "requires": { + "available-typed-arrays": "^1.0.5", + "call-bind": "^1.0.4", + "for-each": "^0.3.3", + "gopd": "^1.0.1", + "has-tostringtag": "^1.0.0" + } + }, "winston": { "version": "2.4.5", "resolved": "https://registry.npmjs.org/winston/-/winston-2.4.5.tgz", @@ -18649,9 +22339,9 @@ } }, "word-wrap": { - "version": "1.2.3", - "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.3.tgz", - "integrity": 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"resolved": "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz", @@ -18799,7 +22475,9 @@ "version": "3.1.1", "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz", "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==", - "dev": true + "dev": true, + "optional": true, + "peer": true }, "zen-observable": { "version": "0.8.15", diff --git a/package.json b/package.json index b2d9239..59c2405 100644 --- a/package.json +++ b/package.json @@ -7,12 +7,13 @@ "start": "node ./dist/src/index.js", "test": "jest", "test:watch": "jest --watch", - "clean": "rm -rf ./dist/* ", - "build": "npm run clean; tsc ", + "cleanAndBuild": "rm -rf ./dist/* && tsc --build", "lint": "eslint . --ext .ts", "lint:fix": "eslint . --ext .ts --fix", - "buildAndRun": "npm run build; npm start", - "admin-project": "node --experimental-modules=node --es-module-specifier-resolution=node admin/run.mjs" + "cbs": "npm run cleanAndBuild && npm start", + "admin-project": "node --experimental-modules=node --es-module-specifier-resolution=node admin/run.mjs", + "post-re-alias-helper": "node --experimental-modules=node --es-module-specifier-resolution=node admin/postReleaseIndicesToAliasesHelper.mjs", + "delete-clinical-indices-helper": "node --experimental-modules=node --es-module-specifier-resolution=node admin/deleteClinicalIndicesFromRelease.mjs" }, "repository": { "type": "git", @@ -38,19 +39,19 @@ "@arranger/middleware": "^2.16.0", "@arranger/server": "^2.16.1", "@awaitjs/express": "^0.8.0", + "@aws-sdk/client-sqs": "^3.438.0", "@elastic/elasticsearch": "^7.9.1", - "aws-sdk": "^2.1035.0", + "ajv": "^8.12.0", "cors": "2.8.5", "dotenv": "^10.0.0", "express": "^4.17.1", "filesize": "^3.6.1", "graphql-parse-resolve-info": "4.11.0", "http-status-codes": "^2.1.4", - "keycloak-connect": "^14.0.0", + "keycloak-connect": "^22.0.5", "lodash": "^4.17.21", "node-cache": "^5.1.2", "node-fetch": "^2.6.5", - "python-shell": "^3.0.0", "regenerator-runtime": "^0.13.9" }, "devDependencies": { @@ -72,7 +73,6 @@ "prettier": "^1.19.1", "supertest": "^6.1.2", "ts-jest": "^27.0.4", - "ts-node": "^10.1.0", "typescript": "^4.3.5" } } diff --git a/resource/py/requirements.txt b/resource/py/requirements.txt deleted file mode 100644 index 9b8d9a7..0000000 --- a/resource/py/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -SurvivalPy==1.0.2 \ No newline at end of file diff --git a/resource/py/survival.py b/resource/py/survival.py deleted file mode 100644 index 741a2b6..0000000 --- a/resource/py/survival.py +++ /dev/null @@ -1,34 +0,0 @@ -from survivalpy.survival import Analyzer -from survivalpy.survival import Datum - -import json -import sys - -def printjson(message): - print(json.dumps({"message":message})) - -data = [] - -try: - for line in sys.stdin: - # Read the participants line by line (ignoring newline character) - participant=json.loads(line[:-1]) - - # Build them into a list of Datums (data? :shrug: ) - time = participant.get('time') - censored = participant.get('censored') - kfid = participant.get('id') - - datum = Datum(time, censored, {'id':kfid}) - - data.append(datum) - - # Do the computations! - analyzer = Analyzer(data) - results = analyzer.compute() - json_results = list(map(lambda interval: interval.to_json_dict(), results)) - - # Spit out the results - printjson(json_results) -except Exception as e: - printjson({'error':str(e)}) diff --git a/src/ElasticSearchClientInstance.ts b/src/ElasticSearchClientInstance.ts index 35f2e23..b8f51bb 100644 --- a/src/ElasticSearchClientInstance.ts +++ b/src/ElasticSearchClientInstance.ts @@ -8,10 +8,10 @@ class EsInstance { constructor() { if (!this.instance) { if (esUser && esPass) { - console.log('Using basic auth'); + console.debug('Using basic auth'); this.instance = new Client({ node: esHost, auth: { username: esUser, password: esPass } }); } else { - console.log('Not using basic auth'); + console.debug('Not using basic auth'); this.instance = new Client({ node: esHost }); } } diff --git a/src/SQS/sendEvent.ts b/src/SQS/sendEvent.ts index 0180586..2f7b7a3 100644 --- a/src/SQS/sendEvent.ts +++ b/src/SQS/sendEvent.ts @@ -1,13 +1,18 @@ -import AWS from 'aws-sdk'; -import { PromiseResult } from 'aws-sdk/lib/request'; +import { SendMessageCommand, SendMessageCommandOutput, SQSClient } from '@aws-sdk/client-sqs'; import { sqsQueueUrl } from '../env'; import { EventCreate, EventDelete, EventUpdate } from './eventTypes'; export const sendSetInSQSQueue = async ( - sqs: AWS.SQS, + sqs: SQSClient, data: EventCreate | EventUpdate | EventDelete, -): Promise> => { - const params = { MessageBody: JSON.stringify(data), QueueUrl: sqsQueueUrl }; - return sqs.sendMessage(params).promise(); +): Promise => { + const command = new SendMessageCommand({ + QueueUrl: sqsQueueUrl, + DelaySeconds: 10, + MessageAttributes: {}, + MessageBody: JSON.stringify(data), + }); + const response = await sqs.send(command); + return response; }; diff --git a/src/app.test.ts b/src/app.test.ts index 9cb2930..0c615b1 100644 --- a/src/app.test.ts +++ b/src/app.test.ts @@ -1,10 +1,11 @@ -import AWS from 'aws-sdk'; +import { SQSClient } from '@aws-sdk/client-sqs'; import { Express } from 'express'; import Keycloak from 'keycloak-connect'; import request from 'supertest'; -import { getToken, publicKey } from '../test/authTestUtils'; +import { fakeKeycloakClient, fakeKeycloakRealm, fakeKeycloakUrl, getToken, publicKey } from '../test/authTestUtils'; import buildApp from './app'; +import { ArrangerProject } from './arrangerUtils'; import { searchAllSources } from './endpoints/searchByIds/searchAllSources'; import { SetNotFoundError } from './endpoints/sets/setError'; import { @@ -16,14 +17,10 @@ import { updateSetTag, } from './endpoints/sets/setsFeature'; import { Set, UpdateSetContentBody, UpdateSetTagBody } from './endpoints/sets/setsTypes'; -import { getStatistics, Statistics } from './endpoints/statistics'; -import { calculateSurvivalForSqonResult } from './endpoints/survival'; -import { keycloakClient, keycloakRealm, keycloakURL } from './env'; +import { getStatistics, getStudiesStatistics, Statistics } from './endpoints/statistics'; import { RiffError } from './riff/riffError'; -import { ArrangerProject } from './sqon/searchSqon'; jest.mock('./endpoints/sets/setsFeature'); -jest.mock('./endpoints/survival'); jest.mock('./endpoints/statistics'); jest.mock('./endpoints/searchByIds/searchAllSources'); @@ -34,15 +31,15 @@ describe('Express app (without Arranger)', () => { const getProject = (_s: string) => ({} as ArrangerProject); beforeEach(() => { - const sqs = new AWS.SQS({ apiVersion: '2012-11-05' }); + const sqs = new SQSClient({}); const publicKeyToVerify = publicKey; keycloakFakeConfig = { - realm: keycloakRealm, + realm: fakeKeycloakRealm, 'confidential-port': 0, 'bearer-only': true, - 'auth-server-url': keycloakURL, + 'auth-server-url': fakeKeycloakUrl, 'ssl-required': 'external', - resource: keycloakClient, + resource: fakeKeycloakClient, 'realm-public-key': publicKeyToVerify, // For test purpose, we use public key to validate token. }; const keycloak = new Keycloak({}, keycloakFakeConfig); @@ -93,6 +90,79 @@ describe('Express app (without Arranger)', () => { samples: 6111, families: 1291, participants: 4330, + variants: 1312312, + genomes: 13575, + transcriptomes: 5454, + sex: { + male: 4387, + female: 4302, + unknown: 4, + other: 3, + }, + downSyndromeStatus: { + T21: 7266, + D21: 1430, + }, + race: { + White: 7029, + 'Black or African American': 618, + Unknown: 408, + Asian: 269, + NoInformation: 131, + other: 66, + 'asked but unknown': 58, + 'More than one race': 37, + unknown: 35, + 'American Indian or Alaska Native': 34, + 'Native Hawaiian or Other Pacific Islander': 8, + 'not available': 3, + }, + diagnosis: [ + { + mondo_id: 'speech disorder (MONDO:0004730)', + count: 2277, + }, + { + mondo_id: 'hearing loss disorder (MONDO:0005365)', + count: 1978, + }, + { + mondo_id: 'intellectual disability (MONDO:0001071)', + count: 1970, + }, + { + mondo_id: 'hypothyroidism (MONDO:0005420)', + count: 1734, + }, + { + mondo_id: 'sleep apnea syndrome (MONDO:0005296)', + count: 1360, + }, + { + mondo_id: 'atrial septal defect (MONDO:0006664)', + count: 1243, + }, + { + mondo_id: 'ventricular septal defect (MONDO:0002070)', + count: 1105, + }, + { + mondo_id: 'specific language impairment (MONDO:0000724)', + count: 1068, + }, + { + mondo_id: 'congenital heart disease (MONDO:0005453)', + count: 991, + }, + { + mondo_id: 'gastroesophageal reflux disease (MONDO:0007186)', + count: 867, + }, + ], + members: { + totalCount: 12343, + publicCount: 345, + }, }; (getStatistics as jest.Mock).mockImplementation(() => expectedStats); @@ -115,6 +185,62 @@ describe('Express app (without Arranger)', () => { }); }); + describe('GET /statistics/public', () => { + beforeEach(() => { + (getStudiesStatistics as jest.Mock).mockReset(); + }); + + it('should return 200 if no error occurs', async () => { + const expectedPublicStats = { + studies: [ + { participant_count: 334, study_code: 'KF-EATF' }, + { + participant_count: 183, + study_code: 'KF-DSD', + }, + { participant_count: 759, study_code: 'KF-OFCAA' }, + { + participant_count: 50, + study_code: 'KF-FASD', + }, + { participant_count: 774, study_code: 'KF-RSBD' }, + { + participant_count: 356, + study_code: 'KF-IGCT', + }, + { participant_count: 599, study_code: 'KF-AIS' }, + { + participant_count: 185, + study_code: 'KF-FALL', + }, + { participant_count: 255, study_code: 'KF-CDL' }, + { + participant_count: 517, + study_code: 'KF-CHARGE', + }, + ], + }; + (getStudiesStatistics as jest.Mock).mockImplementation(() => expectedPublicStats); + + await