From 7545aa3c9dd2d5d8db5e6376635f645209cccb4a Mon Sep 17 00:00:00 2001 From: Alexis Li Date: Thu, 17 Feb 2022 12:32:24 -0500 Subject: [PATCH] use song performance upgraded paginated get analysis endpoint --- .../metadata/study/song/SongStudyDAO.java | 58 +- .../properties/ApplicationProperties.java | 2 + .../DefaultApplicationProperties.java | 6 + .../src/main/resources/config/application.yml | 2 + .../metadata/study/song/SongStudyDAOTest.java | 45 +- .../api/AnalysisCentricIntegrationTest.java | 140 +++- .../api/FileCentricIntegrationTest.java | 146 ++++- .../src/test/resources/config/application.yml | 1 + .../DASH-CA.analysis.response.json | 79 +++ .../EUCANCAN-BE.aws.analysis.response.json | 92 +++ .../EUCANCAN-BE.aws.conflicting.response.json | 92 +++ .../EUCANCAN-BE.response.json | 176 +++++ .../OCCAMS-GB.analysis.response.json | 90 +++ .../TEST-CA.analysis.response.json | 77 +++ .../empty-response.json | 7 + .../LIAD-FR.analysis.response.json | 78 +++ .../LIRI-JP.analysis.response.json | 607 ++++++++++++++++++ .../MALY-DE.analysis.response.json | 247 +++++++ .../PACA-CA.analysis.response.json | 463 +++++++++++++ ...EME-CA.aws.conflicting.study.response.json | 90 +++ .../PEME-CA.aws.study.response.json | 90 +++ .../PEME-CA.study.response.json | 198 ++++++ .../empty-response.json | 7 + .../SongStudyDAOTest/PEME-CA.response.json | 174 +++++ .../SongStudyDAOTest/empty-response.json | 8 + .../metadata/study/GetAnalysisResponse.java | 16 + 26 files changed, 2941 insertions(+), 50 deletions(-) create mode 100644 maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/DASH-CA.analysis.response.json create mode 100644 maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.aws.analysis.response.json create mode 100644 maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.aws.conflicting.response.json create mode 100644 maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.response.json create mode 100644 maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/OCCAMS-GB.analysis.response.json create mode 100644 maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/TEST-CA.analysis.response.json create mode 100644 maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/empty-response.json create mode 100644 maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/LIAD-FR.analysis.response.json create mode 100644 maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/LIRI-JP.analysis.response.json create mode 100644 maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/MALY-DE.analysis.response.json create mode 100644 maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PACA-CA.analysis.response.json create mode 100644 maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.aws.conflicting.study.response.json create mode 100644 maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.aws.study.response.json create mode 100644 maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.study.response.json create mode 100644 maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/empty-response.json create mode 100644 maestro-app/src/test/resources/fixtures/SongStudyDAOTest/PEME-CA.response.json create mode 100644 maestro-app/src/test/resources/fixtures/SongStudyDAOTest/empty-response.json create mode 100644 maestro-domain/src/main/java/bio/overture/maestro/domain/entities/metadata/study/GetAnalysisResponse.java diff --git a/maestro-app/src/main/java/bio/overture/maestro/app/infra/adapter/outbound/metadata/study/song/SongStudyDAO.java b/maestro-app/src/main/java/bio/overture/maestro/app/infra/adapter/outbound/metadata/study/song/SongStudyDAO.java index 7b3fe821..8eec156e 100644 --- a/maestro-app/src/main/java/bio/overture/maestro/app/infra/adapter/outbound/metadata/study/song/SongStudyDAO.java +++ b/maestro-app/src/main/java/bio/overture/maestro/app/infra/adapter/outbound/metadata/study/song/SongStudyDAO.java @@ -24,6 +24,7 @@ import bio.overture.maestro.app.infra.config.properties.ApplicationProperties; import bio.overture.maestro.domain.api.exception.NotFoundException; import bio.overture.maestro.domain.entities.metadata.study.Analysis; +import bio.overture.maestro.domain.entities.metadata.study.GetAnalysisResponse; import bio.overture.maestro.domain.entities.metadata.study.Study; import bio.overture.maestro.domain.port.outbound.metadata.study.GetAllStudiesCommand; import bio.overture.maestro.domain.port.outbound.metadata.study.GetAnalysisCommand; @@ -48,16 +49,15 @@ class SongStudyDAO implements StudyDAO { private static final String STUDY_ANALYSES_URL_TEMPLATE = - "{0}/studies/{1}/analysis?analysisStates={2}"; + "{0}/studies/{1}/analysis/paginated?analysisStates={2}&limit={3}&offset={4}"; private static final String STUDY_ANALYSIS_URL_TEMPLATE = "{0}/studies/{1}/analysis/{2}"; private static final String STUDIES_URL_TEMPLATE = "{0}/studies/all"; - private static final String MSG_STUDY_DOES_NOT_EXIST = - "studyId {0} doesn't exist in the specified repository"; private static final String MSG_ANALYSIS_DOES_NOT_EXIST = "analysis {0} doesn't exist for studyId {1}, repository {2} (or not in a matching state)"; private static final int FALLBACK_SONG_TIMEOUT = 60; private static final int FALLBACK_SONG_ANALYSIS_TIMEOUT = 5; private static final int FALLBACK_SONG_MAX_RETRY = 0; + private static final int DEFAULT_SONG_PAGE_LIMIT = 100; private final WebClient webClient; private final int songMaxRetries; private final int minBackoffSec = 1; @@ -68,11 +68,16 @@ class SongStudyDAO implements StudyDAO { private final int studyCallTimeoutSeconds; private final int analysisCallTimeoutSeconds; + private final int pageLimit; @Inject public SongStudyDAO( @NonNull WebClient webClient, @NonNull ApplicationProperties applicationProperties) { this.webClient = webClient; + this.pageLimit = + applicationProperties.pageLimit() > 0 + ? applicationProperties.pageLimit() + : DEFAULT_SONG_PAGE_LIMIT; this.indexableStudyStatuses = applicationProperties.indexableStudyStatuses(); this.indexableStudyStatusesList = List.of(indexableStudyStatuses.split(",")); this.songMaxRetries = @@ -94,7 +99,6 @@ public Mono> getStudyAnalyses(GetStudyAnalysesCommand getStudyAna log.trace("in getStudyAnalyses, args: {} ", getStudyAnalysesCommand); val repoBaseUrl = getStudyAnalysesCommand.getFilesRepositoryBaseUrl(); val studyId = getStudyAnalysesCommand.getStudyId(); - val analysisListType = new ParameterizedTypeReference>() {}; val retryConfig = Retry.allBut(NotFoundException.class) .retryMax(this.songMaxRetries) @@ -107,14 +111,39 @@ public Mono> getStudyAnalyses(GetStudyAnalysesCommand getStudyAna .exponentialBackoff( Duration.ofSeconds(minBackoffSec), Duration.ofSeconds(maxBackoffSec)); - return this.webClient - .get() - .uri(format(STUDY_ANALYSES_URL_TEMPLATE, repoBaseUrl, studyId, this.indexableStudyStatuses)) - .retrieve() - .onStatus( - HttpStatus.NOT_FOUND::equals, - clientResponse -> error(notFound(MSG_STUDY_DOES_NOT_EXIST, studyId))) - .bodyToMono(analysisListType) + var offset = 0; + val url = + format( + STUDY_ANALYSES_URL_TEMPLATE, + repoBaseUrl, + studyId, + this.indexableStudyStatuses, + this.pageLimit, + offset); + var wrapper = + new Object() { + int offset = 0; + }; + + return fetchItems(url) + .expand( + rep -> { + if (rep.getAnalyses().size() == 0) { + return Mono.empty(); + } + wrapper.offset += this.pageLimit; + val currentUrl = + format( + STUDY_ANALYSES_URL_TEMPLATE, + repoBaseUrl, + studyId, + this.indexableStudyStatuses, + this.pageLimit, + wrapper.offset); + return fetchItems(currentUrl); + }) + .flatMap(rep -> Flux.fromIterable(rep.getAnalyses())) + .collectList() .transform(retryAndTimeout(retryConfig, Duration.ofSeconds(this.studyCallTimeoutSeconds))) .doOnSuccess( (list) -> @@ -124,6 +153,11 @@ public Mono> getStudyAnalyses(GetStudyAnalysesCommand getStudyAna getStudyAnalysesCommand)); } + private Mono fetchItems(@NonNull String url) { + log.trace("get paged analyses, url = {}", url); + return this.webClient.get().uri(url).retrieve().bodyToMono(GetAnalysisResponse.class); + } + @Override public Flux getStudies(@NonNull GetAllStudiesCommand getAllStudiesCommand) { log.trace("in getStudyAnalyses, args: {} ", getAllStudiesCommand); diff --git a/maestro-app/src/main/java/bio/overture/maestro/app/infra/config/properties/ApplicationProperties.java b/maestro-app/src/main/java/bio/overture/maestro/app/infra/config/properties/ApplicationProperties.java index 0dc83cb2..f2d87016 100644 --- a/maestro-app/src/main/java/bio/overture/maestro/app/infra/config/properties/ApplicationProperties.java +++ b/maestro-app/src/main/java/bio/overture/maestro/app/infra/config/properties/ApplicationProperties.java @@ -80,6 +80,8 @@ public interface ApplicationProperties { String indexableStudyStatuses(); + int pageLimit(); + int songAnalysisCallTimeoutSeconds(); Slack.SlackChannelInfo getSlackChannelInfo(); diff --git a/maestro-app/src/main/java/bio/overture/maestro/app/infra/config/properties/DefaultApplicationProperties.java b/maestro-app/src/main/java/bio/overture/maestro/app/infra/config/properties/DefaultApplicationProperties.java index c5b9f7f1..75b15ced 100644 --- a/maestro-app/src/main/java/bio/overture/maestro/app/infra/config/properties/DefaultApplicationProperties.java +++ b/maestro-app/src/main/java/bio/overture/maestro/app/infra/config/properties/DefaultApplicationProperties.java @@ -171,6 +171,11 @@ public String indexableStudyStatuses() { return this.song.getIndexableStudyStatesCsv(); } + @Override + public int pageLimit() { + return this.song.getPageLimit(); + } + @Override public int songAnalysisCallTimeoutSeconds() { return this.song.getTimeoutSec().getAnalysis(); @@ -270,6 +275,7 @@ private static class Song { private int maxRetries = 3; // FIXME: This configuration is called three different things in this codebase private String indexableStudyStatesCsv = "PUBLISHED"; + private int pageLimit = 100; } @Data diff --git a/maestro-app/src/main/resources/config/application.yml b/maestro-app/src/main/resources/config/application.yml index ea014400..b2e80d10 100644 --- a/maestro-app/src/main/resources/config/application.yml +++ b/maestro-app/src/main/resources/config/application.yml @@ -15,6 +15,8 @@ maestro: maxInMemorySize: -1 song: indexableStudyStatesCsv: PUBLISHED + # page limit for getting analysis from song + pageLimit: 50 maxRetries: 3 timeoutSec: study: 100 # some studies take really long, +30 secs, to be downloaded diff --git a/maestro-app/src/test/java/bio/overture/maestro/app/infra/adapter/outbound/metadata/study/song/SongStudyDAOTest.java b/maestro-app/src/test/java/bio/overture/maestro/app/infra/adapter/outbound/metadata/study/song/SongStudyDAOTest.java index 40bc0d95..7d962900 100644 --- a/maestro-app/src/test/java/bio/overture/maestro/app/infra/adapter/outbound/metadata/study/song/SongStudyDAOTest.java +++ b/maestro-app/src/test/java/bio/overture/maestro/app/infra/adapter/outbound/metadata/study/song/SongStudyDAOTest.java @@ -135,23 +135,30 @@ void shouldRetryFetchingAnalysisOnFailure() { @Test @SneakyThrows void shouldRetryFetchingStudyAnalysesOnFailure() { - val analyses = loadJsonString(this.getClass(), "PEME-CA.study.json"); + val analyses = loadJsonString(this.getClass(), "PEME-CA.response.json"); + val emptyResp = loadJsonString(this.getClass(), "empty-response.json"); val analysesList = loadJsonFixture( this.getClass(), "PEME-CA.study.json", new TypeReference>() {}); stubFor( - request("GET", urlEqualTo("/studies/PEME-CA/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlMatching( + "/studies/PEME-CA/analysis/paginated\\?analysisStates=PUBLISHED&limit=100&offset=\\d+")) .inScenario("RANDOM_FAILURE") .whenScenarioStateIs(Scenario.STARTED) .willReturn( aResponse() .withStatus(400) - .withBody("