request(app) + .get('/statistics/studies') + .expect(200, expectedPublicStats); + expect((getStudiesStatistics as jest.Mock).mock.calls.length).toEqual(1); + }); + + it('should return 500 if an error occurs', async () => { + const expectedError = new Error('OOPS'); + (getStudiesStatistics as jest.Mock).mockImplementation(() => { + throw expectedError; + }); + + await request(app) + .get('/statistics/studies') + .expect(500, { error: 'Internal Server Error' }); + expect((getStudiesStatistics as jest.Mock).mock.calls.length).toEqual(1); + }); + }); + describe('GET /sets', () => { beforeEach(() => { (getSets as jest.Mock).mockReset(); @@ -388,97 +514,6 @@ describe('Express app (without Arranger)', () => { }); }); - describe('POST /survival', () => { - const requestBody = { - project: '2021_05_03_v2', - sqon: { - op: 'and', - content: [{ op: 'in', content: { field: 'gender', value: ['Female'] } }], - }, - }; - - beforeEach(() => { - (calculateSurvivalForSqonResult as jest.Mock).mockReset(); - }); - - it('should return 403 if no Authorization header', () => - request(app) - .post('/survival') - .expect(403)); - - it('should return 200 if Authorization header contains valid token and no error occurs', async () => { - const mockSurvivalResponse = [ - { - start: 0, - end: 1, - died: 7, - censored: 467, - cumulativeSurvival: 1, - donors: [ - { - time: 0, - censored: true, - meta: { - id: 'PT_HXDR3ZX6', - }, - }, - ], - }, - { - start: 1, - end: 3, - died: 1, - censored: 1, - cumulativeSurvival: 0.9944223107569721, - donors: [ - { - time: 2, - censored: true, - meta: { - id: 'PT_A0V7V4N0', - }, - }, - { - time: 3, - censored: false, - meta: { - id: 'PT_Y7GFMG49', - }, - }, - ], - }, - ]; - (calculateSurvivalForSqonResult as jest.Mock).mockImplementation(() => mockSurvivalResponse); - - const token = getToken(); - - await request(app) - .post('/survival') - .send(requestBody) - .set('Content-type', 'application/json') - .set({ Authorization: `Bearer ${token}` }) - .expect(200, { data: mockSurvivalResponse }); - expect((calculateSurvivalForSqonResult as jest.Mock).mock.calls.length).toEqual(1); - }); - - it('should return 500 if Authorization header contains valid token but an error occurs', async () => { - const expectedError = new Error('OOPS'); - (calculateSurvivalForSqonResult as jest.Mock).mockImplementation(() => { - throw expectedError; - }); - - const token = getToken(); - - await request(app) - .post('/survival') - .send(requestBody) - .set('Content-type', 'application/json') - .set({ Authorization: `Bearer ${token}` }) - .expect(500, { error: 'Internal Server Error' }); - expect((calculateSurvivalForSqonResult as jest.Mock).mock.calls.length).toEqual(1); - }); - }); - describe('POST /searchByIds', () => { const requestBody = { project: '2021_05_03_v2', diff --git a/src/app.ts b/src/app.ts index af8b0ad..503124c 100644 --- a/src/app.ts +++ b/src/app.ts @@ -1,12 +1,15 @@ import addAsync from '@awaitjs/express'; -import SQS from 'aws-sdk/clients/sqs'; +import { SQSClient } from '@aws-sdk/client-sqs'; import cors from 'cors'; import express, { Express } from 'express'; import { Keycloak } from 'keycloak-connect'; import NodeCache from 'node-cache'; import { dependencies, version } from '../package.json'; +import { ArrangerProject } from './arrangerUtils'; +import { computeAuthorizedStudiesForAllFences } from './endpoints/authorizedStudies/computeAuthorizedStudies'; import genomicFeatureSuggestions, { SUGGESTIONS_TYPES } from './endpoints/genomicFeatureSuggestions'; +import { getPhenotypesNodes } from './endpoints/phenotypes'; import { searchAllSources } from './endpoints/searchByIds/searchAllSources'; import { SearchByIdsResult } from './endpoints/searchByIds/searchByIdsTypes'; import { @@ -18,17 +21,14 @@ import { updateSetTag, } from './endpoints/sets/setsFeature'; import { CreateSetBody, Set, SetSqon, UpdateSetContentBody, UpdateSetTagBody } from './endpoints/sets/setsTypes'; -import { getStatistics } from './endpoints/statistics'; -import { calculateSurvivalForSqonResult } from './endpoints/survival'; -import { cacheTTL, esHost, keycloakURL } from './env'; +import { getStatistics, getStudiesStatistics } from './endpoints/statistics'; +import { cacheTTL, esHost, keycloakURL, userApiURL } from './env'; import { globalErrorHandler, globalErrorLogger } from './errors'; -import { STATISTICS_CACHE_ID, verifyCache } from './middleware/cache'; +import { STATISTICS_CACHE_ID, STATISTICS_PUBLIC_CACHE_ID, verifyCache } from './middleware/cache'; import { injectBodyHttpHeaders } from './middleware/injectBodyHttpHeaders'; import { resolveSetIdMiddleware } from './middleware/resolveSetIdInSqon'; -import { ArrangerProject } from './sqon/searchSqon'; -import { getPhenotypesNodes } from './endpoints/phenotypes'; -export default (keycloak: Keycloak, sqs: SQS, getProject: (projectId: string) => ArrangerProject): Express => { +export default (keycloak: Keycloak, sqs: SQSClient, getProject: (projectId: string) => ArrangerProject): Express => { const app = addAsync.addAsync(express()); const cache = new NodeCache({ stdTTL: cacheTTL }); @@ -53,14 +53,16 @@ export default (keycloak: Keycloak, sqs: SQS, getProject: (projectId: string) => app.useAsync(resolveSetIdMiddleware()); - app.get('/status', (_req, res) => + app.get('/status', (_req, res) => { res.send({ dependencies, version, keycloak: keycloakURL, elasticsearch: esHost, - }), - ); + users: userApiURL, + arrangerNext: true, + }); + }); app.post('/cache-clear', keycloak.protect('realm:ADMIN'), async (_req, res) => { cache.flushAll(); @@ -80,14 +82,10 @@ export default (keycloak: Keycloak, sqs: SQS, getProject: (projectId: string) => res.json(data); }); - app.postAsync('/survival', keycloak.protect(), async (req, res) => { - const accessToken = req.headers.authorization; - const userId = req['kauth']?.grant?.access_token?.content?.sub; - const sqon: SetSqon = req.body.sqon; - const projectId: string = req.body.project; - const data = await calculateSurvivalForSqonResult(sqon, projectId, userId, accessToken, getProject); - - res.send({ data }); + app.getAsync('/statistics/studies', verifyCache(STATISTICS_PUBLIC_CACHE_ID, cache), async (req, res) => { + const data = await getStudiesStatistics(); + cache.set(STATISTICS_PUBLIC_CACHE_ID, data); + res.json(data); }); app.postAsync('/searchByIds', keycloak.protect(), async (req, res) => { @@ -166,6 +164,8 @@ export default (keycloak: Keycloak, sqs: SQS, getProject: (projectId: string) => res.send({ data }); }); + app.postAsync('/authorized-studies', keycloak.protect(), computeAuthorizedStudiesForAllFences); + app.use(globalErrorLogger, globalErrorHandler); return app; diff --git a/src/arrangerUtils.ts b/src/arrangerUtils.ts new file mode 100644 index 0000000..ec3d8da --- /dev/null +++ b/src/arrangerUtils.ts @@ -0,0 +1,8 @@ +import { ExecutionResult } from 'graphql/execution/execute'; + +type RunQuery = ({ query, variables }: { query: unknown; variables: unknown }) => Promise; + +export type ArrangerProject = { + runQuery: ({ query: string, variables: unknown }) => Promise; +}; +export const runProjectQuery = (project: ArrangerProject): RunQuery => project.runQuery; diff --git a/src/endpoints/authorizedStudies/computeAuthorizedStudies.test.ts b/src/endpoints/authorizedStudies/computeAuthorizedStudies.test.ts new file mode 100644 index 0000000..cc1c14e --- /dev/null +++ b/src/endpoints/authorizedStudies/computeAuthorizedStudies.test.ts @@ -0,0 +1,126 @@ +import { computeAuthorizedStudiesForFence } from './computeAuthorizedStudies'; +import { multiSearchFilesAccessCounts, searchAggregatedAuthorizedStudiesForFence } from './searchers'; +import { AuthStudiesData } from './types'; + +jest.mock('./searchers'); +jest.mock('../../ElasticSearchClientInstance', () => jest.fn()); + +describe('Compute Authorized Studies', () => { + describe(`${computeAuthorizedStudiesForFence.name} `, () => { + beforeEach(() => { + (searchAggregatedAuthorizedStudiesForFence as jest.Mock).mockReset(); + (multiSearchFilesAccessCounts as jest.Mock).mockReset(); + }); + + it(`should give proper result when data exists in elasticsearch cluster`, async () => { + (searchAggregatedAuthorizedStudiesForFence as jest.Mock).mockImplementation(() => + Promise.resolve([ + { + key: 'SD_PREASA7S', + doc_count: 100, + top_study_hits: { + hits: { + total: { value: 100, relation: 'eq' }, + hits: [ + { + _source: { + study: { + study_name: 'National Heart, Lung, and Blood Institute...', + study_code: 'KF-CHD', + }, + }, + }, + ], + }, + }, + acls: { + buckets: [ + { key: 'SD_PREASA7S', doc_count: 100 }, + { key: 'phs001138.c999', doc_count: 100 }, + { key: 'phs001138.c1', doc_count: 78 }, + ], + }, + }, + { + key: 'SD_Z6MWD3H0', + doc_count: 4, + top_study_hits: { + hits: { + total: { value: 4, relation: 'eq' }, + hits: [ + { + _source: { + study: { + study_name: 'Kids First: Genomic Analysis of Congenital...', + study_code: 'KF-CHDALL', + }, + }, + }, + ], + }, + }, + acls: { + buckets: [ + { key: 'SD_Z6MWD3H0', doc_count: 4 }, + { key: 'phs002330.c2', doc_count: 4 }, + { key: 'phs002330.c999', doc_count: 4 }, + { key: 'open_access', doc_count: 10 }, + ], + }, + }, + ]), + ); + + (multiSearchFilesAccessCounts as jest.Mock).mockImplementation(() => + Promise.resolve([ + { + hits: { total: { value: 100, relation: 'eq' }, max_score: null, hits: [] }, + status: 200, + }, + { + hits: { total: { value: 0, relation: 'eq' }, max_score: null, hits: [] }, + status: 200, + }, + { + hits: { total: { value: 100, relation: 'eq' }, max_score: null, hits: [] }, + status: 200, + }, + { + hits: { total: { value: 10, relation: 'eq' }, max_score: null, hits: [] }, + status: 200, + }, + ]), + ); + + const r: { data: AuthStudiesData } = await computeAuthorizedStudiesForFence(null, 'gen3', [ + 'phs001138.c1', + 'phs001138.c999', + 'phs002330.c2', + ]); + + expect((searchAggregatedAuthorizedStudiesForFence as jest.Mock).mock.calls.length).toEqual(1); + expect((multiSearchFilesAccessCounts as