some wierd unexpected text

") + .withBody("

some weird unexpected text

") .withHeader("content-type", "text/html")) .willSetStateTo("WORKING")); stubFor( - request("GET", urlEqualTo("/studies/PEME-CA/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .inScenario("RANDOM_FAILURE") .whenScenarioStateIs("WORKING") .willReturn( @@ -159,6 +166,19 @@ void shouldRetryFetchingStudyAnalysesOnFailure() { .withBody(analyses) .withStatus(200) .withHeader("content-type", "application/json"))); + // Mock the second/last request: + stubFor( + request( + "GET", + urlEqualTo( + "/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .inScenario("RANDOM_FAILURE") + .whenScenarioStateIs("WORKING") + .willReturn( + aResponse() + .withBody(emptyResp) + .withStatus(200) + .withHeader("content-type", "application/json"))); val analysesMono = songStudyDAO.getStudyAnalyses( @@ -179,11 +199,24 @@ void fetchingStudyAnalysesShouldReturnRetryExhaustedException() { .studyId("PEME-CA") .build(); stubFor( - request("GET", urlEqualTo("/studies/PEME-CA/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(400) - .withBody("

Some wierd unexpected text

") + .withBody("

Some weird unexpected text

") + .withHeader("content-type", "text/html"))); + stubFor( + request( + "GET", + urlEqualTo( + "/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(400) + .withBody("

Some weird unexpected text

") .withHeader("content-type", "text/html"))); // when diff --git a/maestro-app/src/test/java/bio/overture/maestro/domain/api/AnalysisCentricIntegrationTest.java b/maestro-app/src/test/java/bio/overture/maestro/domain/api/AnalysisCentricIntegrationTest.java index 31a81426..3a9f8a43 100644 --- a/maestro-app/src/test/java/bio/overture/maestro/domain/api/AnalysisCentricIntegrationTest.java +++ b/maestro-app/src/test/java/bio/overture/maestro/domain/api/AnalysisCentricIntegrationTest.java @@ -224,17 +224,33 @@ void shouldIndexStudyRepositoryWithExclusionsApplied() throws InterruptedExcepti elasticSearchJsonMapper, Map.of("COLLAB_REPO_URL", applicationProperties.repositories().get(0).getUrl()))); + val emptyResp = loadJsonString(this.getClass(), "empty-response.json"); for (Study study : studies) { val studyId = study.getStudyId(); - val studyAnalyses = getStudyAnalysesAsString(studyId); + val resp = getAnalysisResponse(studyId); stubFor( request( "GET", - urlEqualTo("/collab/studies/" + studyId + "/analysis?analysisStates=PUBLISHED")) + urlEqualTo( + "/collab/studies/" + + studyId + + "/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(200) - .withBody(studyAnalyses) + .withBody(resp) + .withHeader("Content-Type", "application/json"))); + stubFor( + request( + "GET", + urlEqualTo( + "/collab/studies/" + + studyId + + "/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(emptyResp) .withHeader("Content-Type", "application/json"))); } @@ -275,7 +291,8 @@ void shouldIndexStudyRepositoryWithExclusionsApplied() throws InterruptedExcepti void shouldIndexStudyWithExclusionsApplied() throws InterruptedException, IOException { // Given @SuppressWarnings("all") - val analyses = loadJsonString(this.getClass(), "EUCANCAN-BE.studies.json"); + val analyses = loadJsonString(this.getClass(), "EUCANCAN-BE.response.json"); + val emptyResp = loadJsonString(this.getClass(), "empty-response.json"); val expectedDoc0 = loadJsonFixture( this.getClass(), @@ -292,12 +309,25 @@ void shouldIndexStudyWithExclusionsApplied() throws InterruptedException, IOExce Map.of("COLLAB_REPO_URL", applicationProperties.repositories().get(0).getUrl())); stubFor( - request("GET", urlEqualTo("/collab/studies/EUCANCAN-BE/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/collab/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(200) .withBody(analyses) .withHeader("Content-Type", "application/json"))); + stubFor( + request( + "GET", + urlEqualTo( + "/collab/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(emptyResp) + .withHeader("Content-Type", "application/json"))); // test val result = @@ -334,6 +364,8 @@ void shouldIndexStudyWithExclusionsApplied() throws InterruptedException, IOExce void shouldDeleteSingleAnalysis() throws InterruptedException, IOException { @SuppressWarnings("all") val collabAnalyses = loadJsonString(this.getClass(), "EUCANCAN-BE.studies.json"); + val resp = loadJsonString(this.getClass(), "EUCANCAN-BE.response.json"); + val emptyResp = loadJsonString(this.getClass(), "empty-response.json"); val expectedDoc0 = loadJsonFixture( this.getClass(), @@ -350,10 +382,23 @@ void shouldDeleteSingleAnalysis() throws InterruptedException, IOException { Map.of("COLLAB_REPO_URL", applicationProperties.repositories().get(0).getUrl())); stubFor( - request("GET", urlEqualTo("/collab/studies/EUCANCAN-BE/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/collab/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() - .withBody(collabAnalyses) + .withBody(resp) + .withHeader("Content-Type", "application/json") + .withStatus(200))); + stubFor( + request( + "GET", + urlEqualTo( + "/collab/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withBody(emptyResp) .withHeader("Content-Type", "application/json") .withStatus(200))); @@ -388,9 +433,11 @@ void shouldDeleteSingleAnalysis() throws InterruptedException, IOException { void shouldUpdateExistingDocRepository() throws InterruptedException, IOException { // Given @SuppressWarnings("all") - val collabAnalyses = loadJsonString(this.getClass(), "EUCANCAN-BE.studies.json"); + val collabAnalyses = loadJsonString(this.getClass(), "EUCANCAN-BE.response.json"); @SuppressWarnings("all") - val awsStudyAnalyses = loadJsonString(this.getClass(), "EUCANCAN-BE.aws.analysis.json"); + val awsStudyAnalyses = + loadJsonString(this.getClass(), "EUCANCAN-BE.aws.analysis.response.json"); + val emptyResp = loadJsonString(this.getClass(), "empty-response.json"); val expectedDoc0 = loadJsonFixture( @@ -418,20 +465,46 @@ void shouldUpdateExistingDocRepository() throws InterruptedException, IOExceptio "COLLAB_REPO_URL", applicationProperties.repositories().get(0).getUrl(), "AWS_REPO_URL", applicationProperties.repositories().get(1).getUrl())); stubFor( - request("GET", urlEqualTo("/collab/studies/EUCANCAN-BE/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/collab/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(200) .withBody(collabAnalyses) .withHeader("Content-Type", "application/json"))); + stubFor( + request( + "GET", + urlEqualTo( + "/collab/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(emptyResp) + .withHeader("Content-Type", "application/json"))); stubFor( - request("GET", urlEqualTo("/aws/studies/EUCANCAN-BE/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/aws/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(200) .withBody(awsStudyAnalyses) .withHeader("Content-Type", "application/json"))); + stubFor( + request( + "GET", + urlEqualTo( + "/aws/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(emptyResp) + .withHeader("Content-Type", "application/json"))); // test // step 1 @@ -475,11 +548,15 @@ void shouldDetectAndNotifyConflictingDocuments() throws InterruptedException, IO // Given @SuppressWarnings("all") val collabAnalyses = loadJsonString(this.getClass(), "EUCANCAN-BE.studies.json"); + val resp = loadJsonString(this.getClass(), "EUCANCAN-BE.response.json"); + val emptyResp = loadJsonString(this.getClass(), "empty-response.json"); // Conflicting analysis 43f07e4d-e26b-4f4a-b07e-4de26b9f4a50 has a different analysis state: @SuppressWarnings("all") val awsStudyAnalyses = loadJsonString(this.getClass(), "EUCANCAN-BE.aws.conflicting.study.json"); + val awsAnalysisResp = + loadJsonString(this.getClass(), "EUCANCAN-BE.aws.conflicting.response.json"); val awsStudyAnalysesList = loadJsonFixture( this.getClass(), @@ -505,19 +582,47 @@ void shouldDetectAndNotifyConflictingDocuments() throws InterruptedException, IO NotificationName.ANALYSIS_CONFLICT, getConflicts(expectedDoc1, awsStudyAnalysesList.get(0).getAnalysisId())); + // stub collab requests: stubFor( - request("GET", urlEqualTo("/collab/studies/EUCANCAN-BE/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/collab/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(200) - .withBody(collabAnalyses) + .withBody(resp) .withHeader("Content-Type", "application/json"))); stubFor( - request("GET", urlEqualTo("/aws/studies/EUCANCAN-BE/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/collab/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) .willReturn( aResponse() .withStatus(200) - .withBody(awsStudyAnalyses) + .withBody(emptyResp) + .withHeader("Content-Type", "application/json"))); + // stub aws repo requests: + stubFor( + request( + "GET", + urlEqualTo( + "/aws/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(awsAnalysisResp) + .withHeader("Content-Type", "application/json"))); + stubFor( + request( + "GET", + urlEqualTo( + "/aws/studies/EUCANCAN-BE/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(emptyResp) .withHeader("Content-Type", "application/json"))); // test @@ -618,6 +723,11 @@ private String getStudyAnalysesAsString(String studyId) { return loadJsonString(getClass(), studyId + ".analysis.json"); } + @SneakyThrows + private String getAnalysisResponse(String studyId) { + return loadJsonString(getClass(), studyId + ".analysis.response.json"); + } + @NotNull private List getAnalysisCentricDocuments() throws IOException { val searchRequest = new SearchRequest(alias); diff --git a/maestro-app/src/test/java/bio/overture/maestro/domain/api/FileCentricIntegrationTest.java b/maestro-app/src/test/java/bio/overture/maestro/domain/api/FileCentricIntegrationTest.java index 8ca80676..48520550 100644 --- a/maestro-app/src/test/java/bio/overture/maestro/domain/api/FileCentricIntegrationTest.java +++ b/maestro-app/src/test/java/bio/overture/maestro/domain/api/FileCentricIntegrationTest.java @@ -265,6 +265,7 @@ void shouldIndexStudyRepositoryWithExclusionsApplied() throws InterruptedExcepti // study LIAD-FR and donor DO52693 should be excluded // Given val studiesArray = loadJsonFixture(this.getClass(), "studies.json", String[].class); + val emptyResp = loadJsonString(this.getClass(), "empty-response.json"); val studies = Arrays.stream(studiesArray) .map(s -> Study.builder().studyId(s).build()) @@ -284,12 +285,27 @@ void shouldIndexStudyRepositoryWithExclusionsApplied() throws InterruptedExcepti stubFor( request( "GET", - urlEqualTo("/collab/studies/" + studyId + "/analysis?analysisStates=PUBLISHED")) + urlEqualTo( + "/collab/studies/" + + studyId + + "/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(200) .withBody(studyAnalyses) .withHeader("Content-Type", "application/json"))); + stubFor( + request( + "GET", + urlEqualTo( + "/collab/studies/" + + studyId + + "/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(emptyResp) + .withHeader("Content-Type", "application/json"))); } stubFor( @@ -329,7 +345,8 @@ void shouldIndexStudyRepositoryWithExclusionsApplied() throws InterruptedExcepti void shouldIndexStudyWithExclusionsApplied() throws InterruptedException, IOException { // Given @SuppressWarnings("all") - val analyses = loadJsonString(this.getClass(), "PEME-CA.study.json"); + val analyses = loadJsonString(this.getClass(), "PEME-CA.study.response.json"); + val emptyResp = loadJsonString(this.getClass(), "empty-response.json"); val expectedDoc0 = loadJsonFixture( this.getClass(), @@ -346,12 +363,25 @@ void shouldIndexStudyWithExclusionsApplied() throws InterruptedException, IOExce Map.of("COLLAB_REPO_URL", applicationProperties.repositories().get(0).getUrl())); stubFor( - request("GET", urlEqualTo("/collab/studies/PEME-CA/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/collab/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(200) .withBody(analyses) .withHeader("Content-Type", "application/json"))); + stubFor( + request( + "GET", + urlEqualTo( + "/collab/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(emptyResp) + .withHeader("Content-Type", "application/json"))); // test val result = @@ -387,9 +417,11 @@ void shouldIndexStudyWithExclusionsApplied() throws InterruptedException, IOExce void shouldDeleteSingleAnalysis() throws InterruptedException, IOException { // Given @SuppressWarnings("all") - val collabAnalyses = loadJsonString(this.getClass(), "PEME-CA.study.json"); + val collabAnalyses = loadJsonString(this.getClass(), "PEME-CA.study.response.json"); @SuppressWarnings("all") - val awsStudyAnalyses = loadJsonString(this.getClass(), "PEME-CA.aws.study.json"); + val awsStudyAnalyses = loadJsonString(this.getClass(), "PEME-CA.aws.study.response.json"); + val emptyResp = loadJsonString(this.getClass(), "empty-response.json"); + val expectedDoc0 = loadJsonFixture( this.getClass(), @@ -406,19 +438,45 @@ void shouldDeleteSingleAnalysis() throws InterruptedException, IOException { Map.of("COLLAB_REPO_URL", applicationProperties.repositories().get(0).getUrl())); stubFor( - request("GET", urlEqualTo("/collab/studies/PEME-CA/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/collab/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withBody(collabAnalyses) .withHeader("Content-Type", "application/json") .withStatus(200))); stubFor( - request("GET", urlEqualTo("/aws/studies/PEME-CA/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/collab/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withBody(emptyResp) + .withHeader("Content-Type", "application/json") + .withStatus(200))); + stubFor( + request( + "GET", + urlEqualTo( + "/aws/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withBody(awsStudyAnalyses) .withHeader("Content-Type", "application/json") .withStatus(200))); + stubFor( + request( + "GET", + urlEqualTo( + "/aws/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withBody(emptyResp) + .withHeader("Content-Type", "application/json") + .withStatus(200))); populateIndexWithCollabStudy(expectedDoc0, expectedDoc1); @@ -450,10 +508,10 @@ void shouldDeleteSingleAnalysis() throws InterruptedException, IOException { void shouldUpdateExistingFileDocRepository() throws InterruptedException, IOException { // Given @SuppressWarnings("all") - val collabAnalyses = loadJsonString(this.getClass(), "PEME-CA.study.json"); + val collabAnalyses = loadJsonString(this.getClass(), "PEME-CA.study.response.json"); @SuppressWarnings("all") - val awsStudyAnalyses = loadJsonString(this.getClass(), "PEME-CA.aws.study.json"); - + val awsStudyAnalyses = loadJsonString(this.getClass(), "PEME-CA.aws.study.response.json"); + val emptyResp = loadJsonString(this.getClass(), "empty-response.json"); val expectedDoc0 = loadJsonFixture( this.getClass(), @@ -480,20 +538,46 @@ void shouldUpdateExistingFileDocRepository() throws InterruptedException, IOExce "COLLAB_REPO_URL", applicationProperties.repositories().get(0).getUrl(), "AWS_REPO_URL", applicationProperties.repositories().get(1).getUrl())); stubFor( - request("GET", urlEqualTo("/collab/studies/PEME-CA/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/collab/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(200) .withBody(collabAnalyses) .withHeader("Content-Type", "application/json"))); + stubFor( + request( + "GET", + urlEqualTo( + "/collab/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(emptyResp) + .withHeader("Content-Type", "application/json"))); stubFor( - request("GET", urlEqualTo("/aws/studies/PEME-CA/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/aws/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(200) .withBody(awsStudyAnalyses) .withHeader("Content-Type", "application/json"))); + stubFor( + request( + "GET", + urlEqualTo( + "/aws/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(emptyResp) + .withHeader("Content-Type", "application/json"))); // test // step 1 @@ -534,11 +618,13 @@ void shouldUpdateExistingFileDocRepository() throws InterruptedException, IOExce void shouldDetectAndNotifyConflictingDocuments() throws InterruptedException, IOException { // Given @SuppressWarnings("all") - val collabAnalyses = loadJsonString(this.getClass(), "PEME-CA.study.json"); + val collabAnalyses = loadJsonString(this.getClass(), "PEME-CA.study.response.json"); + val emptyResp = loadJsonString(this.getClass(), "empty-response.json"); // this has a different analysis id than the one in previous files @SuppressWarnings("all") - val awsStudyAnalyses = loadJsonString(this.getClass(), "PEME-CA.aws.conflicting.study.json"); + val awsStudyAnalyses = + loadJsonString(this.getClass(), "PEME-CA.aws.conflicting.study.response.json"); val awsStudyAnalysesList = loadJsonFixture( this.getClass(), @@ -565,19 +651,45 @@ void shouldDetectAndNotifyConflictingDocuments() throws InterruptedException, IO getConflicts(expectedDoc1, awsStudyAnalysesList.get(0).getAnalysisId())); stubFor( - request("GET", urlEqualTo("/collab/studies/PEME-CA/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/collab/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(200) .withBody(collabAnalyses) .withHeader("Content-Type", "application/json"))); stubFor( - request("GET", urlEqualTo("/aws/studies/PEME-CA/analysis?analysisStates=PUBLISHED")) + request( + "GET", + urlEqualTo( + "/collab/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(emptyResp) + .withHeader("Content-Type", "application/json"))); + stubFor( + request( + "GET", + urlEqualTo( + "/aws/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=0")) .willReturn( aResponse() .withStatus(200) .withBody(awsStudyAnalyses) .withHeader("Content-Type", "application/json"))); + stubFor( + request( + "GET", + urlEqualTo( + "/aws/studies/PEME-CA/analysis/paginated?analysisStates=PUBLISHED&limit=100&offset=100")) + .willReturn( + aResponse() + .withStatus(200) + .withBody(emptyResp) + .withHeader("Content-Type", "application/json"))); // test populateIndexWithCollabStudy(expectedDoc0, expectedDoc1); @@ -694,6 +806,6 @@ private List getFileCentricDocuments() throws IOException { @SneakyThrows private String getStudyAnalysesAsString(String studyId) { - return loadJsonString(getClass(), studyId + ".analysis.json"); + return loadJsonString(getClass(), studyId + ".analysis.response.json"); } } diff --git a/maestro-app/src/test/resources/config/application.yml b/maestro-app/src/test/resources/config/application.yml index b4c8bc88..c2d8d371 100644 --- a/maestro-app/src/test/resources/config/application.yml +++ b/maestro-app/src/test/resources/config/application.yml @@ -15,6 +15,7 @@ maestro: song: indexableStudyStatus: PUBLISHED maxRetries: 3 + pageLimit: 100 timeoutSec: study: 5 analysis: 5 diff --git a/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/DASH-CA.analysis.response.json b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/DASH-CA.analysis.response.json new file mode 100644 index 00000000..0192c5f1 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/DASH-CA.analysis.response.json @@ -0,0 +1,79 @@ +{ + "analyses": + [ + { + "analysisId": "a07fe97f-80e1-4e69-bfe9-7f80e18e6969", + "studyId": "DASH-CA", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "sampleId": "SA619219", + "specimenId": "SP219218", + "submitterSampleId": "dashsa-1", + "matchedNormalSubmitterSampleId": null, + "sampleType": "Amplified DNA", + "specimen": { + "specimenId": "SP219218", + "donorId": "DO259142", + "submitterSpecimenId": "dashsp-1", + "tumourNormalDesignation": "Normal", + "specimenTissueSource": "Blood derived", + "specimenType": "Normal" + }, + "donor": { + "donorId": "DO259142", + "studyId": "DASH-CA", + "gender": "Male", + "submitterDonorId": "DASH-1" + } + } + ], + "files": [ + { + "objectId": "fc019c84-dc29-5362-8069-dee7aea67735", + "studyId": "DASH-CA", + "analysisId": "a07fe97f-80e1-4e69-bfe9-7f80e18e6969", + "fileName": "dash-1-normal.bam", + "fileSize": 24, + "fileType": "BAM", + "fileMd5sum": "4d6e35e3290ccce08c8c7517dc29d624", + "fileAccess": "controlled", + "dataType": "Submitted Reads" + } + ], + "analysisType": { + "name": "sequencing_experiment", + "version": 3 + }, + "experiment": { + "platform": "ILLUMINA", + "platform_model": null, + "sequencing_date": null, + "sequencing_center": null, + "experimental_strategy": "WGS", + "submitter_sequencing_experiment_id": "DASH-SE-1" + }, + "read_groups": [ + { + "file_r1": "dash-1-normal.bam", + "file_r2": null, + "insert_size": null, + "library_name": "Dashboard-Testing", + "is_paired_end": false, + "platform_unit": "Dashboard-Testing", + "read_length_r1": null, + "read_length_r2": null, + "sample_barcode": null, + "submitter_read_group_id": "dash-1-rg-1" + } + ], + "read_group_count": 1 + } + ], + "totalAnalyses": 1, + "currentTotalAnalyses": 1 +} + diff --git a/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.aws.analysis.response.json b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.aws.analysis.response.json new file mode 100644 index 00000000..241dc150 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.aws.analysis.response.json @@ -0,0 +1,92 @@ +{ + "analyses": + [ + { + "analysisId": "43f07e4d-e26b-4f4a-b07e-4de26b9f4a50", + "studyId": "EUCANCAN-BE", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "sampleId": "SA610334", + "specimenId": "SP210307", + "submitterSampleId": "insilico_2_tumor", + "matchedNormalSubmitterSampleId": "insilico_2_normal", + "sampleType": "Total DNA", + "specimen": { + "specimenId": "SP210307", + "donorId": "DO250284", + "submitterSpecimenId": "insilico_2_tumor", + "tumourNormalDesignation": "Tumour", + "specimenTissueSource": "Blood derived", + "specimenType": "Primary tumour" + }, + "donor": { + "donorId": "DO250284", + "studyId": "EUCANCAN-BE", + "gender": "Female", + "submitterDonorId": "insilico_2" + } + } + ], + "files": [ + { + "objectId": "882e4591-b004-5564-b2ec-1a210f8cba6b", + "studyId": "EUCANCAN-BE", + "analysisId": "43f07e4d-e26b-4f4a-b07e-4de26b9f4a50", + "fileName": "EUCANCAN-BE.DO250284.SA610334.wgs.20200413.sanger-wgs.somatic.snv.vcf.gz", + "fileSize": 927567, + "fileType": "VCF", + "fileMd5sum": "0d38c7ed8d5ca347deca7b5ef155823b", + "fileAccess": "controlled", + "dataType": "somatic_snv" + }, + { + "objectId": "c6d6eee4-a2cd-513d-a8e5-4d06098d54fe", + "studyId": "EUCANCAN-BE", + "analysisId": "43f07e4d-e26b-4f4a-b07e-4de26b9f4a50", + "fileName": "EUCANCAN-BE.DO250284.SA610334.wgs.20200413.sanger-wgs.somatic.snv.vcf.gz.tbi", + "fileSize": 168704, + "fileType": "TBI", + "fileMd5sum": "acd5e3780a91ed0364af7ce8106edd3d", + "fileAccess": "controlled", + "dataType": "vcf_index" + } + ], + "analysisType": { + "name": "variant_calling", + "version": 2 + }, + "workflow": { + "name": "sanger-wgs-variant-calling", + "inputs": [ + { + "analysis_type": "sequencing_alignment", + "tumour_analysis_id": "13b13548-6e32-412d-b135-486e32512dbe" + }, + { + "analysis_type": "sequencing_alignment", + "normal_analysis_id": "0efe5aeb-3e21-48a5-be5a-eb3e2118a502" + } + ], + "run_id": "wise_brown", + "version": "0.1.0-dev", + "short_name": "sanger-wgs" + }, + "experiment": { + "library_strategy": "WGS" + }, + "variant_type": [ + "snv" + ], + "variant_class": [ + "somatic" + ] + } + ], + "totalAnalyses": 1, + "currentTotalAnalyses": 1 +} + diff --git a/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.aws.conflicting.response.json b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.aws.conflicting.response.json new file mode 100644 index 00000000..874ee611 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.aws.conflicting.response.json @@ -0,0 +1,92 @@ +{ + "analyses": + [ + { + "analysisId": "43f07e4d-e26b-4f4a-b07e-4de26b9f4a50", + "studyId": "EUCANCAN-BE", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "sampleId": "SA610334", + "specimenId": "SP210307", + "submitterSampleId": "insilico_2_tumor", + "matchedNormalSubmitterSampleId": "insilico_2_normal", + "sampleType": "Total DNA", + "specimen": { + "specimenId": "SP210307", + "donorId": "DO250284", + "submitterSpecimenId": "insilico_2_tumor", + "tumourNormalDesignation": "Tumour", + "specimenTissueSource": "Blood derived", + "specimenType": "Primary tumour" + }, + "donor": { + "donorId": "DO250284", + "studyId": "EUCANCAN-BE", + "gender": "Female", + "submitterDonorId": "insilico_2" + } + } + ], + "files": [ + { + "objectId": "882e4591-b004-5564-b2ec-1a210f8cba6b", + "studyId": "EUCANCAN-BE", + "analysisId": "43f07e4d-e26b-4f4a-b07e-4de26b9f4a50", + "fileName": "EUCANCAN-BE.DO250284.SA610334.wgs.20200413.sanger-wgs.somatic.snv.vcf.gz", + "fileSize": 927567, + "fileType": "VCF", + "fileMd5sum": "0d38c7ed8d5ca347deca7b5ef155823b", + "fileAccess": "controlled", + "dataType": "somatic_snv" + }, + { + "objectId": "c6d6eee4-a2cd-513d-a8e5-4d06098d54fe", + "studyId": "EUCANCAN-BE", + "analysisId": "43f07e4d-e26b-4f4a-b07e-4de26b9f4a50", + "fileName": "EUCANCAN-BE.DO250284.SA610334.wgs.20200413.sanger-wgs.somatic.snv.vcf.gz.tbi", + "fileSize": 168704, + "fileType": "TBI", + "fileMd5sum": "acd5e3780a91ed0364af7ce8106edd3d", + "fileAccess": "controlled", + "dataType": "vcf_index" + } + ], + "analysisType": { + "name": "sequencingRead", + "version": 2 + }, + "workflow": { + "name": "sanger-wgs-variant-calling", + "inputs": [ + { + "analysis_type": "sequencing_alignment", + "tumour_analysis_id": "13b13548-6e32-412d-b135-486e32512dbe" + }, + { + "analysis_type": "sequencing_alignment", + "normal_analysis_id": "0efe5aeb-3e21-48a5-be5a-eb3e2118a502" + } + ], + "run_id": "wise_brown", + "version": "0.1.0-dev", + "short_name": "sanger-wgs" + }, + "experiment": { + "library_strategy": "WGS" + }, + "variant_type": [ + "snv" + ], + "variant_class": [ + "somatic" + ] + } + ], + "totalAnalyses": 1, + "currentTotalAnalyses": 1 +} + diff --git a/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.response.json b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.response.json new file mode 100644 index 00000000..852f947f --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/EUCANCAN-BE.response.json @@ -0,0 +1,176 @@ +{ + "analyses": + [ + { + "analysisId": "cf1432f7-985e-4858-9432-f7985ee858e4", + "studyId": "EUCANCAN-BE", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "sampleId": "SA610334", + "specimenId": "SP210307", + "submitterSampleId": "insilico_2_tumor", + "matchedNormalSubmitterSampleId": "insilico_2_normal", + "sampleType": "Total DNA", + "specimen": { + "specimenId": "SP210307", + "donorId": "DO250284", + "submitterSpecimenId": "insilico_2_tumor", + "tumourNormalDesignation": "Tumour", + "specimenTissueSource": "Blood derived", + "specimenType": "Primary tumour" + }, + "donor": { + "donorId": "DO250284", + "studyId": "EUCANCAN-BE", + "gender": "Female", + "submitterDonorId": "insilico_2" + } + } + ], + "files": [ + { + "objectId": "94ef9598-537f-574b-842d-1486fac84ade", + "studyId": "EUCANCAN-BE", + "analysisId": "cf1432f7-985e-4858-9432-f7985ee858e4", + "fileName": "EUCANCAN-BE.DO250284.SA610334.wgs.20200413.sanger-wgs.somatic.sv.vcf.gz", + "fileSize": 695576, + "fileType": "VCF", + "fileMd5sum": "f8f8dc5a4899b927fe565183a0798a2a", + "fileAccess": "controlled", + "dataType": "somatic_sv" + }, + { + "objectId": "f215e48c-2d76-5c32-b920-20a95305801f", + "studyId": "EUCANCAN-BE", + "analysisId": "cf1432f7-985e-4858-9432-f7985ee858e4", + "fileName": "EUCANCAN-BE.DO250284.SA610334.wgs.20200413.sanger-wgs.somatic.sv.vcf.gz.tbi", + "fileSize": 11732, + "fileType": "TBI", + "fileMd5sum": "a48ef040c536807e6bf7107a216b54f2", + "fileAccess": "controlled", + "dataType": "vcf_index" + } + ], + "analysisType": { + "name": "variant_calling", + "version": 2 + }, + "workflow": { + "name": "sanger-wgs-variant-calling", + "inputs": [ + { + "analysis_type": "sequencing_alignment", + "tumour_analysis_id": "13b13548-6e32-412d-b135-486e32512dbe" + }, + { + "analysis_type": "sequencing_alignment", + "normal_analysis_id": "0efe5aeb-3e21-48a5-be5a-eb3e2118a502" + } + ], + "run_id": "wise_brown", + "version": "0.1.0-dev", + "short_name": "sanger-wgs" + }, + "experiment": { + "library_strategy": "WGS" + }, + "variant_type": [ + "sv" + ], + "variant_class": [ + "somatic" + ] + }, + { + "analysisId": "43f07e4d-e26b-4f4a-b07e-4de26b9f4a50", + "studyId": "EUCANCAN-BE", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "sampleId": "SA610334", + "specimenId": "SP210307", + "submitterSampleId": "insilico_2_tumor", + "matchedNormalSubmitterSampleId": "insilico_2_normal", + "sampleType": "Total DNA", + "specimen": { + "specimenId": "SP210307", + "donorId": "DO250284", + "submitterSpecimenId": "insilico_2_tumor", + "tumourNormalDesignation": "Tumour", + "specimenTissueSource": "Blood derived", + "specimenType": "Primary tumour" + }, + "donor": { + "donorId": "DO250284", + "studyId": "EUCANCAN-BE", + "gender": "Female", + "submitterDonorId": "insilico_2" + } + } + ], + "files": [ + { + "objectId": "882e4591-b004-5564-b2ec-1a210f8cba6b", + "studyId": "EUCANCAN-BE", + "analysisId": "43f07e4d-e26b-4f4a-b07e-4de26b9f4a50", + "fileName": "EUCANCAN-BE.DO250284.SA610334.wgs.20200413.sanger-wgs.somatic.snv.vcf.gz", + "fileSize": 927567, + "fileType": "VCF", + "fileMd5sum": "0d38c7ed8d5ca347deca7b5ef155823b", + "fileAccess": "controlled", + "dataType": "somatic_snv" + }, + { + "objectId": "c6d6eee4-a2cd-513d-a8e5-4d06098d54fe", + "studyId": "EUCANCAN-BE", + "analysisId": "43f07e4d-e26b-4f4a-b07e-4de26b9f4a50", + "fileName": "EUCANCAN-BE.DO250284.SA610334.wgs.20200413.sanger-wgs.somatic.snv.vcf.gz.tbi", + "fileSize": 168704, + "fileType": "TBI", + "fileMd5sum": "acd5e3780a91ed0364af7ce8106edd3d", + "fileAccess": "controlled", + "dataType": "vcf_index" + } + ], + "analysisType": { + "name": "variant_calling", + "version": 2 + }, + "workflow": { + "name": "sanger-wgs-variant-calling", + "inputs": [ + { + "analysis_type": "sequencing_alignment", + "tumour_analysis_id": "13b13548-6e32-412d-b135-486e32512dbe" + }, + { + "analysis_type": "sequencing_alignment", + "normal_analysis_id": "0efe5aeb-3e21-48a5-be5a-eb3e2118a502" + } + ], + "run_id": "wise_brown", + "version": "0.1.0-dev", + "short_name": "sanger-wgs" + }, + "experiment": { + "library_strategy": "WGS" + }, + "variant_type": [ + "snv" + ], + "variant_class": [ + "somatic" + ] + } + ], + "totalAnalyses": 2, + "currentTotalAnalyses": 2 +} + diff --git a/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/OCCAMS-GB.analysis.response.json b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/OCCAMS-GB.analysis.response.json new file mode 100644 index 00000000..f494ae87 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/OCCAMS-GB.analysis.response.json @@ -0,0 +1,90 @@ +{ + "analyses": + [ + { + "analysisId": "6332d367-dc6a-4994-b2d3-67dc6a9994d0", + "studyId": "OCCAMS-GB", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "sampleId": "SA528813", + "specimenId": "SP111002", + "submitterSampleId": "LP6007504-DNA_A01", + "matchedNormalSubmitterSampleId": "LP6007566-DNA_A01", + "sampleType": "Total DNA", + "specimen": { + "specimenId": "SP111002", + "donorId": "DO50327", + "submitterSpecimenId": "COU1-0084-lesion-30-3-11-A-", + "tumourNormalDesignation": "Tumour", + "specimenTissueSource": "Solid tissue", + "specimenType": "Primary tumour" + }, + "donor": { + "donorId": "DO50327", + "studyId": "OCCAMS-GB", + "gender": "Male", + "submitterDonorId": "OCCAMS-AH-021" + } + } + ], + "files": [ + { + "objectId": "43d4f83b-1a18-5868-8a44-5e3a6930e89c", + "studyId": "OCCAMS-GB", + "analysisId": "6332d367-dc6a-4994-b2d3-67dc6a9994d0", + "fileName": "OCCAMS-GB.DO50327.SA528813.wgs.20200409.sanger-wgs.somatic.snv.vcf.gz", + "fileSize": 8857968, + "fileType": "VCF", + "fileMd5sum": "2d43e6fa316aa12db74fd6c862939139", + "fileAccess": "controlled", + "dataType": "somatic_snv" + }, + { + "objectId": "7c943e62-7d92-545a-837a-c6b7b57bb930", + "studyId": "OCCAMS-GB", + "analysisId": "6332d367-dc6a-4994-b2d3-67dc6a9994d0", + "fileName": "OCCAMS-GB.DO50327.SA528813.wgs.20200409.sanger-wgs.somatic.snv.vcf.gz.tbi", + "fileSize": 536077, + "fileType": "TBI", + "fileMd5sum": "6fc6cda076c91f909174b9df69c939d7", + "fileAccess": "controlled", + "dataType": "vcf_index" + } + ], + "analysisType": { + "name": "variant_calling", + "version": 2 + }, + "workflow": { + "name": "sanger-wgs-variant-calling", + "inputs": [ + { + "analysis_type": "sequencing_alignment", + "tumour_analysis_id": "04a2db76-f3ef-415d-a2db-76f3ef615d1b" + }, + { + "analysis_type": "sequencing_alignment", + "normal_analysis_id": "77e7ba17-2aee-40f9-a7ba-172aee60f92c" + } + ], + "run_id": "naughty_galileo", + "version": "0.1.0-dev", + "short_name": "sanger-wgs" + }, + "experiment": { + "library_strategy": "WGS" + }, + "variant_type": [ + "snv" + ], + "variant_class": "somatic" + } + ], + "totalAnalyses": 1, + "currentTotalAnalyses": 1 +} + diff --git a/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/TEST-CA.analysis.response.json b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/TEST-CA.analysis.response.json new file mode 100644 index 00000000..8b1e9978 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/TEST-CA.analysis.response.json @@ -0,0 +1,77 @@ +{ + "analyses": + [ + { + "analysisId": "d0b62734-d955-4b74-b627-34d955eb745e", + "studyId": "TEST-CA", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "sampleId": "SA610512", + "specimenId": "SP210509", + "submitterSampleId": "DEMO_SA_1", + "matchedNormalSubmitterSampleId": "sample_x24_11a", + "sampleType": "Total RNA", + "specimen": { + "specimenId": "SP210509", + "donorId": "DO250326", + "submitterSpecimenId": "DEMO_SP_1", + "tumourNormalDesignation": "Tumour", + "specimenTissueSource": "Solid tissue", + "specimenType": "Primary tumour" + }, + "donor": { + "donorId": "DO250326", + "studyId": "TEST-CA", + "gender": "Female", + "submitterDonorId": "DEMO_DO_1" + } + } + ], + "files": [ + { + "objectId": "5230eb04-6702-5e11-ade3-9dc8abbe69a0", + "studyId": "TEST-CA", + "analysisId": "d0b62734-d955-4b74-b627-34d955eb745e", + "fileName": "example.vcf.gz", + "fileSize": 52, + "fileType": "VCF", + "fileMd5sum": "9a793e90d0d1e11301ea8da996446e59", + "fileAccess": "open", + "dataType": "SOME_DATA_TYPE" + }, + { + "info": { + "rob": "somevalue2" + }, + "objectId": "30ab4c21-a514-5d86-a127-3dc6e17a567c", + "studyId": "TEST-CA", + "analysisId": "d0b62734-d955-4b74-b627-34d955eb745e", + "fileName": "example.vcf.gz.idx", + "fileSize": 25, + "fileType": "IDX", + "fileMd5sum": "c03274816eb4907a92b8e5632cd6eb81", + "fileAccess": "controlled", + "dataType": "robdatatype2" + } + ], + "analysisType": { + "name": "variantCall", + "version": 1 + }, + "info": { + "description": "This is extra info in a JSON format" + }, + "experiment": { + "variantCallingTool": "silver bullet", + "matchedNormalSampleSubmitterId": "sample_x24_11a" + } + } + ], + "totalAnalyses": 1, + "currentTotalAnalyses": 1 +} + diff --git a/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/empty-response.json b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/empty-response.json new file mode 100644 index 00000000..78d7dd61 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/AnalysisCentricIntegrationTest/empty-response.json @@ -0,0 +1,7 @@ +{ + "analyses": + [ + ], + "totalAnalyses": 2, + "currentTotalAnalyses": 0 +} diff --git a/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/LIAD-FR.analysis.response.json b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/LIAD-FR.analysis.response.json new file mode 100644 index 00000000..48b46055 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/LIAD-FR.analysis.response.json @@ -0,0 +1,78 @@ +{ + "analyses": + [ + { + "analysisType": { + "name": "sequencingRead", + "version": 1 + }, + "info": { + "dcc_project_code": "LIAD-FR", + "isPcawg": false + }, + "analysisId": "EGAR00001165965", + "studyId": "LIAD-FR", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA520689", + "specimenId": "SP109375", + "submitterSampleId": "CHC1124T", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP109375", + "donorId": "DO49691", + "submitterSpecimenId": "CHC1124T", + "specimenType": "Primary tumour - solid tissue" + }, + "donor": { + "donorId": "DO49691", + "submitterDonorId": "CHC1124", + "studyId": "LIAD-FR", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "71729c60-d87a-5458-a88c-38e6dc294733", + "studyId": "LIAD-FR", + "analysisId": "EGAR00001165965", + "fileName": "bundle.EGAR00001165965.xml", + "fileSize": 8904, + "fileType": "XML", + "fileMd5sum": "7243c2e2fa5cbabea1ad9d5e9972524a", + "fileAccess": "open", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "cf8d06de-f994-5b32-ad1d-ea815f037fd2", + "studyId": "LIAD-FR", + "analysisId": "EGAR00001165965", + "fileName": "d309e3cdd1fc38b0fa8b5486a48e4b94.CHC1124T.sorted.bam", + "fileSize": 7494108451, + "fileType": "BAM", + "fileMd5sum": "d309e3cdd1fc38b0fa8b5486a48e4b94", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "analysisId": "EGAR00001165965", + "aligned": false, + "libraryStrategy": "WXS", + "info": {} + } + } + ], + "totalAnalyses": 1, + "currentTotalAnalyses": 1 +} diff --git a/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/LIRI-JP.analysis.response.json b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/LIRI-JP.analysis.response.json new file mode 100644 index 00000000..49d66e96 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/LIRI-JP.analysis.response.json @@ -0,0 +1,607 @@ +{ + "analyses": + [ + { + "analysisType": { + "name": "variantCall", + "version": 1 + }, + "info": {}, + "analysisId": "909614f0-ceeb-11e5-8498-af7e4d100685", + "studyId": "LIRI-JP", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA515389", + "specimenId": "SP107109", + "submitterSampleId": "RK202_C01", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP107109", + "donorId": "DO48736", + "submitterSpecimenId": "RK202_C01", + "specimenType": "Primary tumour - solid tissue" + }, + "donor": { + "donorId": "DO48736", + "submitterDonorId": "RK202", + "studyId": "LIRI-JP", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "b63dff38-e239-5a5d-9c36-ec851049fd12", + "studyId": "LIRI-JP", + "analysisId": "909614f0-ceeb-11e5-8498-af7e4d100685", + "fileName": "1fd69adc-c623-11e3-bf01-24c6515278c0.svcp_1-0-6.20150511.somatic.indel.vcf.gz", + "fileSize": 44440835, + "fileType": "VCF", + "fileMd5sum": "93354882b0fc014b49be1b24df8f435e", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "eb2832eb-ad54-574b-bb60-1abf74489ed8", + "studyId": "LIRI-JP", + "analysisId": "909614f0-ceeb-11e5-8498-af7e4d100685", + "fileName": "1fd69adc-c623-11e3-bf01-24c6515278c0.svcp_1-0-6.20150511.somatic.indel.vcf.gz.tbi", + "fileSize": 1458418, + "fileType": "TBI", + "fileMd5sum": "ade04a5fd0e9d4052b0ec0b280a9be60", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "feecfb7d-2aa9-5434-a0a0-56a6c5ee4a70", + "studyId": "LIRI-JP", + "analysisId": "909614f0-ceeb-11e5-8498-af7e4d100685", + "fileName": "1fd69adc-c623-11e3-bf01-24c6515278c0.svfix2_4-0-12.20160209.somatic.sv.vcf.gz", + "fileSize": 11431, + "fileType": "VCF", + "fileMd5sum": "ae2e0a8eb02414569fa06cd56a3e809e", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "e14e73a5-a869-5b9a-a89c-be77fa54135e", + "studyId": "LIRI-JP", + "analysisId": "909614f0-ceeb-11e5-8498-af7e4d100685", + "fileName": "1fd69adc-c623-11e3-bf01-24c6515278c0.svfix2_4-0-12.20160209.somatic.sv.vcf.gz.tbi", + "fileSize": 1756, + "fileType": "TBI", + "fileMd5sum": "9ce7cdedb7450a05c03e419235ed56a6", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "3106300b-3666-52b7-a3fa-a5096a51814b", + "studyId": "LIRI-JP", + "analysisId": "909614f0-ceeb-11e5-8498-af7e4d100685", + "fileName": "1fd69adc-c623-11e3-bf01-24c6515278c0.svcp_1-0-6.20150511.somatic.cnv.vcf.gz", + "fileSize": 3648, + "fileType": "VCF", + "fileMd5sum": "492989e81699bd5a56b7956e0be7416d", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "ad4e821d-1908-5e37-8b09-f2bcbe841a6b", + "studyId": "LIRI-JP", + "analysisId": "909614f0-ceeb-11e5-8498-af7e4d100685", + "fileName": "1fd69adc-c623-11e3-bf01-24c6515278c0.svcp_1-0-6.20150511.somatic.cnv.vcf.gz.tbi", + "fileSize": 5539, + "fileType": "TBI", + "fileMd5sum": "acdf137ad635f95ee93412fa9153d066", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "bed33bd4-eec1-5905-8480-5def36d7f6de", + "studyId": "LIRI-JP", + "analysisId": "909614f0-ceeb-11e5-8498-af7e4d100685", + "fileName": "1fd69adc-c623-11e3-bf01-24c6515278c0.svcp_1-0-6.20150511.somatic.snv_mnv.vcf.gz", + "fileSize": 1418099, + "fileType": "VCF", + "fileMd5sum": "1f3cfd1e1ad462cff9871eb2373935ac", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "deab15a3-6820-5bcc-926a-bca2ab5ddaa0", + "studyId": "LIRI-JP", + "analysisId": "909614f0-ceeb-11e5-8498-af7e4d100685", + "fileName": "1fd69adc-c623-11e3-bf01-24c6515278c0.svcp_1-0-6.20150511.somatic.snv_mnv.vcf.gz.tbi", + "fileSize": 236926, + "fileType": "TBI", + "fileMd5sum": "2233fb90872d759d279395b1a7ad3461", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "233bc863-114c-5ec4-842b-7f44d189eab0", + "studyId": "LIRI-JP", + "analysisId": "909614f0-ceeb-11e5-8498-af7e4d100685", + "fileName": "909614f0-ceeb-11e5-8498-af7e4d100685.xml", + "fileSize": 58853, + "fileType": "XML", + "fileMd5sum": "4f8a5a5a1a040f7538760c3b8b944c86", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "info": {}, + "analysisId": "909614f0-ceeb-11e5-8498-af7e4d100685", + "variantCallingTool": "Sanger variant call pipeline", + "matchedNormalSampleSubmitterId": "RK202_B01" + } + }, + { + "info": {}, + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "studyId": "LIRI-JP", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA270462", + "specimenId": "SP50179", + "submitterSampleId": "RK156_C01", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP50179", + "donorId": "DO23549", + "submitterSpecimenId": "RK156_C01", + "specimenType": "Primary tumour - solid tissue" + }, + "donor": { + "donorId": "DO23549", + "submitterDonorId": "RK156", + "studyId": "LIRI-JP", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "24329157-e218-5854-8f45-7fa6b9e046c6", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-snowman-10.20151220.germline.indel.vcf.gz", + "fileSize": 10536170, + "fileType": "VCF", + "fileMd5sum": "7d0676c6a85696e1cb2919836b0ab71e", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "ad8a45f3-ec8d-5391-ae93-b19dc982698a", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-snowman-10.20151220.germline.indel.vcf.gz.idx", + "fileSize": 1031078, + "fileType": "IDX", + "fileMd5sum": "8269ee64b80e6ec66e590767f697d37b", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "4d070189-bd33-5391-b7af-ea32c6782875", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-dRanger_snowman-10.20151220.somatic.sv.vcf.gz", + "fileSize": 59633, + "fileType": "VCF", + "fileMd5sum": "1d0a8bcf2abf8373c6f8cc63cb748aa8", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "14e94abe-1fd1-5a85-8d26-a7291edd80ef", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-dRanger_snowman-10.20151220.somatic.sv.vcf.gz.idx", + "fileSize": 11325, + "fileType": "IDX", + "fileMd5sum": "fdb961feac82a7912bf657450e02c44d", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "107c83c7-595e-5b36-957b-ae706611d5b9", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-snowman-10.20151220.somatic.sv.vcf.gz", + "fileSize": 