jest.Mock).mock.calls.length).toEqual(1); + expect(r).toHaveProperty(['data']); + expect(r.data).toEqual([ + { + study_id: 'SD_PREASA7S', + user_acl_in_study: ['phs001138.c999', 'phs001138.c1'], + study_code: 'KF-CHD', + title: 'National Heart, Lung, and Blood Institute...', + authorized_controlled_files_count: 100, + total_files_count: 100, + total_authorized_files_count: 100, + }, + { + study_id: 'SD_Z6MWD3H0', + user_acl_in_study: ['phs002330.c2', 'open_access'], + study_code: 'KF-CHDALL', + title: 'Kids First: Genomic Analysis of Congenital...', + authorized_controlled_files_count: 4, + total_files_count: 100, + total_authorized_files_count: 14, + }, + ]); + }); + }); +}); diff --git a/src/endpoints/authorizedStudies/computeAuthorizedStudies.ts b/src/endpoints/authorizedStudies/computeAuthorizedStudies.ts new file mode 100644 index 0000000..adc9388 --- /dev/null +++ b/src/endpoints/authorizedStudies/computeAuthorizedStudies.ts @@ -0,0 +1,134 @@ +import { Client } from '@elastic/elasticsearch'; +import { Request, Response } from 'express'; +import { StatusCodes } from 'http-status-codes'; + +import EsInstance from '../../ElasticSearchClientInstance'; +import { multiSearchFilesAccessCounts, searchAggregatedAuthorizedStudiesForFence } from './searchers'; +import { AuthStudiesData, ResponseResult, SearchBucket, StudyDataGlobal, StudyDataSpecific } from './types'; + +const SUPPORTED_FENCES = ['gen3', 'dcf']; + +export const computeAuthorizedStudiesForFence = async ( + client: Client, + fence: string, + userAclForFence: string[], +): Promise<{ data: AuthStudiesData }> => { + const buckets: SearchBucket[] = await searchAggregatedAuthorizedStudiesForFence(client, fence, userAclForFence); + if (buckets.length === 0) { + return { + data: [], + }; + } + + const dataAggregations: StudyDataSpecific[] = buckets.map((b: SearchBucket) => ({ + study_id: b.key, + // Filtering out study files acls that are not included in the user's acls. + // It Would be better to do the filtering in the query itself, but it is simpler here. + user_acl_in_study: b.acls.buckets.filter(b => userAclForFence.includes(b.key)).map(b => b.key), + study_code: b.top_study_hits.hits.hits[0]._source.study.study_code, + title: b.top_study_hits.hits.hits[0]._source.study.study_name, + authorized_controlled_files_count: b.doc_count, + })); + + const allStudyIds = dataAggregations.map(x => x.study_id); + const M_SEARCH = { + indexOfTotalNOfFiles: 0, + indexOfOpenAccessNOfFiles: 1, + }; + + //Get all files count per candidate study + const accessCounts = await multiSearchFilesAccessCounts(client, fence, allStudyIds); + + const countFailures = + accessCounts?.filter(x => x._shards?.failures && x._shards.failures.length > 0)?.map(x => x._shards.failures) || + []; + // eslint-disable-next-line no-console + console.assert(countFailures.length === 0, 'failures detected', countFailures); + const size = Object.keys(M_SEARCH).length; //there are "size" response elements per study + // eslint-disable-next-line no-console + console.assert( + accessCounts.length % size === 0, + '`Authorized-Studies: Unexpected chunks size from files counts multi-search', + ); + return { + data: dataAggregations.map((x: StudyDataSpecific, i: number): StudyDataSpecific | StudyDataGlobal => { + const extractMSearchHitsTotal = (index: number) => + accessCounts.slice(i * size, i * size + size)[index].hits.total.value; + const openAccessCount = extractMSearchHitsTotal(M_SEARCH.indexOfOpenAccessNOfFiles); + const containsOpenAccess = openAccessCount > 0; + const total_authorized_files_count = openAccessCount + x.authorized_controlled_files_count; + + return { + ...x, + total_files_count: extractMSearchHitsTotal(M_SEARCH.indexOfTotalNOfFiles), + total_authorized_files_count, + user_acl_in_study: containsOpenAccess ? [...x.user_acl_in_study, 'open_access'] : x.user_acl_in_study, + }; + }), + }; +}; + +export const computeAuthorizedStudiesForAllFences = async (req: Request, res: Response): Promise => { + const body: { + gen3: { + acl: string[]; + }; + dcf: { + acl: string[]; + }; + } = req.body; + + //===== INPUT Validations + const fences = Object.keys(body); + const fencesAreProcessable = + Array.isArray(fences) && fences.length > 0 && fences.every(f => SUPPORTED_FENCES.includes(f)); + if (!fencesAreProcessable) { + return res.status(StatusCodes.UNPROCESSABLE_ENTITY).send('Unsupported Fence(s) format or value'); + } + + const MAX_ACL_SIZE = 500; + const MAX_ALC_LENGTH_VALUE = 100; + const aclAreProcessable = Object.values(body).every( + x => + Array.isArray(x.acl) && + x.acl.length <= MAX_ACL_SIZE && + x.acl.every(a => typeof a === 'string' && a.length < MAX_ALC_LENGTH_VALUE), + ); + if (!aclAreProcessable) { + return res + .status(StatusCodes.UNPROCESSABLE_ENTITY) + .send(`Acls must be a list of acl values for each fence and not exceed a certain size`); + } + + const state: ResponseResult = Object.fromEntries( + Object.entries({ + gen3: { + data: [], + error: false, + }, + dcf: { + data: [], + error: false, + }, + }).filter(([k]) => fences.includes(k)), + ); + + const client = EsInstance.getInstance(); + for (const fence of fences) { + try { + const { data } = await computeAuthorizedStudiesForFence(client, fence, body[fence].acl); + state[fence] = { + ...state[fence], + data, + }; + } catch (e) { + console.error(`Authorized-Studies (${computeAuthorizedStudiesForFence.name}):\n`, e); + state[fence] = { + ...state[fence], + error: true, + }; + } + } + + return res.send(state); +}; diff --git a/src/endpoints/authorizedStudies/searchers.ts b/src/endpoints/authorizedStudies/searchers.ts new file mode 100644 index 0000000..73f636b --- /dev/null +++ b/src/endpoints/authorizedStudies/searchers.ts @@ -0,0 +1,103 @@ +import { Client } from '@elastic/elasticsearch'; + +import { esFileIndex } from '../../env'; +import { FileAccessCountsResponse, SearchBucket } from './types'; + +const MAX_SIZE_FOR_HITS = 10000; + +export const searchAggregatedAuthorizedStudiesForFence = async ( + client: Client, + fence: string, + userAcl: string[], +): Promise => { + const r = await client.search({ + index: esFileIndex, + body: { + size: 0, + track_total_hits: true, + query: { + bool: { + must: [ + { + terms: { + acl: userAcl, + }, + }, + { + term: { + repository: { + value: fence, + }, + }, + }, + ], + }, + }, + aggs: { + study_ids: { + terms: { + field: 'study_id', + size: MAX_SIZE_FOR_HITS, + }, + aggs: { + // Nice to have/do: filter out all the acl values that the user does not have. + acls: { + terms: { + field: 'acl', + size: MAX_SIZE_FOR_HITS, + }, + }, + top_study_hits: { + top_hits: { + _source: { + includes: ['study.study_name', 'study.study_code'], + }, + //In theory, only one doc suffice to get all the needed information + size: 1, + }, + }, + }, + }, + }, + }, + }); + return r.body?.aggregations?.study_ids.buckets || []; +}; + +export const multiSearchFilesAccessCounts = async ( + client: Client, + fence: string, + studyIds: string[], +): Promise => { + const { body: bodyMSearch } = await client.msearch({ + body: studyIds + .map((s: string) => [ + { index: esFileIndex }, + { + track_total_hits: true, + size: 0, + query: { + bool: { + must: [{ term: { study_id: { value: s } } }, { term: { repository: { value: fence } } }], + }, + }, + }, + { index: esFileIndex }, + { + track_total_hits: true, + size: 0, + query: { + bool: { + must: [ + { term: { study_id: { value: s } } }, + { term: { acl: { value: 'open_access' } } }, + { term: { repository: { value: fence } } }, + ], + }, + }, + }, + ]) + .flat(), + }); + return bodyMSearch.responses || []; +}; diff --git a/src/endpoints/authorizedStudies/types.ts b/src/endpoints/authorizedStudies/types.ts new file mode 100644 index 0000000..28f882f --- /dev/null +++ b/src/endpoints/authorizedStudies/types.ts @@ -0,0 +1,52 @@ +export type SearchBucket = { + key: string; + acls: { buckets: { key: string }[] }; + top_study_hits: { hits: { hits: { _source: { study: { study_name: string; study_code: string } } }[] } }; + doc_count: number; +}; + +export type StudyDataSpecific = { + study_id: string; + user_acl_in_study: string[]; + title: string; + authorized_controlled_files_count: number; +}; + +export type StudyDataGlobal = { + total_files_count: number; + total_authorized_files_count: number; +}; + +export type AuthStudiesData = (StudyDataSpecific | StudyDataGlobal)[]; + +export type ResponseResult = { + [k: string]: { + data: AuthStudiesData; + error: boolean; + }; +}; + +export type FileAccessCountsResponse = { + hits: { total: { value: number } }; + status: number; + _shards: { + total: number; + successful: number; + skipped: number; + failed: number; + failures: { + shard: number; + index: string; + node: string; + reason: { + reason: string; + index: string; + index_uuid: string; + caused_by: { + type: string; + reason: string; + }; + }; + }[]; + }; +}; diff --git a/src/endpoints/phenotypes.ts b/src/endpoints/phenotypes.ts index 6a607fe..809cb63 100644 --- a/src/endpoints/phenotypes.ts +++ b/src/endpoints/phenotypes.ts @@ -1,17 +1,101 @@ -import { idKey } from '../env'; -import { ArrangerProject, searchSqon } from '../sqon/searchSqon'; -import { SetSqon } from './sets/setsTypes'; +import { ExecutionResult } from 'graphql/execution/execute'; import { get } from 'lodash'; + +import { runProjectQuery } from '../arrangerUtils'; +import { ArrangerProject } from '../arrangerUtils'; +import { idKey } from '../env'; +import { throwErrorsFromGqlQueryIfExist } from '../errors'; import { replaceSetByIds } from '../sqon/setSqon'; +import { SetSqon } from './sets/setsTypes'; const MAX_PHENOTYPES = 100000; +const extractPsIds = (resp): string[] => (resp?.data?.participant?.hits?.edges || []).map(edge => edge.node[idKey]); + const getParticipantIds = async ( sqon: SetSqon, projectId: string, getProject: (projectId: string) => ArrangerProject, ) => { - return await searchSqon(sqon, projectId, 'participant', [], idKey, getProject); + const project = getProject(projectId); + const runQuery = runProjectQuery(project); + + const countRes: ExecutionResult = await runQuery({ + query: `query getParticipantCount($sqon: JSON) { + participant { + hits(filters: $sqon) { + total + } + } + } + `, + variables: { sqon }, + }); + const psCount = countRes?.data?.participant?.hits?.total ?? 