51548, + "fileType": "VCF", + "fileMd5sum": "fc246f5e1f670b1f756b8e4294f59504", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "c5496778-0d72-5cc6-aac4-98777cfbc0c2", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-snowman-10.20151220.somatic.sv.vcf.gz.idx", + "fileSize": 10447, + "fileType": "IDX", + "fileMd5sum": "5aeb4749609bd0a4d81ecffd673a36e1", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "da524891-37af-5a21-9867-c6812018aa22", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-snowman-10.20151220.germline.sv.vcf.gz", + "fileSize": 1710383, + "fileType": "VCF", + "fileMd5sum": "1f22fff9e578244ba16762a4c82792e8", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "d87c4599-bba4-5c23-b7a2-57bbeed7eacb", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-snowman-10.20151220.germline.sv.vcf.gz.idx", + "fileSize": 61514, + "fileType": "IDX", + "fileMd5sum": "ade5449b588c81496e4e7d2b0b49e3d0", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "46194bd5-b131-55f7-b7b1-99293ba1d6b9", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-snowman-10.20151220.somatic.indel.vcf.gz", + "fileSize": 31242, + "fileType": "VCF", + "fileMd5sum": "e75eef7af227c5c80d0b499ffd39c43b", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "55283d00-b1a2-521c-99e1-e9d8d88c660d", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-snowman-10.20151220.somatic.indel.vcf.gz.idx", + "fileSize": 14606, + "fileType": "IDX", + "fileMd5sum": "8cae7bbcd28b6a78ad5c53642ae9695c", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "ae5b1daf-05d5-5e41-be2a-9f1d3369d517", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-dRanger-10.20151220.somatic.sv.vcf.gz", + "fileSize": 10191, + "fileType": "VCF", + "fileMd5sum": "f199c6714f7a6880d30bf7aa56e00625", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "c4d10f9f-7e9e-5cb3-a30a-0ff8865952ce", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-dRanger-10.20151220.somatic.sv.vcf.gz.idx", + "fileSize": 4212, + "fileType": "IDX", + "fileMd5sum": "139ce5f29fc0e877d5ae5a5d5e03c3f0", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "8b28796a-1630-5d12-92a7-d8264ee57bc6", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-mutect-v3.20160222.somatic.snv_mnv.vcf.gz", + "fileSize": 382815, + "fileType": "VCF", + "fileMd5sum": "d641e6e373d21d2fc882f2e4550b7b2c", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "a99d2a9c-96c4-5788-9149-79a146f0f925", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "f064f762-c622-11e3-bf01-24c6515278c0.broad-mutect-v3.20160222.somatic.snv_mnv.vcf.gz.idx", + "fileSize": 151104, + "fileType": "IDX", + "fileMd5sum": "797e4ef5c348d4a23e9e83790812d857", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "bd7aa748-d781-523e-99dc-cb7e3469ddc6", + "studyId": "LIRI-JP", + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "fileName": "0a3c8def-5ef9-4470-b64d-91f62da29abf.xml", + "fileSize": 38858, + "fileType": "XML", + "fileMd5sum": "486853e9fc33dd7f1429c90a6b526b0d", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "info": {}, + "analysisId": "0a3c8def-5ef9-4470-b64d-91f62da29abf", + "variantCallingTool": "Broad variant call pipeline", + "matchedNormalSampleSubmitterId": "RK156_B01" + }, + "analysisType": { + "name": "variantCall", + "version": 1 + } + }, + { + "info": {}, + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "studyId": "LIRI-JP", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA501653", + "specimenId": "SP99145", + "submitterSampleId": "RK091_C01", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP99145", + "donorId": "DO45211", + "submitterSpecimenId": "RK091_C01", + "specimenType": "Primary tumour - solid tissue" + }, + "donor": { + "donorId": "DO45211", + "submitterDonorId": "RK091", + "studyId": "LIRI-JP", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "316177db-022d-5121-aba8-ce72a92ee778", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-snowman-11.20160302.somatic.sv.vcf.gz", + "fileSize": 404406, + "fileType": "VCF", + "fileMd5sum": "33b96c263be31852de8d5d15775561c9", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "97c3147f-dd1d-507f-a73d-8646f7ce2a0b", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-snowman-11.20160302.somatic.sv.vcf.gz.idx", + "fileSize": 27885, + "fileType": "IDX", + "fileMd5sum": "3ed262dbc3b1c427177bdd5af5ef5633", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "18917df0-2cc6-5ac5-88d8-f48acf24c92e", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-snowman-11.20160302.germline.sv.vcf.gz", + "fileSize": 1853889, + "fileType": "VCF", + "fileMd5sum": "d3227038bd37e74ff88b07e5408c76ed", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "9abe4aad-9d35-5d4f-955c-8bceb559827e", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-snowman-11.20160302.germline.sv.vcf.gz.idx", + "fileSize": 67312, + "fileType": "IDX", + "fileMd5sum": "a7cf0d572f1649c8791cda7892c7be55", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "5c222a32-a79d-55e0-a490-440217c63393", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-snowman-11.20160302.germline.indel.vcf.gz", + "fileSize": 10429379, + "fileType": "VCF", + "fileMd5sum": "64ef1b8daf5b6eec161555f5cdad3420", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "ad68b7cb-e91c-506e-acae-812ae2ea7678", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-snowman-11.20160302.germline.indel.vcf.gz.idx", + "fileSize": 1032907, + "fileType": "IDX", + "fileMd5sum": "78b2dd0696a1f2ea8ac8e25a77c4e239", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "2af2e398-c27b-5645-b60b-b932a916184d", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-dRanger_snowman-11.20160302.somatic.sv.vcf.gz", + "fileSize": 400597, + "fileType": "VCF", + "fileMd5sum": "7e7f3e23aa8869bfd82ce16382b7bc7d", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "bbb31cb3-f175-52c4-ba66-569e1a1d2ed7", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-dRanger_snowman-11.20160302.somatic.sv.vcf.gz.idx", + "fileSize": 27877, + "fileType": "IDX", + "fileMd5sum": "130e37274d3c7bebcb41d027eea9148d", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "d9388ed4-1603-584f-9b18-5ff53b9bffeb", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-snowman-11.20160302.somatic.indel.vcf.gz", + "fileSize": 25270, + "fileType": "VCF", + "fileMd5sum": "ee313d9cbe077063174d92050dde03e0", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "95e7563e-e8d1-5377-8cfc-1c45a72448da", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-snowman-11.20160302.somatic.indel.vcf.gz.idx", + "fileSize": 12044, + "fileType": "IDX", + "fileMd5sum": "941a7d48a3250de6edcbbde1cbb4b7e1", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "60307755-185e-536e-aa3b-190fb9934844", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-dRanger-11.20160302.somatic.sv.vcf.gz", + "fileSize": 2540, + "fileType": "VCF", + "fileMd5sum": "cbafecb01dea96496176bf7497cb9e80", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "221e532c-a0c8-5573-8399-81f785423e57", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-dRanger-11.20160302.somatic.sv.vcf.gz.idx", + "fileSize": 1336, + "fileType": "IDX", + "fileMd5sum": "de502cd9a25efe6f868f3156e8fd302e", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "2664e052-ba85-5be4-89e0-4f2f06a998c0", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-mutect-v3.20160222.somatic.snv_mnv.vcf.gz", + "fileSize": 422502, + "fileType": "VCF", + "fileMd5sum": "ca10e3bd248498c9427b2b5e324f0242", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "87d9f1f2-3d13-5dd2-8ed5-d175952e2586", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "aabddb20-c622-11e3-bf01-24c6515278c0.broad-mutect-v3.20160222.somatic.snv_mnv.vcf.gz.idx", + "fileSize": 160972, + "fileType": "IDX", + "fileMd5sum": "9029f92d2d1ea6d76b3a88795756aacc", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "8d8a4db8-071d-5385-9266-06e93ca029d0", + "studyId": "LIRI-JP", + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "fileName": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9.xml", + "fileSize": 41214, + "fileType": "XML", + "fileMd5sum": "080be308183242812e07359f7c9c1566", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "info": {}, + "analysisId": "cbc64c23-1d6f-40db-a49e-dc54ef222ae9", + "variantCallingTool": "Broad variant call pipeline", + "matchedNormalSampleSubmitterId": "RK091_B01" + }, + "analysisType": { + "name": "variantCall", + "version": 1 + } + } + ], + "totalAnalyses": 3, + "currentTotalAnalyses": 3 +} diff --git a/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/MALY-DE.analysis.response.json b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/MALY-DE.analysis.response.json new file mode 100644 index 00000000..ea9598af --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/MALY-DE.analysis.response.json @@ -0,0 +1,247 @@ +{ + "analyses": + [ + { + "analysisType": { + "name": "variantCall", + "version": 1 + }, + "info": {}, + "analysisId": "0a1df2a2-029d-48cc-839c-0a7c89ff972f", + "studyId": "MALY-DE", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA557689", + "specimenId": "SP124981", + "submitterSampleId": "tumor_4128852", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP124981", + "donorId": "DO221129", + "submitterSpecimenId": "tumor_4128852", + "specimenType": "Primary tumour - lymph node" + }, + "donor": { + "donorId": "DO221129", + "submitterDonorId": "4128852", + "studyId": "MALY-DE", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "316612a4-4c23-5434-976a-810f8cde06b7", + "studyId": "MALY-DE", + "analysisId": "0a1df2a2-029d-48cc-839c-0a7c89ff972f", + "fileName": "e2fa7251-507e-4d76-95a3-a228adc3885a.MUSE_1-0rc-vcf.20151107.somatic.snv_mnv.vcf.gz", + "fileSize": 273787, + "fileType": "VCF", + "fileMd5sum": "f83b0f9099e8594b589440819ab119cd", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "a9c47630-491b-5587-a58d-6736734d6163", + "studyId": "MALY-DE", + "analysisId": "0a1df2a2-029d-48cc-839c-0a7c89ff972f", + "fileName": "e2fa7251-507e-4d76-95a3-a228adc3885a.MUSE_1-0rc-vcf.20151107.somatic.snv_mnv.vcf.gz.idx", + "fileSize": 146924, + "fileType": "IDX", + "fileMd5sum": "f5629a05fe5b8dd6a63381de259aa935", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "95cbd8c1-1cb1-5c18-8c2d-6f54867d7b72", + "studyId": "MALY-DE", + "analysisId": "0a1df2a2-029d-48cc-839c-0a7c89ff972f", + "fileName": "0a1df2a2-029d-48cc-839c-0a7c89ff972f.xml", + "fileSize": 36818, + "fileType": "XML", + "fileMd5sum": "7240205cac78b6e94a131d2db14de07b", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "info": {}, + "analysisId": "0a1df2a2-029d-48cc-839c-0a7c89ff972f", + "variantCallingTool": "MUSE variant call pipeline", + "matchedNormalSampleSubmitterId": "control_4128852" + } + }, + { + "analysisType": { + "name": "variantCall", + "version": 1 + }, + "info": {}, + "analysisId": "64e6f498-20ae-4c59-a5f5-36b18f81bd99", + "studyId": "MALY-DE", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA542152", + "specimenId": "SP116718", + "submitterSampleId": "tumor_4113191", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP116718", + "donorId": "DO52693", + "submitterSpecimenId": "tumor_4113191", + "specimenType": "Primary