0; + if (psCount === 0) { + return []; + } + const batchSize = 5000; + const gqlVariables = { sqon, sort: [{ field: idKey, order: 'asc' }], first: batchSize }; + const psResp = await runQuery({ + query: ` + query ($sqon: JSON, $sort: [Sort], $first: Int) { + participant { + hits(filters: $sqon, sort: $sort, first: $first) { + edges { + node { + ${idKey} + } + } + } + } + } + `, + variables: gqlVariables, + }); + + throwErrorsFromGqlQueryIfExist(psResp); + + const state = { searchAfter: [], ids: extractPsIds(psResp) }; + const nOfBatches = Math.ceil(psCount / batchSize); + const remainingNOfBatches = nOfBatches - 1; //subtract 1 since first batch has been consumed already + const it = Array(remainingNOfBatches).keys(); + let x = it.next(); + while (!x.done) { + const lastFetchedId = state.ids.slice(-1); + const psResp = await runQuery({ + query: ` + query ($sqon: JSON, $sort: [Sort], $first: Int, $searchAfter: JSON) { + participant { + hits(filters: $sqon, sort: $sort, first: $first, searchAfter: $searchAfter) { + edges { + searchAfter + node { + ${idKey} + } + } + } + } + } + `, + variables: { ...gqlVariables, searchAfter: lastFetchedId }, + }); + + throwErrorsFromGqlQueryIfExist(psResp); + + state.ids = [...state.ids, ...extractPsIds(psResp)]; + x = it.next(); + } + + if (psCount !== state.ids.length) { + const duplicateDetected = new Set(state.ids).size !== state.ids.length; + throw new Error( + `Participants count differs from the number of retrieve ids. Got ${psCount} for count but got ${ + state.ids.length + } for the number of retrieved ids. ${duplicateDetected ? 'Besides, duplicates were detected.' : ''}`, + ); + } + return state.ids; }; export const getPhenotypesNodes = async ( @@ -27,7 +111,7 @@ export const getPhenotypesNodes = async ( const participantIds = await getParticipantIds(newSqon as SetSqon, projectId, getProject); - return await getPhenotypesNodesByIds(participantIds, projectId, getProject, type, aggregations_filter_themselves); + return getPhenotypesNodesByIds(participantIds, projectId, getProject, type, aggregations_filter_themselves); }; const getPhenotypesNodesByIds = async ( diff --git a/src/endpoints/searchByIds/executePagedQuery.ts b/src/endpoints/searchByIds/executePagedQuery.ts index ffa2d34..37964be 100644 --- a/src/endpoints/searchByIds/executePagedQuery.ts +++ b/src/endpoints/searchByIds/executePagedQuery.ts @@ -1,6 +1,6 @@ import { get } from 'lodash'; -import { ArrangerProject } from '../../sqon/searchSqon'; +import { ArrangerProject } from '../../arrangerUtils'; import { SetSqon } from '../sets/setsTypes'; import { normalizeResults } from './normalizeResults'; diff --git a/src/endpoints/searchByIds/searchAllSources.ts b/src/endpoints/searchByIds/searchAllSources.ts index 4b8c5d6..2bd3212 100644 --- a/src/endpoints/searchByIds/searchAllSources.ts +++ b/src/endpoints/searchByIds/searchAllSources.ts @@ -1,6 +1,6 @@ import { flatten } from 'lodash'; -import { ArrangerProject } from '../../sqon/searchSqon'; +import { ArrangerProject } from '../../arrangerUtils'; import { byBiospecimenId } from './byBiospecimenId'; import { byFamilyId } from './byFamilyId'; import { byId } from './byId'; diff --git a/src/endpoints/sets/setsFeature.test.ts b/src/endpoints/sets/setsFeature.test.ts index cfb4d10..5f4f08d 100644 --- a/src/endpoints/sets/setsFeature.test.ts +++ b/src/endpoints/sets/setsFeature.test.ts @@ -1,16 +1,17 @@ -import AWS from 'aws-sdk'; +import { SQS } from '@aws-sdk/client-sqs'; +import { ArrangerProject } from '../../arrangerUtils'; import { CreateUpdateBody, deleteRiff, getRiffs, + Output as RiffOutput, postRiff, putRiff, - Output, RIFF_TYPE_SET, } from '../../riff/riffClient'; import { resolveSetsInSqon } from '../../sqon/resolveSetInSqon'; -import { ArrangerProject, searchSqon } from '../../sqon/searchSqon'; +import { searchSqon } from '../../sqon/searchSqon'; import { sendSetInSQSQueue } from '../../SQS/sendEvent'; import { createSet, deleteSet, getSets, SubActionTypes, updateSetContent, updateSetTag } from './setsFeature'; import { CreateSetBody, Set, Sort, UpdateSetContentBody, UpdateSetTagBody } from './setsTypes'; @@ -42,7 +43,7 @@ describe('Set management', () => { const mockParticipantIds = ['participant_1', 'participant_2']; - const riff = { + const riff: RiffOutput = { id: setId, alias: tag, content: { @@ -50,17 +51,22 @@ describe('Set management', () => { sqon, riffType: RIFF_TYPE_SET, setType: type, + idField: 'fhir_id', + sort: [], }, sharedPublicly: false, uid: 'abcedfghijkl', creationDate: new Date(), updatedDate: new Date(), - } as Output; + }; const setFromRiff: Set = { id: setId, tag, - size: mockParticipantIds.length + size: mockParticipantIds.length, + setType: type, + updated_date: riff.updatedDate, + created_date: riff.creationDate, }; describe('Get user sets using Riff API', () => { @@ -70,7 +76,16 @@ describe('Set management', () => { it('should send get riffs and return result filtered to keep only set with tag and convert to Set', async () => { const mockUserRiffs = [riff, { ...riff, content: {} }, { ...riff, alias: '' }]; - const expectedSets = [{ id: riff.id, tag: riff.alias, size: riff.content.ids.length } as Set]; + const expectedSets: Set[] = [ + { + id: riff.id, + tag: riff.alias, + size: riff.content.ids.length, + setType: riff.content.setType, + created_date: riff.creationDate, + updated_date: riff.updatedDate, + }, + ]; (getRiffs as jest.Mock).mockImplementation(() => mockUserRiffs); const result = await getSets(accessToken, userId); @@ -117,7 +132,7 @@ describe('Set management', () => { }, }; - const sqs = new AWS.SQS({ apiVersion: '2012-11-05' }); + const sqs = new SQS({ apiVersion: '2012-11-05' }); beforeEach(() => { (resolveSetsInSqon as jest.Mock).mockReset(); @@ -273,13 +288,13 @@ describe('Set management', () => { content: riff.content, }; - const updatedRiff: Output = { + const updatedRiff: RiffOutput = { ...riff, alias: 'tag updated', updatedDate: new Date(), }; - const sqs = new AWS.SQS({ apiVersion: '2012-11-05' }); + const sqs = new SQS({ apiVersion: '2012-11-05' }); beforeEach(() => { (getRiffs as jest.Mock).mockReset(); @@ -288,7 +303,11 @@ describe('Set management', () => { }); it('should send put riff and return result', async () => { - const setFromUpdatedRiff: Set = { ...setFromRiff, tag: 'tag updated' }; + const setFromUpdatedRiff: Set = { + ...setFromRiff, + tag: 'tag updated', + updated_date: updatedRiff.updatedDate, + }; (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); (putRiff as jest.Mock).mockImplementation(() => updatedRiff); @@ -306,7 +325,7 @@ describe('Set management', () => { }); it('should not send message in SQS for empty tag sets', async () => { - const setFromUpdatedRiff: Set = { ...setFromRiff, tag: '' }; + const setFromUpdatedRiff: Set = { ...setFromRiff, tag: '', updated_date: updatedRiff.updatedDate }; (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); (putRiff as jest.Mock).mockImplementation(() => ({ ...updatedRiff, alias: '' })); @@ -370,7 +389,7 @@ describe('Set management', () => { const updateSetContentRemoveSqon = { ...updateSetContentAddSqon, subAction: SubActionTypes.REMOVE_IDS }; - const sqs = new AWS.SQS({ apiVersion: '2012-11-05' }); + const sqs = new SQS({ apiVersion: '2012-11-05' }); beforeEach(() => { (getRiffs as jest.Mock).mockReset(); @@ -381,25 +400,27 @@ describe('Set management', () => { }); it('should send put riff and return result - case add ids', async () => { - const setFromUpdatedRiff: Set = { ...setFromRiff, size: 3 }; const expectedAddSqon = { op: 'or', content: [sqon, newSqon] }; - const expectedUpdateRiffBody: CreateUpdateBody = { - alias: riff.alias, - sharedPublicly: riff.sharedPublicly, + const updatedRiff = { + ...riff, content: { ...riff.content, sqon: expectedAddSqon, ids: ['participant_1', 'participant_2', 'participant_3'], }, + updatedDate: new Date(), }; - const updatedRiff = { - ...riff, + + const setFromUpdatedRiff: Set = { ...setFromRiff, size: 3, updated_date: updatedRiff.updatedDate }; + + const expectedUpdateRiffBody: CreateUpdateBody = { + alias: riff.alias, + sharedPublicly: riff.sharedPublicly, content: { ...riff.content, sqon: expectedAddSqon, ids: ['participant_1', 'participant_2', 'participant_3'], }, - updatedDate: new Date(), }; (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); @@ -430,25 +451,26 @@ describe('Set management', () => { op: 'and', content: [{ op: 'in', content: { field: 'kf_id', value: mockNewSqonParticipantIds } }], }; - const setFromUpdatedRiff: Set = { ...setFromRiff, size: 3 }; const expectedAddSqon = { op: 'or', content: [sqon, newSqonWithSetId] }; - const expectedUpdateRiffBody: CreateUpdateBody = { - alias: riff.alias, - sharedPublicly: riff.sharedPublicly, + const updatedRiff = { + ...riff, content: { ...riff.content, sqon: expectedAddSqon, ids: ['participant_1', 'participant_2', 'participant_3'], }, + updatedDate: new Date(), }; - const updatedRiff = { - ...riff, + const setFromUpdatedRiff: Set = { ...setFromRiff, size: 3, updated_date: updatedRiff.updatedDate }; + + const expectedUpdateRiffBody: CreateUpdateBody = { + alias: riff.alias, + sharedPublicly: riff.sharedPublicly, content: { ...riff.content, sqon: expectedAddSqon, ids: ['participant_1', 'participant_2', 'participant_3'], }, - updatedDate: new Date(), }; (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); @@ -480,9 +502,8 @@ describe('Set management', () => { }); it('should not send message in SQS for empty tag sets', async () => { - const setFromUpdatedRiff: Set = { ...setFromRiff, size: 3, tag: '' }; const expectedAddSqon = { op: 'or', content: [sqon, newSqon] }; - const updatedRiff: Output = { + const updatedRiff: RiffOutput = { ...riff, alias: '', content: { @@ -493,6 +514,8 @@ describe('Set management', () => { updatedDate: new Date(), }; + const setFromUpdatedRiff: Set = { ...setFromRiff, size: 3, tag: '', updated_date: updatedRiff.updatedDate }; + (getRiffs as jest.Mock).mockImplementation(() => [{ ...riff, tag: '' }]); (resolveSetsInSqon as jest.Mock).mockImplementation(sqon => sqon); (searchSqon as jest.Mock).mockImplementation(() => mockNewSqonParticipantIds); @@ -509,28 +532,29 @@ describe('Set management', () => { }); it('should send put riff and return result - case remove ids', async () => { - const setFromUpdatedRiff: Set = { ...setFromRiff, size: 1 }; const expectedRemoveSqon = { op: 'and', content: [sqon, { op: 'not', content: [newSqon] }], }; - const expectedUpdateRiffBody: CreateUpdateBody = { - alias: riff.alias, - sharedPublicly: riff.sharedPublicly, + const updatedRiff = { + ...riff, content: { ...riff.content, sqon: expectedRemoveSqon, ids: ['participant_2'], }, + updatedDate: new Date(), }; - const updatedRiff = { - ...riff, + const setFromUpdatedRiff: Set = { ...setFromRiff, size: 1, updated_date: updatedRiff.updatedDate }; + + const expectedUpdateRiffBody: CreateUpdateBody = { + alias: riff.alias, + sharedPublicly: riff.sharedPublicly, content: { ...riff.content, sqon: expectedRemoveSqon, ids: ['participant_2'], }, - updatedDate: new Date(), }; (getRiffs as jest.Mock).mockImplementation(() => mockExistingSets); @@ -598,7 +622,7 @@ describe('Set management', () => { }); describe('Delete set using Riff API', () => { - const sqs = new AWS.SQS({ apiVersion: '2012-11-05' }); + const sqs = new SQS({ apiVersion: '2012-11-05' }); beforeEach(() => { (searchSqon as jest.Mock).mockReset(); diff --git a/src/endpoints/sets/setsFeature.ts b/src/endpoints/sets/setsFeature.ts index 5a77997..065e7af 100644 --- a/src/endpoints/sets/setsFeature.ts +++ b/src/endpoints/sets/setsFeature.ts @@ -1,32 +1,30 @@ -import SQS from 'aws-sdk/clients/sqs'; +import { SQSClient } from '@aws-sdk/client-sqs'; import { difference, dropRight, get, union } from 'lodash'; +import { ArrangerProject } from '../../arrangerUtils'; import { maxSetContentSize, project, PROJECT_INCLUDE, sendUpdateToSqs } from '../../env'; import { CreateUpdateBody, deleteRiff, getRiffs, - Output, + Output as RiffOutput, postRiff, putRiff, RIFF_TYPE_SET, } from '../../riff/riffClient'; import { addSqonToSetSqon, removeSqonToSetSqon } from '../../sqon/manipulateSqon'; import { resolveSetsInSqon } from '../../sqon/resolveSetInSqon'; -import { ArrangerProject, searchSqon } from '../../sqon/searchSqon'; -import { - EventCreate, - EventCreateValue, - EventDelete, - EventDeleteValues, - EventUpdate, - UpdateContentValue, - UpdateTagValue, -} from '../../SQS/eventTypes'; +import { searchSqon } from '../../sqon/searchSqon'; import { sendSetInSQSQueue } from '../../SQS/sendEvent'; +import { + deleteUserContent, + getUserContents, + Output as UserSetOutput, + postUserContent, + putUserContent, +} from '../../userApi/userApiClient'; import { SetNotFoundError } from './setError'; import { CreateSetBody, Set, UpdateSetContentBody, UpdateSetTagBody } from './setsTypes'; -import { deleteUserContent, getUserContents, postUserContent, putUserContent } from '../../userApi/userApiClient'; const projectType = project; @@ -42,12 +40,14 @@ const ActionTypes = { UPDATE: 'UPDATE', }; -export const getUserSet = async (accessToken: string, userId: string, setId: string): Promise => { - let existingSetsFilterById; +export const getUserSet = async (accessToken: string, userId: string, setId: string): Promise => { + let existingSetsFilterById: UserSetOutput[]; if (projectType === PROJECT_INCLUDE) { existingSetsFilterById = (await getUserContents(accessToken)).filter(r => r.id === setId); } else { - existingSetsFilterById = (await getRiffs(accessToken, userId)).filter(r => r.id === setId); + existingSetsFilterById = (await getRiffs(accessToken, userId)) + .filter(r => r.id === setId) + .map(s => mapRiffOutputToUserOutput(s)); } if (existingSetsFilterById.length !== 1) { @@ -61,13 +61,13 @@ export const getSets = async (accessToken: string, userId: string): Promise mapResultToSet(set)); + return userContents.map(set => mapUserResultToSet(set)); } else { const userContents = await getRiffs(accessToken, userId); return userContents .filter(riff => get(riff, 'content.riffType', '') === RIFF_TYPE_SET) .filter(riff => riff.alias) - .map(riff => mapResultToSet(riff)); + .map(riff => mapRiffResultToSet(riff)); } }; @@ -75,7 +75,7 @@ export const createSet = async ( requestBody: CreateSetBody, accessToken: string, userId: string, - sqs: SQS, + sqs: SQSClient, getProject: (projectId: string) => ArrangerProject, ): Promise => { const { sqon, sort, projectId, type, idField, tag } = requestBody; @@ -84,39 +84,39 @@ export const createSet = async ( const truncatedIds = truncateIds(ids); - const payload = { + const payload: CreateUpdateBody = { alias: tag, sharedPublicly: false, content: { ids: truncatedIds, riffType: RIFF_TYPE_SET, setType: type, sqon, sort, idField }, - } as CreateUpdateBody; + }; - let createResult; + let setResult: Set; if (projectType === PROJECT_INCLUDE) { if (!payload.alias || !payload.content.ids) { throw Error(`Set must have ${!payload.alias ? 'a name' : 'no set ids'}`); } - createResult = await postUserContent(accessToken, payload); + const createResult = await postUserContent(accessToken, payload); + setResult = mapUserResultToSet(createResult); } else { - createResult = await postRiff(accessToken, payload); + const createResult = await postRiff(accessToken, payload); + setResult = mapRiffResultToSet(createResult); } - const setResult: Set = mapResultToSet(createResult); - - if (sendUpdateToSqs && createResult.alias) { + if (sendUpdateToSqs && setResult.tag) { await sendSetInSQSQueue(sqs, { actionType: ActionTypes.CREATE, values: { userId, - setId: createResult.id, + setId: setResult.id, ids: truncatedIds, size: truncatedIds.length, sqon, path: idField, type, tag, - createdAt: createResult.creationDate, - } as EventCreateValue, - } as EventCreate); + createdAt: setResult.created_date, + }, + }); } return setResult; }; @@ -126,31 +126,31 @@ export const updateSetTag = async ( accessToken: string, userId: string, setId: string, - sqs: SQS, + sqs: SQSClient, ): Promise => { - const setToUpdate = await getUserSet(accessToken, userId, setId); + const setToUpdate: UserSetOutput = await getUserSet(accessToken, userId, setId); - const payload = { + const payload: CreateUpdateBody = { alias: requestBody.newTag, - sharedPublicly: setToUpdate.sharedPublicly, + sharedPublicly: setToUpdate.sharedpublicly, content: setToUpdate.content, - } as CreateUpdateBody; + }; - let updateResult; + let setResult: Set; if (projectType === PROJECT_INCLUDE) { - updateResult = await putUserContent(accessToken, payload, setId); + const updateResult = await putUserContent(accessToken, payload, setId); + setResult = mapUserResultToSet(updateResult); } else { - updateResult = await putRiff(accessToken, payload, setId); + const updateResult = await putRiff(accessToken, payload, setId); + setResult = mapRiffResultToSet(updateResult); } - const setResult: Set = mapResultToSet(updateResult); - - if (sendUpdateToSqs && updateResult.alias) { + if (sendUpdateToSqs && setResult.tag) { await sendSetInSQSQueue(sqs, { actionType: ActionTypes.UPDATE, subActionType: requestBody.subAction, - values: { userId, setId, newTag: updateResult.alias } as UpdateTagValue, - } as EventUpdate); + values: { userId, setId, newTag: setResult.tag }, + }); } return setResult; @@ -161,7 +161,7 @@ export const updateSetContent = async ( accessToken: string, userId: string, setId: string, - sqs: SQS, + sqs: SQSClient, getProject: (projectId: string) => ArrangerProject, ): Promise => { const setToUpdate = await getUserSet(accessToken, userId, setId); @@ -192,38 +192,43 @@ export const updateSetContent = async ( requestBody.subAction === SubActionTypes.ADD_IDS ? union(ids, newSqonIds) : difference(ids, newSqonIds); const truncatedIds = truncateIds(existingIdsWithNewIds); - const payload = { + const payload: CreateUpdateBody = { alias: setToUpdate.alias, - sharedPublicly: setToUpdate.sharedPublicly, + sharedPublicly: setToUpdate.sharedpublicly, content: { ...setToUpdate.content, sqon: existingSqonWithNewSqon, ids: truncatedIds }, - } as CreateUpdateBody; + }; - let updateResult; + let setResult: Set; if (projectType === PROJECT_INCLUDE) { - updateResult = await putUserContent(accessToken, payload, setId); + const updateResult = await putUserContent(accessToken, payload, setId); + setResult = mapUserResultToSet(updateResult); } else { - updateResult = await putRiff(accessToken, payload, setId); + const updateResult = await putRiff(accessToken, payload, setId); + setResult = mapRiffResultToSet(updateResult); } - const setResult: Set = mapResultToSet(updateResult); - - if (sendUpdateToSqs && updateResult.alias) { + if (sendUpdateToSqs && setResult.tag) { await sendSetInSQSQueue(sqs, { actionType: ActionTypes.UPDATE, subActionType: requestBody.subAction, values: { userId, setId, - tag: updateResult.alias, + tag: setResult.tag, ids: truncatedIds, - createdAt: updateResult.creationDate, - } as UpdateContentValue, - } as EventUpdate); + createdAt: setResult.created_date, + }, + }); } return setResult; }; -export const deleteSet = async (accessToken: string, setId: string, userId: string, sqs: SQS): Promise => { +export const deleteSet = async ( + accessToken: string, + setId: string, + userId: string, + sqs: SQSClient, +): Promise => { let deleteResult; if (projectType === PROJECT_INCLUDE) { @@ -235,20 +240,39 @@ export const deleteSet = async (accessToken: string, setId: string, userId: stri if (sendUpdateToSqs) { await sendSetInSQSQueue(sqs, { actionType: ActionTypes.DELETE, - values: { setIds: [setId], userId } as EventDeleteValues, - } as EventDelete); + values: { setIds: [setId], userId }, + }); } return deleteResult; }; -const mapResultToSet = (output: Output): Set => - ({ - id: output.id, - tag: output.alias, - size: output.content.ids.length, - updated_date: output.updated_date, - setType: output.content.setType, - } as Set); +const mapUserResultToSet = (output: UserSetOutput): Set => ({ + id: output.id, + tag: output.alias, + size: output.content.ids.length, + updated_date: output.updated_date, + setType: output.content.setType, + created_date: output.creation_date, +}); + +const mapRiffResultToSet = (output: RiffOutput): Set => ({ + id: output.id, + tag: output.alias, + size: output.content.ids.length, + updated_date: output.updatedDate, + setType: output.content.setType, + created_date: output.creationDate, +}); + +export const mapRiffOutputToUserOutput = (output: RiffOutput): UserSetOutput => ({ + id: output.id, + keycloak_id: output.uid, + content: output.content, + alias: output.alias, + sharedpublicly: output.sharedPublicly, + creation_date: output.creationDate, + updated_date: output.updatedDate, +}); const truncateIds = (ids: string[]): string[] => { if (ids.length <= maxSetContentSize) { diff --git a/src/endpoints/sets/setsTypes.ts b/src/endpoints/sets/setsTypes.ts index 582301e..0e36fb7 100644 --- a/src/endpoints/sets/setsTypes.ts +++ b/src/endpoints/sets/setsTypes.ts @@ -34,5 +34,7 @@ export type Set = { id: string; tag: string; size: number; + setType: string; + updated_date: Date; + created_date: Date; }; - diff --git a/src/endpoints/statistics/index.ts b/src/endpoints/statistics/index.ts index dd44e9e..eaa6779 100644 --- a/src/endpoints/statistics/index.ts +++ b/src/endpoints/statistics/index.ts @@ -5,7 +5,9 @@ import EsInstance from '../../ElasticSearchClientInstance'; import { esFileIndex, esParticipantIndex, - esStudyIndex, familyIdKey, + esStudyIndex, + esVariantIndex, + familyIdKey, fileIdKey, participantIdKey, project, @@ -16,6 +18,16 @@ import { import { fetchBiospecimenStats as fetchIncludeBiospecimen } from './includeBiospecimen'; import { fetchBiospecimenStats as fetchKidsfirstBiospecimen } from './kidsfirstBiospecimen'; +export type Diagnosis = { + mondo_id: string; + count: number; +}; + +export type MembersCount = { + totalCount: number; + publicCount: number; +}; + export type Statistics = { files: number; fileSize: string; @@ -23,6 +35,14 @@ export type Statistics = { samples: number; families: number; participants: number; + variants: number; + genomes: number; + transcriptomes: number; + sex: Record; + downSyndromeStatus: Record; + race: Record; + diagnosis: Diagnosis[]; + members: MembersCount; }; const fetchFileStats = async (client: Client): Promise => { @@ -92,23 +112,260 @@ const fetchBiospecimenStats = async (client: Client): Promise => { return Promise.resolve(0); }; +export const fetchVariantStats = async (client: Client): Promise => { + const { body } = await client.count({ + index: esVariantIndex, + }); + return body?.count; +}; + +export const fetchGenomesStats = async (client: Client): Promise => { + const { body } = await client.count({ + index: esParticipantIndex, + body: { + query: { + bool: { + must: [ + { + nested: { + path: 'files', + query: { + term: { + 'files.file_format': 'cram', + }, + }, + }, + }, + { + bool: { + should: [ + { + nested: { + path: 'files.sequencing_experiment', + query: { + term: { + 'files.sequencing_experiment.experiment_strategy': + 'Whole Genome Sequencing', + }, + }, + }, + }, + { + nested: { + path: 'files.sequencing_experiment', + query: { + term: { + 'files.sequencing_experiment.experiment_strategy': 'WGS', + }, + }, + }, + }, + ], + }, + }, + ], + }, + }, + }, + }); + + return body?.count; +}; + +export const fetchTranscriptomesStats = async (client: Client): Promise => { + const { body } = await client.count({ + index: esParticipantIndex, + body: { + query: { + bool: { + must: [ + { + nested: { + path: 'files.sequencing_experiment', + query: { + term: { + 'files.sequencing_experiment.experiment_strategy': 'RNA-Seq', + }, + }, + }, + }, + { + bool: { + should: [ + { + nested: { + path: 'files', + query: { + term: { + 'files.file_format': 'cram', + }, + }, + }, + }, + { + nested: { + path: 'files', + query: { + term: { + 'files.file_format': 'fastq', + }, + }, + }, + }, + { + nested: { + path: 'files', + query: { + term: { + 'files.file_format': 'bam', + }, + }, + }, + }, + ], + }, + }, + ], + }, + }, + }, + }); + + return body?.count; +}; + +export const fetchDemographicsStats = async (client: Client): Promise[]> => { + const response = await client.msearch({ + body: [ + { index: esParticipantIndex }, + { size: 0, aggs: { sex: { terms: { field: 'sex', size: 10 } } } }, + { index: esParticipantIndex }, + { size: 0, aggs: { down_syndrome_status: { terms: { field: 'down_syndrome_status', size: 10 } } } }, + { index: esParticipantIndex }, + { size: 0, aggs: { race: { terms: { field: 'race', size: 20 } } } }, + ], + }); + + const sex = response.body.responses[0].aggregations.sex.buckets.reduce((acc, curr) => { + acc[curr.key] = curr.doc_count; + return acc; + }, {}); + const downSyndromeStatus = response.body.responses[1].aggregations.down_syndrome_status.buckets.reduce( + (acc, curr) => { + acc[curr.key] = curr.doc_count; + return acc; + }, + {}, + ); + const race = response.body.responses[2].aggregations.race.buckets.reduce((acc, curr) => { + acc[curr.key] = curr.doc_count; + return acc; + }, {}); + + return [sex, downSyndromeStatus, race]; +}; + +export const fetchTopDiagnosis = async (client: Client): Promise => { + const response = await client.search({ + index: esParticipantIndex, + body: { + size: 0, + aggs: { + top_diagnosis_ids: { + nested: { + path: 'diagnosis', + }, + aggs: { + filtered_diagnosis_ids: { + terms: { + field: 'diagnosis.mondo_display_term', + size: 10, + exclude: '.*MONDO:(0700030|0008608|0700129|0700127|0700130|0700128|0700126).*', + }, + }, + }, + }, + }, + }, + }); + + return response.body.aggregations.top_diagnosis_ids.filtered_diagnosis_ids.buckets.map(bucket => ({ + mondo_id: bucket.key, + count: bucket.doc_count, + })); +}; + +export const fetchMemberStats = async (client: Client): Promise => { + const membersExists = await client.indices.exists({ + index: 'members', + }); + + const publicMembersExists = await client.indices.exists({ + index: 'members-public', + }); + + if (!membersExists?.body || !publicMembersExists?.body) return; + + const { body: members } = await client.count({ + index: 'members', + }); + + const { body: publicMembers } = await client.count({ + index: 'members-public', + }); + return { + totalCount: members?.count, + publicCount: publicMembers?.count, + }; +}; + export const getStatistics = async (): Promise => { const client = EsInstance.getInstance(); - const result = await Promise.all([ + const results = await Promise.all([ fetchFileStats(client), fetchStudyStats(client), fetchParticipantStats(client), - fetchFamilyStats(client), fetchBiospecimenStats(client), + fetchFamilyStats(client), fetchFileSizeStats(client), + fetchVariantStats(client), + fetchGenomesStats(client), + fetchTranscriptomesStats(client), + fetchDemographicsStats(client), ]); + const diagnosis = await fetchTopDiagnosis(client); + + const members = await fetchMemberStats(client); + return { - files: result[0], - studies: result[1], - participants: result[2], - families: result[3], - samples: result[4], - fileSize: result[5], - } as Statistics; + files: results[0], + studies: results[1], + participants: results[2], + samples: results[3], + families: results[4], + fileSize: results[5], + variants: results[6], + genomes: results[7], + transcriptomes: results[8], + sex: results[9][0], + downSyndromeStatus: results[9][1], + race: results[9][2], + diagnosis, + members, + }; +}; + +export const getStudiesStatistics = async (): Promise> => { + const client = EsInstance.getInstance(); + + const { body } = await client.search({ + index: esStudyIndex, + body: { + size: 500, + _source: ['participant_count', 'study_code'], + }, + }); + + return body.hits.hits.map(hit => hit._source); }; diff --git a/src/endpoints/survival.ts b/src/endpoints/survival.ts deleted file mode 100644 index 5d8cbb5..0000000 --- a/src/endpoints/survival.ts +++ /dev/null @@ -1,159 +0,0 @@ -import { get, min } from 'lodash'; -import { Options, PythonShell } from 'python-shell'; - -import { idKey, pythonPath, survivalPyFile } from '../env'; -import { resolveSetsInSqon } from '../sqon/resolveSetInSqon'; -import { ArrangerProject } from '../sqon/searchSqon'; -import { SetSqon } from './sets/setsTypes'; - -const pyOptions: Options = { pythonPath, mode: 'text', pythonOptions: ['-u'] }; - -const ALIVE = 'Alive'; -const DECEASED = 'Deceased'; -const STATUSES = [ALIVE, DECEASED]; - -const convertCensored = (value: string): boolean => { - switch (value) { - case ALIVE: - return true; - case DECEASED: - return false; - } -}; - -const getDiagnosesAge = diagnoses => { - const ages = diagnoses - .map(diagnosis => parseInt(get(diagnosis, 'node.age_at_event_days'))) - .filter(age => !isNaN(age)); - return min(ages); -}; - -const getParticipants = async ( - sqon: SetSqon, - projectId: string, - userId: string, - accessToken: string, - getProject: (projectId: string) => ArrangerProject, -) => { - const sqonWithSetContent = await resolveSetsInSqon(sqon, userId, accessToken); - - const query = `query ($sqon: JSON, $size: Int, $offset: Int) { - participant{ - hits (filters: $sqon, first:$size, offset:$offset){ - edges { - node { - ${idKey} - outcome { - age_at_event_days - vital_status - } - diagnoses { - hits { - edges { - node { - age_at_event_days - } - } - } - } - } - } - } - } - } - `; - - const participants = []; - let complete = false; - let offset = 0; - const size = 1000; - - const project = getProject(projectId); - if (!project) { - throw new Error(`ProjectID '${projectId}' cannot be established.