tumour - lymph node" + }, + "donor": { + "donorId": "DO52693", + "submitterDonorId": "4113191", + "studyId": "MALY-DE", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "5d360754-ee81-581f-9b51-dfdd24f7a8d2", + "studyId": "MALY-DE", + "analysisId": "64e6f498-20ae-4c59-a5f5-36b18f81bd99", + "fileName": "64e6f498-20ae-4c59-a5f5-36b18f81bd99.xml", + "fileSize": 31669, + "fileType": "XML", + "fileMd5sum": "8f6ef3b2f3904c523b811e9c5191e159", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "0bafbb56-728e-5e6c-bb87-88e7bb789dab", + "studyId": "MALY-DE", + "analysisId": "64e6f498-20ae-4c59-a5f5-36b18f81bd99", + "fileName": "4e7e6e1f-c648-446f-bdf6-0b1fcc6dfa83.consensus.20160830.somatic.snv_mnv.vcf.gz", + "fileSize": 188550, + "fileType": "VCF", + "fileMd5sum": "02b4602861de0a5529e42d3e66eaa2a6", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "21126ff1-cd5e-5bb2-a55e-3c9f68b2ad14", + "studyId": "MALY-DE", + "analysisId": "64e6f498-20ae-4c59-a5f5-36b18f81bd99", + "fileName": "4e7e6e1f-c648-446f-bdf6-0b1fcc6dfa83.consensus.20160830.somatic.snv_mnv.vcf.gz.tbi", + "fileSize": 101608, + "fileType": "TBI", + "fileMd5sum": "c00c6672cb752c71dd2d1ef23ea559fa", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "info": {}, + "analysisId": "64e6f498-20ae-4c59-a5f5-36b18f81bd99", + "variantCallingTool": " PCAWG SNV-MNV callers", + "matchedNormalSampleSubmitterId": "control_4113191" + } + }, + { + "analysisType": { + "name": "variantCall", + "version": 1 + }, + "info": {}, + "analysisId": "327c74cd-ee0b-4885-bafd-741e17b8b163", + "studyId": "MALY-DE", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA542043", + "specimenId": "SP116638", + "submitterSampleId": "tumor_4166503", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP116638", + "donorId": "DO52662", + "submitterSpecimenId": "tumor_4166503", + "specimenType": "Primary tumour - lymph node" + }, + "donor": { + "donorId": "DO52662", + "submitterDonorId": "4166503", + "studyId": "MALY-DE", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "46c2fec8-fd4a-5b62-8819-647bf23ac15c", + "studyId": "MALY-DE", + "analysisId": "327c74cd-ee0b-4885-bafd-741e17b8b163", + "fileName": "327c74cd-ee0b-4885-bafd-741e17b8b163.xml", + "fileSize": 35287, + "fileType": "XML", + "fileMd5sum": "91733724f431b0d91b47e37778e6c20e", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "7b32b455-d8e2-5e51-bcad-dad7945c8b15", + "studyId": "MALY-DE", + "analysisId": "327c74cd-ee0b-4885-bafd-741e17b8b163", + "fileName": "866ecfe7-caa6-4565-9418-6b9d6c8a3b43.consensus.20161006.somatic.indel.vcf.gz", + "fileSize": 38671, + "fileType": "VCF", + "fileMd5sum": "020a444fb10ec02b40e141aa9cd0de87", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "4ba753ee-bbb7-5f57-9cda-6e15c519f834", + "studyId": "MALY-DE", + "analysisId": "327c74cd-ee0b-4885-bafd-741e17b8b163", + "fileName": "866ecfe7-caa6-4565-9418-6b9d6c8a3b43.consensus.20161006.somatic.indel.vcf.gz.tbi", + "fileSize": 19306, + "fileType": "TBI", + "fileMd5sum": "7c606af5d37d3788850da1a5f1705feb", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "info": {}, + "analysisId": "327c74cd-ee0b-4885-bafd-741e17b8b163", + "variantCallingTool": "PCAWG InDel callers", + "matchedNormalSampleSubmitterId": "control_4166503" + } + } + ], + "totalAnalyses": 3, + "currentTotalAnalyses": 3 +} diff --git a/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PACA-CA.analysis.response.json b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PACA-CA.analysis.response.json new file mode 100644 index 00000000..cbe29043 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PACA-CA.analysis.response.json @@ -0,0 +1,463 @@ +{ + "analyses": + [ + { + "analysisType": { + "name": "variantCall", + "version": 1 + }, + "info": {}, + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "studyId": "PACA-CA", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA533729", + "specimenId": "SP125730", + "submitterSampleId": "PCSI_0233_Pa_P_526", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP125730", + "donorId": "DO51523", + "submitterSpecimenId": "PCSI_0233_Pa_P_526", + "specimenType": "Primary tumour - other" + }, + "donor": { + "donorId": "DO51523", + "submitterDonorId": "PCSI_0233", + "studyId": "PACA-CA", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "e86158ec-0eb6-50e2-bbb5-7bfed4745db0", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.dkfz-snvCalling_1-0-132-1.20150722.somatic.snv_mnv.vcf.gz", + "fileSize": 543337, + "fileType": "VCF", + "fileMd5sum": "14ded2a7342f9124421ace5aa920510d", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "bb949d15-334f-5712-9f04-41225a7beb8d", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.dkfz-snvCalling_1-0-132-1.20150722.somatic.snv_mnv.vcf.gz.tbi", + "fileSize": 224729, + "fileType": "TBI", + "fileMd5sum": "99f0b87f5113494e2fc2284c91dc15e0", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "0474e5f1-3b49-5ec5-8186-a1ffc6952f37", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.dkfz-indelCalling_1-0-132-1.20150722.somatic.indel.vcf.gz", + "fileSize": 5565355, + "fileType": "VCF", + "fileMd5sum": "0e1e3c924b37d90c99bb04f719a56ce4", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "2910e07c-268b-57a5-877a-0cec35298319", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.dkfz-indelCalling_1-0-132-1.20150722.somatic.indel.vcf.gz.tbi", + "fileSize": 546153, + "fileType": "TBI", + "fileMd5sum": "1abed463bc92e0d8486699b37af73737", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "54abbcb5-485f-5acd-88e9-50261e0c8e17", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.dkfz-snvCalling_1-0-132-1.20150722.germline.snv_mnv.vcf.gz", + "fileSize": 101384873, + "fileType": "VCF", + "fileMd5sum": "19b56e546bdcdb7f68dfd603b1b7a8d7", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "425898fd-35d3-5ee2-ac00-50dfd724f4c6", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.dkfz-snvCalling_1-0-132-1.20150722.germline.snv_mnv.vcf.gz.tbi", + "fileSize": 1541330, + "fileType": "TBI", + "fileMd5sum": "a6113c54193fd7539dffd06f50f04779", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "0d7ee358-01fe-59ce-b62b-0663bec8596d", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.dkfz-indelCalling_1-0-132-1.20150722.germline.indel.vcf.gz", + "fileSize": 72850649, + "fileType": "VCF", + "fileMd5sum": "c102abc0bfa0b63b2e1ea2ae62e18b80", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "04c24136-c19d-5042-a3cd-36f63c7b4d6b", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.dkfz-indelCalling_1-0-132-1.20150722.germline.indel.vcf.gz.tbi", + "fileSize": 1502241, + "fileType": "TBI", + "fileMd5sum": "156880f52b94b3119afa3ac6dd7b8ced", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "432779b5-95db-5caf-a529-85a36a707c04", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.dkfz-copyNumberEstimation_1-0-189-hpc-fix.1508271702.somatic.cnv.vcf.gz", + "fileSize": 23763, + "fileType": "VCF", + "fileMd5sum": "93b219c94687e12b5fda564399fa3319", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "51306186-092d-5e3f-bb3c-028873052eb2", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.dkfz-copyNumberEstimation_1-0-189-hpc-fix.1508271702.somatic.cnv.vcf.gz.tbi", + "fileSize": 10691, + "fileType": "TBI", + "fileMd5sum": "68d76af7c7b9b7c00fa0438101739798", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "4f2bee69-e66e-5af5-856a-a0f3c34b12ff", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.embl-delly_1-0-0-preFilter.20150722.somatic.sv.vcf.gz", + "fileSize": 18226, + "fileType": "VCF", + "fileMd5sum": "6ebd4aa8a821da40955d7fcb879be82a", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "e5d387a1-3b51-5526-ae22-270df2e1fd2f", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.embl-delly_1-0-0-preFilter.20150722.somatic.sv.vcf.gz.tbi", + "fileSize": 6134, + "fileType": "TBI", + "fileMd5sum": "96b05a083d371ae8317651ceffb0f48b", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "3f571505-3bea-5065-956a-4b5a793ad1ed", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.embl-delly_1-0-0-preFilter.20150722.germline.sv.vcf.gz", + "fileSize": 161511, + "fileType": "VCF", + "fileMd5sum": "f3a99bd737b3b416aa34e131b939b2a0", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "e8569e7c-6ae4-5aeb-ae50-b94366aae5df", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "bcef0b6c-6584-4090-9d28-ef784a7e5fbb.embl-delly_1-0-0-preFilter.20150722.germline.sv.vcf.gz.tbi", + "fileSize": 19769, + "fileType": "TBI", + "fileMd5sum": "cb856f2d5837c5f065c7c598dcd795b5", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "bbbbc35b-9ea3-5191-b6c8-9092975d8033", + "studyId": "PACA-CA", + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "fileName": "744c62bf-4747-4ab2-aca9-50879cea82e0.xml", + "fileSize": 60087, + "fileType": "XML", + "fileMd5sum": "64db344f980be12737566635acf5820f", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "info": {}, + "analysisId": "744c62bf-4747-4ab2-aca9-50879cea82e0", + "variantCallingTool": "DKFZ/EMBL variant call pipeline", + "matchedNormalSampleSubmitterId": "PCSI_0233_Ly_R" + } + }, + { + "analysisType": { + "name": "variantCall", + "version": 1 + }, + "info": {}, + "analysisId": "916b5a92-cea6-11e5-af30-d4714d100685", + "studyId": "PACA-CA", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA533758", + "specimenId": "SP125791", + "submitterSampleId": "ASHPC_0022_Pa_P", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP125791", + "donorId": "DO51498", + "submitterSpecimenId": "ASHPC_0022_Pa_P", + "specimenType": "Primary tumour - other" + }, + "donor": { + "donorId": "DO51498", + "submitterDonorId": "PCSI_0450", + "studyId": "PACA-CA", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "e122b153-c98b-530d-879a-11871a427d1b", + "studyId": "PACA-CA", + "analysisId": "916b5a92-cea6-11e5-af30-d4714d100685", + "fileName": "94652d14-2e4d-4f4a-a4f7-8df77df788c0.svcp_1-0-8.20150911.somatic.indel.vcf.gz", + "fileSize": 58091383, + "fileType": "VCF", + "fileMd5sum": "4824d68baf7c2b06f5a652bb5462b9b4", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "b26a535c-3531-55ad-8725-17aa6afb22c2", + "studyId": "PACA-CA", + "analysisId": "916b5a92-cea6-11e5-af30-d4714d100685", + "fileName": "94652d14-2e4d-4f4a-a4f7-8df77df788c0.svcp_1-0-8.20150911.somatic.indel.vcf.gz.tbi", + "fileSize": 1524609, + "fileType": "TBI", + "fileMd5sum": "894fa70742c16ed7f845abd68609f20c", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "36ede5a5-fcde-5b6a-95c1-af28321fbd39", + "studyId": "PACA-CA", + "analysisId": "916b5a92-cea6-11e5-af30-d4714d100685", + "fileName": "94652d14-2e4d-4f4a-a4f7-8df77df788c0.svfix2_4-0-12.20160208.somatic.sv.vcf.gz", + "fileSize": 59407, + "fileType": "VCF", + "fileMd5sum": "0502184e75c3a3fb83e2aa6ab536e78a", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "b9800f14-13d5-55cf-9383-a65b5446116a", + "studyId": "PACA-CA", + "analysisId": "916b5a92-cea6-11e5-af30-d4714d100685", + "fileName": "94652d14-2e4d-4f4a-a4f7-8df77df788c0.svfix2_4-0-12.20160208.somatic.sv.vcf.gz.tbi", + "fileSize": 