`); - } - - while (!complete) { - const results = await project.runQuery({ - query, - variables: { sqon: sqonWithSetContent, size, offset }, - }); - offset += size; - - const edges = get(results, 'data.participant.hits.edges', []); - if (edges.length < size) { - complete = true; - } - - const filteredList = edges - // get values we need - .map(edge => ({ - id: edge.node[idKey], - outcomeAge: parseInt(edge.node.outcome.age_at_event_days), - censored: convertCensored(edge.node.outcome.vital_status), - diagnosesAge: getDiagnosesAge(get(edge, 'node.diagnoses.hits.edges', [])), - status: edge.node.outcome.vital_status, - })) - // Make sure all fields have useable values - .filter( - item => - item.id && - !isNaN(item.outcomeAge) && - !isNaN(item.diagnosesAge) && - item.outcomeAge >= item.diagnosesAge && - STATUSES.includes(item.status), - ); - const formattedResults = filteredList - // Calculate time and format for survivalPy - .map(item => ({ - id: item.id, - censored: item.censored, - time: item.outcomeAge - item.diagnosesAge, - })); - participants.push(...formattedResults); - } - - return participants; -}; - -const calculateSurvival = async participants => - new Promise((resolve, reject) => { - const data = []; - try { - const pyShell = new PythonShell(survivalPyFile, pyOptions); - pyShell.on('error', err => { - reject(err); - }); - pyShell.on('message', payload => { - const message = JSON.parse(payload).message; - // Only expecting one response from our script, but for extra security we add to array, return only uses first message - data.push(message); - }); - - participants.forEach(participant => { - pyShell.send(JSON.stringify(participant)); - }); - - pyShell.end(err => { - if (err) { - reject(err); - } else { - resolve(data[0]); - } - }); - } catch (error) { - reject(error); - } - }); - -export const calculateSurvivalForSqonResult = async ( - sqon: SetSqon, - projectId: string, - userId: string, - accessToken: string, - getProject: (projectId: string) => ArrangerProject, -) => { - const participants = await getParticipants(sqon, projectId, userId, accessToken, getProject); - - return calculateSurvival(participants); -}; diff --git a/src/env.ts b/src/env.ts index d01365f..211646b 100644 --- a/src/env.ts +++ b/src/env.ts @@ -21,6 +21,7 @@ export const esFileIndex = process.env.ES_FILE_INDEX || 'file_centric'; export const esStudyIndex = process.env.ES_STUDY_INDEX || 'study_centric'; export const esParticipantIndex = process.env.ES_PARTICIPANT_INDEX || 'participant_centric'; export const esBiospecimenIndex = process.env.ES_BIOSPECIMEN_INDEX || 'biospecimen_centric'; +export const esVariantIndex = process.env.ES_VARIANT_INDEX || 'variant_centric'; export const maxNOfGenomicFeatureSuggestions = process.env.MAX_NUMBER_OF_GF_SUGGESTIONS || 5; @@ -32,17 +33,12 @@ export const userApiURL = process.env.USER_API_URL || 'https://include-users-api export const sendUpdateToSqs = process.env.SEND_UPDATE_TO_SQS !== 'false'; export const sqsQueueUrl = process.env.SQS_QUEUE_URL || ''; export const maxSetContentSize: number = Number.parseInt(process.env.MAX_SET_CONTENT_SIZE) || 100000; - -export const survivalPyFile = process.env.SURVIVAL_PY_FILE || 'resource/py/survival.py'; -export const pythonPath = process.env.PYTHON_PATH || '/usr/local/bin/python3'; - export const idKey = process.env.ID_KEY || 'kf_id'; export const fileIdKey = process.env.FILE_ID_KEY || 'kf_id'; export const studyIdKey = process.env.STUDY_ID_KEY || 'kf_id'; export const participantIdKey = process.env.PARTICIPANT_ID_KEY || 'kf_id'; export const biospecimenIdKey = process.env.BIOSPECIMEN_ID_KEY || 'kf_id'; export const familyIdKey = process.env.FAMILY_ID_KEY || 'family_id'; - export const participantKey = process.env.TO_PARTICIPANT_ID_KEY || 'kf_id'; export const participantFileKey = process.env.TO_PARTICIPANT_FILE_ID_KEY || 'kf_id'; export const participantBiospecimenKey = process.env.TO_PARTICIPANT_BIOSPECIMEN_ID_KEY || 'kf_id'; diff --git a/src/errors.ts b/src/errors.ts index c454a0c..b0acf6f 100644 --- a/src/errors.ts +++ b/src/errors.ts @@ -1,4 +1,5 @@ import { NextFunction, Request, Response } from 'express'; +import { ExecutionResult } from 'graphql/execution/execute'; import { getReasonPhrase, StatusCodes } from 'http-status-codes'; import { SetNotFoundError } from './endpoints/sets/setError'; @@ -21,3 +22,9 @@ export const globalErrorLogger = (err: unknown, _req: Request, _res: Response, n console.error(err); next(err); }; + +export const throwErrorsFromGqlQueryIfExist = (resp: ExecutionResult): void | never => { + if (resp.errors) { + throw new Error(resp.errors.join(',')); + } +}; diff --git a/src/index.ts b/src/index.ts index 629dbed..b46a7bd 100644 --- a/src/index.ts +++ b/src/index.ts @@ -3,11 +3,11 @@ import 'regenerator-runtime/runtime.js'; import Arranger from '@arranger/server'; import { getProject } from '@arranger/server'; -import SQS from 'aws-sdk/clients/sqs'; +import { SQSClient } from '@aws-sdk/client-sqs'; import Keycloak from 'keycloak-connect'; import buildApp from './app'; -import { esHost, esUser, esPass, port } from './env'; +import { esHost, esPass, esUser, port } from './env'; import keycloakConfig from './keycloak'; process.on('uncaughtException', err => { @@ -26,7 +26,8 @@ process.on('SIGINT', () => { }); const keycloak = new Keycloak({}, keycloakConfig); -const sqs = new SQS({ apiVersion: '2012-11-05' }); + +const sqs = new SQSClient({}); const app = buildApp(keycloak, sqs, getProject); const externalContext = (req, _res, _con) => ({ auth: req.kauth?.grant?.access_token || {} }); @@ -41,7 +42,16 @@ Arranger({ app.get('/*/ping', router); app.use(keycloak.protect(), router); + const k: any = keycloak; + const originalValidateGrant = k.grantManager.validateGrant; + k.grantManager.validateGrant = grant => + originalValidateGrant.call(k.grantManager, grant).catch(err => { + console.error('Grant Validation Error', err); + throw err; + }); + app.listen(port, async () => { + console.log('Arranger-Next Starting'); console.log(`⚡️ Listening on port ${port} ⚡️`); }); }); diff --git a/src/middleware/cache.ts b/src/middleware/cache.ts index 4628caf..871dfda 100644 --- a/src/middleware/cache.ts +++ b/src/middleware/cache.ts @@ -3,6 +3,8 @@ import NodeCache from 'node-cache'; export const STATISTICS_CACHE_ID = 'statistics'; +export const STATISTICS_PUBLIC_CACHE_ID = 'statistics_studies'; + export const verifyCache = (cacheId: string, cache: NodeCache) => ( _req: Request, res: Response, diff --git a/src/riff/riffClient.ts b/src/riff/riffClient.ts index 06a076c..e65e770 100644 --- a/src/riff/riffClient.ts +++ b/src/riff/riffClient.ts @@ -29,7 +29,6 @@ export type Output = { sharedPublicly: boolean; creationDate: Date; updatedDate: Date; - updated_date: Date; }; export const getRiffs = async (accessToken: string, userId: string): Promise => { diff --git a/src/sqon/resolveSetInSqon.test.ts b/src/sqon/resolveSetInSqon.test.ts index c0e6b5c..988563c 100644 --- a/src/sqon/resolveSetInSqon.test.ts +++ b/src/sqon/resolveSetInSqon.test.ts @@ -1,12 +1,18 @@ +/* eslint-disable @typescript-eslint/no-var-requires */ import { SetSqon } from '../endpoints/sets/setsTypes'; -import { getRiffs, Output, RIFF_TYPE_SET } from '../riff/riffClient'; -import { resolveSetsInSqon } from './resolveSetInSqon'; +import { getRiffs, Output as RiffOutput, RIFF_TYPE_SET } from '../riff/riffClient'; +import { getSharedSet, getUserContents, Output as UserSetOutput } from '../userApi/userApiClient'; +import { resolveSetsInSqon, retrieveSetsFromUsers } from './resolveSetInSqon'; jest.mock('../riff/riffClient'); +jest.mock('../userApi/userApiClient'); +jest.mock('../env'); -describe('resolveSetsInSqon', () => { +describe('resolveSetsInSqon - legacy KF', () => { beforeEach(() => { (getRiffs as jest.Mock).mockReset(); + const env = require('../env'); + env.project = 'Kidsfirst'; }); it('should return the input sqon if not set id in it', async () => { @@ -50,50 +56,56 @@ describe('resolveSetsInSqon', () => { ], }; - const riff1ez = { + const riff1ez: RiffOutput = { id: '1ez', alias: 'tag-1ez', content: { ids: ['participant_1', 'participant_2'], - sqon: {}, + sqon: { op: 'and', content: [] }, riffType: RIFF_TYPE_SET, setType: 'participant', + idField: 'fhir_id', + sort: [], }, sharedPublicly: false, uid: 'uid-1ez', creationDate: new Date(), updatedDate: new Date(), - } as Output; + }; - const riff1ey = { + const riff1ey: RiffOutput = { id: '1ey', alias: 'tag-1ey', content: { ids: ['participant_1', 'participant_3'], - sqon: {}, + sqon: { op: 'and', content: [] }, riffType: RIFF_TYPE_SET, setType: 'participant', + idField: 'fhir_id', + sort: [], }, sharedPublicly: false, uid: 'uid-1ey', creationDate: new Date(), updatedDate: new Date(), - } as Output; + }; - const anotherRiff = { + const anotherRiff: RiffOutput = { id: '1ea', alias: 'tag-1ea', content: { ids: ['participant_2', 'participant_3'], - sqon: {}, + sqon: { op: 'and', content: [] }, riffType: RIFF_TYPE_SET, setType: 'participant', + idField: 'fhir_id', + sort: [], }, sharedPublicly: false, uid: 'uid-1ea', creationDate: new Date(), updatedDate: new Date(), - } as Output; + }; const getRiffsMockResponse = [riff1ey, anotherRiff, riff1ez]; @@ -146,35 +158,39 @@ describe('resolveSetsInSqon', () => { ], }; - const riff1ez = { + const riff1ez: RiffOutput = { id: '1ez', alias: 'tag-1ez', content: { ids: ['participant_1', 'participant_2'], - sqon: {}, + sqon: { op: 'and', content: [] }, riffType: RIFF_TYPE_SET, setType: 'participant', + idField: 'fhir_id', + sort: [], }, sharedPublicly: false, uid: 'uid-1ez', creationDate: new Date(), updatedDate: new Date(), - } as Output; + }; - const anotherRiff = { + const anotherRiff: RiffOutput = { id: '1ea', alias: 'tag-1ea', content: { ids: ['participant_2', 'participant_3'], - sqon: {}, + sqon: { op: 'and', content: [] }, riffType: RIFF_TYPE_SET, setType: 'participant', + idField: 'fhir_id', + sort: [], }, sharedPublicly: false, uid: 'uid-1ea', creationDate: new Date(), updatedDate: new Date(), - } as Output; + }; const getRiffsMockResponse = [anotherRiff, riff1ez]; @@ -206,3 +222,102 @@ describe('resolveSetsInSqon', () => { expect((getRiffs as jest.Mock).mock.calls.length).toEqual(1); }); }); + +describe('retrieveSetsFromUsers', () => { + beforeEach(() => { + (getUserContents as jest.Mock).mockReset(); + (getSharedSet as jest.Mock).mockReset(); + const env = require('../env'); + env.project = 'Include'; + }); + + const setIds = ['setId1', 'setId2']; + const setId1: UserSetOutput = { + id: 'setId1', + alias: 'my first set', + content: { + ids: ['participant_1', 'participant_2'], + sqon: { op: 'and', content: [] }, + idField: 'fhir_id', + sort: [], + riffType: RIFF_TYPE_SET, + setType: 'participant', + }, + sharedpublicly: false, + keycloak_id: 'uid-1ez', + creation_date: new Date(), + updated_date: new Date(), + }; + const setId2: UserSetOutput = { + id: 'setId2', + alias: 'my second set', + content: { + ids: ['participant_3', 'participant_4'], + sqon: { op: 'and', content: [] }, + idField: 'fhir_id', + sort: [], + riffType: RIFF_TYPE_SET, + setType: 'participant', + }, + sharedpublicly: false, + keycloak_id: 'uid-1ez', + creation_date: new Date(), + updated_date: new Date(), + }; + const sharedSet: UserSetOutput = { + id: 'sharedSet', + alias: 'not my set', + content: { + ids: ['participant_5', 'participant_6'], + sqon: { op: 'and', content: [] }, + idField: 'fhir_id', + sort: [], + riffType: RIFF_TYPE_SET, + setType: 'participant', + }, + sharedpublicly: true, + keycloak_id: 'uid-2ab', + creation_date: new Date(), + updated_date: new Date(), + }; + + it('should include user sets', async () => { + (getUserContents as jest.Mock).mockImplementation(() => [setId1, setId2]); + + const result = await retrieveSetsFromUsers('access_token', setIds); + + expect(result.length).toEqual(2); + expect(result).toEqual(expect.arrayContaining([setId1, setId2])); + expect((getUserContents as jest.Mock).mock.calls.length).toEqual(1); + expect((getSharedSet as jest.Mock).mock.calls.length).toEqual(0); + }); + + it('should add all shared sets', async () => { + (getUserContents as jest.Mock).mockImplementation(() => [setId1, setId2]); + (getSharedSet as jest.Mock).mockImplementation(() => sharedSet); + + const result = await retrieveSetsFromUsers('access_token', [...setIds, 'sharedSet']); + + expect(result.length).toEqual(3); + expect(result).toEqual(expect.arrayContaining([setId1, setId2, sharedSet])); + + expect((getUserContents as jest.Mock).mock.calls.length).toEqual(1); + expect((getSharedSet as jest.Mock).mock.calls.length).toEqual(1); + }); + + it('should fail if the shared set is not public (ie not returned by users-api)', async () => { + (getUserContents as jest.Mock).mockImplementation(() => [setId1, setId2]); + (getSharedSet as jest.Mock).mockImplementation(() => { + throw new Error('User Set #sharedSet does not exist.'); + }); + + try { + await retrieveSetsFromUsers('access_token', [...setIds, 'sharedSet']); + } catch (e) { + expect(e.message).toEqual('User Set #sharedSet does not exist.'); + } finally { + expect((getUserContents as jest.Mock).mock.calls.length).toEqual(1); + expect((getSharedSet as jest.Mock).mock.calls.length).toEqual(1); + } + }); +}); diff --git a/src/sqon/resolveSetInSqon.ts b/src/sqon/resolveSetInSqon.ts index e11b42f..5887755 100644 --- a/src/sqon/resolveSetInSqon.ts +++ b/src/sqon/resolveSetInSqon.ts @@ -1,11 +1,10 @@ import { Dictionary, flattenDeep, get, isArray, zipObject } from 'lodash'; +import { mapRiffOutputToUserOutput } from '../endpoints/sets/setsFeature'; import { SetSqon } from '../endpoints/sets/setsTypes'; -import { getRiffs } from '../riff/riffClient'; import { project, PROJECT_INCLUDE } from '../env'; -import { getUserContents } from '../userApi/userApiClient'; - -const projectType = project; +import { getRiffs } from '../riff/riffClient'; +import { getSharedSet, getUserContents, Output as UserSetOutput } from '../userApi/userApiClient'; const getSetIdsFromSqon = (sqon: SetSqon, collection = []) => (isArray(sqon.content) @@ -35,11 +34,11 @@ const injectIdsIntoSqon = (sqon: SetSqon, setIdsToValueMap: Dictionary export const resolveSetsInSqon = async (sqon: SetSqon, userId: string, accessToken: string): Promise => { const setIds: string[] = getSetIdsFromSqon(sqon || ({} as SetSqon)); if (setIds.length) { - let userSets; - if (projectType === PROJECT_INCLUDE) { - userSets = await getUserContents(accessToken); + let userSets: UserSetOutput[]; + if (project === PROJECT_INCLUDE) { + userSets = await retrieveSetsFromUsers(accessToken, setIds); } else { - userSets = await getRiffs(accessToken, userId); + userSets = (await getRiffs(accessToken, userId)).map(s => mapRiffOutputToUserOutput(s)); } const ids = setIds.map(setId => get(userSets.filter(r => r.id === setId)[0], 'content.ids', [])); @@ -53,3 +52,20 @@ export const resolveSetsInSqon = async (sqon: SetSqon, userId: string, accessTok return sqon; } }; + +export const retrieveSetsFromUsers = async (accessToken: string, setIds: string[]): Promise => { + // Get all user sets + const userSets = await getUserContents(accessToken); + const userSetsIds = userSets.map(us => us.id); + + for (const setId of setIds) { + // if set is a shared set, fetch it and add it to user sets + if (!userSetsIds.includes(setId)) { + const sharedSet = await getSharedSet(accessToken, setId); + userSets.push(sharedSet); + userSetsIds.push(sharedSet.id); + } + } + + return userSets; +}; diff --git a/src/sqon/searchSqon.ts b/src/sqon/searchSqon.ts index b17be19..04176d2 100644 --- a/src/sqon/searchSqon.ts +++ b/src/sqon/searchSqon.ts @@ -1,12 +1,10 @@ import { graphql } from 'graphql'; import { get } from 'lodash'; +import { ArrangerProject } from '../arrangerUtils'; import { SetSqon, Sort } from '../endpoints/sets/setsTypes'; -import { idKey, maxSetContentSize } from '../env'; +import { maxSetContentSize } from '../env'; -export type ArrangerProject = { - runQuery: ({ query: string, variables: unknown }) => Promise; -}; export const searchSqon = async ( sqon: SetSqon, projectId: string, @@ -44,7 +42,7 @@ export const searchSqon = async ( throw new Error(get(results, 'errors', undefined)); } - const ids: string[] = get(results, `data.${type}.hits.edges`, []).map(edge => edge.node[idKey]); + const ids: string[] = get(results, `data.${type}.hits.edges`, []).map(edge => edge.node[idField]); return ids; }; diff --git a/src/sqon/setSqon.ts b/src/sqon/setSqon.ts index 0f31db0..ac4f653 100644 --- a/src/sqon/setSqon.ts +++ b/src/sqon/setSqon.ts @@ -1,6 +1,6 @@ +import { getUserSet } from '../endpoints/sets/setsFeature'; import { SetSqon } from '../endpoints/sets/setsTypes'; import { participantBiospecimenKey, participantFileKey, participantKey } from '../env'; -import { getUserSet } from '../endpoints/sets/setsFeature'; const setRegex = /^set_id:(.+)$/gm; @@ -14,24 +14,33 @@ const getPathToParticipantId = (type: string) => { } }; -export const replaceSetByIds = async (sqon: SetSqon, accessToken, userId) => { +const CAPTURING_GROUP_OF_SET_ID_VALUE = 1; +export const replaceSetByIds = async (sqon: SetSqon, accessToken: string, userId: string): Promise => { if (!sqon) { throw new Error('Sqon is missing'); } - let contents = []; - - for (let i = 0; i < sqon.content.length; i++) { - const c = sqon.content[i]; + const contents = []; - if (c.content.value[0].match(setRegex)) { - const match = setRegex.exec(c.content.value[0])[1]; - const set = await getUserSet(accessToken, userId, match); - const newContent = { ...c }; - newContent.content.field = getPathToParticipantId(set.content.setType); - newContent.content.value = set.content.ids; - contents.push(newContent); + for (const content of sqon.content) { + const handleContent = async content => { + const matchesSet = setRegex.exec(content?.content?.value?.[0]); + const setId: string | null = matchesSet && matchesSet[CAPTURING_GROUP_OF_SET_ID_VALUE]; + if (setId) { + const set = await getUserSet(accessToken, userId, setId); + const newContent = { ...content }; + newContent.content.field = getPathToParticipantId(set.content.setType); + newContent.content.value = set.content.ids; + contents.push(newContent); + } else { + contents.push(content); + } + }; + if (Array.isArray(content.content)) { + for (const deepContent of content.content) { + await handleContent(deepContent); + } } else { - contents.push(c); + await handleContent(content); } } return { op: 'and', content: contents }; diff --git a/src/userApi/userApiClient.ts b/src/userApi/userApiClient.ts index 04028dc..e3c47d3 100644 --- a/src/userApi/userApiClient.ts +++ b/src/userApi/userApiClient.ts @@ -1,8 +1,48 @@ import fetch from 'node-fetch'; +import { SetSqon, Sort } from '../endpoints/sets/setsTypes'; import { userApiURL } from '../env'; +import { CreateUpdateBody } from '../riff/riffClient'; import { UserApiError } from './userApiError'; -import { CreateUpdateBody, Output } from '../riff/riffClient'; + +export type Content = { + setType: string; + riffType: string; + ids: string[]; + sqon: SetSqon; + sort: Sort[]; + idField: string; +}; + +export type Output = { + id: string; + keycloak_id: string; + content: Content; + alias: string; + sharedpublicly: boolean; + creation_date: Date; + updated_date: Date; +}; + +export const getSharedSet = async (accessToken: string, setId: string): Promise => { + const uri = `${userApiURL}/user-sets/shared/${setId}`; + + const response = await fetch(encodeURI(uri), { + method: 'get', + headers: { + Authorization: accessToken, + 'Content-Type': 'application/json', + }, + }); + + const body = await response.json(); + + if (response.status === 200) { + return body; + } + + throw new UserApiError(response.status, body); +}; export const getUserContents = async (accessToken: string): Promise => { const uri = `${userApiURL}/user-sets`; diff --git a/test/authTestUtils.ts b/test/authTestUtils.ts index ade25b4..652c905 100644 --- a/test/authTestUtils.ts +++ b/test/authTestUtils.ts @@ -14,10 +14,14 @@ JBCiTrVNMy4wmZruwoG/sae517Jl6cIFePSifpOTsA== export const publicKey = `MFwwDQYJKoZIhvcNAQEBBQADSwAwSAJBAJgoVgqi7/C9uSoUsfQeep2Dbw5HfXWQIyypg+XZ3NqsxTA2k2Fr2vmBu82iGsNgwWBKac5IOzSGvyob1l64MkUCAwEAAQ==`; +export const fakeKeycloakRealm = 'fake_realm'; +export const fakeKeycloakClient = 'fake_client'; +export const fakeKeycloakUrl = 'https://fake_keycloak_url.com/auth'; + export const getToken = (expire = 1000, sub = '12345-678-90abcdef', roles = []) => jwt.sign( { - iss: 'https://kf-keycloak-qa.kf-strides.org/auth/realms/kidsfirstdrc', + iss: `${fakeKeycloakUrl}/realms/${fakeKeycloakRealm}`, sub: sub, aud: 'kf-api-arranger', jti: '2c166d55-5ae6-4fb4-9daa-a1d5e1f535d7',