2961, + "fileType": "TBI", + "fileMd5sum": "1ba234eb0c457dba2942215d3fc4741a", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "5c1fcacb-7c66-53a6-8fb6-93d1281e55b8", + "studyId": "PACA-CA", + "analysisId": "916b5a92-cea6-11e5-af30-d4714d100685", + "fileName": "94652d14-2e4d-4f4a-a4f7-8df77df788c0.svcp_1-0-8.20150911.somatic.cnv.vcf.gz", + "fileSize": 2964, + "fileType": "VCF", + "fileMd5sum": "bafebb1c613c348c696dc8f940ce1039", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "52db8e51-5b3e-56ce-b939-0a96b4dfbce3", + "studyId": "PACA-CA", + "analysisId": "916b5a92-cea6-11e5-af30-d4714d100685", + "fileName": "94652d14-2e4d-4f4a-a4f7-8df77df788c0.svcp_1-0-8.20150911.somatic.cnv.vcf.gz.tbi", + "fileSize": 4783, + "fileType": "TBI", + "fileMd5sum": "725becdd11e63c371e57a987420846bd", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "e704d3f5-1274-5cdd-924f-609159e121cc", + "studyId": "PACA-CA", + "analysisId": "916b5a92-cea6-11e5-af30-d4714d100685", + "fileName": "94652d14-2e4d-4f4a-a4f7-8df77df788c0.svcp_1-0-8.20150911.somatic.snv_mnv.vcf.gz", + "fileSize": 1704966, + "fileType": "VCF", + "fileMd5sum": "37ee70b282788eb0660f7d965f355898", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "6b32cfec-e82c-5528-b908-8e00ae927578", + "studyId": "PACA-CA", + "analysisId": "916b5a92-cea6-11e5-af30-d4714d100685", + "fileName": "94652d14-2e4d-4f4a-a4f7-8df77df788c0.svcp_1-0-8.20150911.somatic.snv_mnv.vcf.gz.tbi", + "fileSize": 303747, + "fileType": "TBI", + "fileMd5sum": "91dece67c383a67123caae382a130cb9", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "47fc8458-df52-5ad1-a0fc-cd2c277ecb93", + "studyId": "PACA-CA", + "analysisId": "916b5a92-cea6-11e5-af30-d4714d100685", + "fileName": "916b5a92-cea6-11e5-af30-d4714d100685.xml", + "fileSize": 60346, + "fileType": "XML", + "fileMd5sum": "a2a10568288e3756745dddaee91df5d5", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "info": {}, + "analysisId": "916b5a92-cea6-11e5-af30-d4714d100685", + "variantCallingTool": "Sanger variant call pipeline", + "matchedNormalSampleSubmitterId": "ASHPC_0022_Pa_R" + } + }, + { + "analysisType": { + "name": "variantCall", + "version": 1 + }, + "info": {}, + "analysisId": "b8e09611-225a-4de6-87dc-104753072252", + "studyId": "PACA-CA", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA520221", + "specimenId": "SP125732", + "submitterSampleId": "PCSI_0083_Pa_P_526", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP125732", + "donorId": "DO35442", + "submitterSpecimenId": "PCSI_0083_Pa_P_526", + "specimenType": "Primary tumour - other" + }, + "donor": { + "donorId": "DO35442", + "submitterDonorId": "PCSI_0083", + "studyId": "PACA-CA", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "ca8479dc-8f00-5757-b433-c3cf5b76f255", + "studyId": "PACA-CA", + "analysisId": "b8e09611-225a-4de6-87dc-104753072252", + "fileName": "b8e09611-225a-4de6-87dc-104753072252.xml", + "fileSize": 33270, + "fileType": "XML", + "fileMd5sum": "bc3d7e8d1acc6a2d20608e10d6a6ed05", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "9727c61d-3871-54f1-a65a-2d1d91acd242", + "studyId": "PACA-CA", + "analysisId": "b8e09611-225a-4de6-87dc-104753072252", + "fileName": "536dedba-46c4-4a21-b112-13c030b13069.consensus.20161006.somatic.indel.vcf.gz", + "fileSize": 329863, + "fileType": "VCF", + "fileMd5sum": "01e54034c70b85812e9aac58f2525594", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "08519ab5-8665-58dc-8476-1c40cae5b789", + "studyId": "PACA-CA", + "analysisId": "b8e09611-225a-4de6-87dc-104753072252", + "fileName": "536dedba-46c4-4a21-b112-13c030b13069.consensus.20161006.somatic.indel.vcf.gz.tbi", + "fileSize": 148925, + "fileType": "TBI", + "fileMd5sum": "5b83369174136b88f16a08ab87bb67f7", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "info": {}, + "analysisId": "b8e09611-225a-4de6-87dc-104753072252", + "variantCallingTool": "PCAWG InDel callers", + "matchedNormalSampleSubmitterId": "PCSI_0083_Du_R" + } + } + ], + "totalAnalyses": 3, + "currentTotalAnalyses": 3 +} diff --git a/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.aws.conflicting.study.response.json b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.aws.conflicting.study.response.json new file mode 100644 index 00000000..818959d1 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.aws.conflicting.study.response.json @@ -0,0 +1,90 @@ +{ + "analyses": + [ + { + "analysisType": { + "name": "sequencingRead", + "version": 1 + }, + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false + }, + "analysisId": "EGAZ00001254245", + "studyId": "PEME-CA", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA604905", + "specimenId": "SP200947", + "submitterSampleId": "MDT-AP-0432_control", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP200947", + "donorId": "DO232959", + "submitterSpecimenId": "MDT-AP-0432_control_specimen", + "specimenType": "Normal - blood derived" + }, + "donor": { + "donorId": "DO232959", + "submitterDonorId": "MDT-AP-0432", + "studyId": "PEME-CA", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "464116e4-afc9-5879-b567-6f54513a32dc", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "bundle.EGAZ00001254247.xml", + "fileSize": 6352, + "fileType": "XML", + "fileMd5sum": "cad2b396e0f7dc5384a5275f89ccad3a", + "fileAccess": "open", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "6aa8d318-e168-520e-9d1e-cef127ee6b65", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "b2e40ebb719e1754e99be2e752239639.control_MDT-AP-0432_merged.mdup.bam.bai", + "fileSize": 8982928, + "fileType": "BAI", + "fileMd5sum": "227a2a11d660a8a53a7375c6623034e2", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "9ce9358d-c93a-5f83-8032-4addcb84b51a", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "b2e40ebb719e1754e99be2e752239639.control_MDT-AP-0432_merged.mdup.bam", + "fileSize": 77675501639, + "fileType": "BAM", + "fileMd5sum": "b2e40ebb719e1754e99be2e752239639", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "analysisId": "EGAZ00001254247", + "aligned": true, + "libraryStrategy": "WGS", + "info": {} + } + } + ], + "totalAnalyses": 1, + "currentTotalAnalyses": 1 +} diff --git a/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.aws.study.response.json b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.aws.study.response.json new file mode 100644 index 00000000..445aea36 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.aws.study.response.json @@ -0,0 +1,90 @@ +{ + "analyses": + [ + { + "analysisType": { + "name": "sequencingRead", + "version": 1 + }, + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false + }, + "analysisId": "EGAZ00001254247", + "studyId": "PEME-CA", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA604905", + "specimenId": "SP200947", + "submitterSampleId": "MDT-AP-0432_control", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP200947", + "donorId": "DO232959", + "submitterSpecimenId": "MDT-AP-0432_control_specimen", + "specimenType": "Normal - blood derived" + }, + "donor": { + "donorId": "DO232959", + "submitterDonorId": "MDT-AP-0432", + "studyId": "PEME-CA", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "464116e4-afc9-5879-b567-6f54513a32dc", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "bundle.EGAZ00001254247.xml", + "fileSize": 6352, + "fileType": "XML", + "fileMd5sum": "cad2b396e0f7dc5384a5275f89ccad3a", + "fileAccess": "open", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "6aa8d318-e168-520e-9d1e-cef127ee6b65", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "b2e40ebb719e1754e99be2e752239639.control_MDT-AP-0432_merged.mdup.bam.bai", + "fileSize": 8982928, + "fileType": "BAI", + "fileMd5sum": "227a2a11d660a8a53a7375c6623034e2", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "9ce9358d-c93a-5f83-8032-4addcb84b51a", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "b2e40ebb719e1754e99be2e752239639.control_MDT-AP-0432_merged.mdup.bam", + "fileSize": 77675501639, + "fileType": "BAM", + "fileMd5sum": "b2e40ebb719e1754e99be2e752239639", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "analysisId": "EGAZ00001254247", + "aligned": true, + "libraryStrategy": "WGS", + "info": {} + } + } + ], + "totalAnalyses": 1, + "currentTotalAnalyses": 1 +} diff --git a/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.study.response.json b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.study.response.json new file mode 100644 index 00000000..e22637a7 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/PEME-CA.study.response.json @@ -0,0 +1,198 @@ +{ + "analyses": + [ + { + "analysisType": { + "name": "sequencingRead", + "version": 1 + }, + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false + }, + "analysisId": "EGAZ00001254368", + "studyId": "PEME-CA", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "sampleId": "SA604924", + "specimenId": "SP201301", + "submitterSampleId": "MDT-AP-0749_tumor", + "sampleType": "DNA", + "specimen": { + "specimenId": "SP201301", + "donorId": "DO232978", + "submitterSpecimenId": "MDT-AP-0749_tumor_specimen", + "specimenType": "Primary tumour - solid tissue", + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false + } + }, + "donor": { + "donorId": "DO232978", + "submitterDonorId": "MDT-AP-0749", + "studyId": "PEME-CA", + "gender": "Female", + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false + } + }, + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false + } + } + ], + "files": [ + { + "objectId": "41ba4fb3-9428-50b5-af6c-d779cd59b04d", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254368", + "fileName": "bundle.EGAZ00001254368.xml", + "fileSize": 6342, + "fileType": "XML", + "fileMd5sum": "fb157ece007dc31b3d34add273efedcb", + "fileAccess": "open", + "dataType": "AlignedReads", + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false + } + }, + { + "objectId": "d819f154-2292-56f7-94f3-bbe03fb45bc5", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254368", + "fileName": "29ff9df727803d20834b9997bc17e970.tumor_MDT-AP-0749_merged.mdup.bam.bai", + "fileSize": 8939816, + "fileType": "BAI", + "fileMd5sum": "e2a83668aa4cfe4f4048e75212d44f19", + "fileAccess": "controlled", + "dataType": "AlignedReads", + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false, + "nested": { + "nestedAgain": [ + { + "theeNested": "word" + } + ] + } + } + }, + { + "objectId": "43d29864-6756-51f0-bb2a-ba7cff860778", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254368", + "fileName": "29ff9df727803d20834b9997bc17e970.tumor_MDT-AP-0749_merged.mdup.bam", + "fileSize": 88906416144, + "fileType": "BAM", + "fileMd5sum": "29ff9df727803d20834b9997bc17e970", + "fileAccess": "controlled", + "dataType": "AlignedReads", + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false + } + } + ], + "experiment": { + "analysisId": "EGAZ00001254368", + "aligned": true, + "libraryStrategy": "WGS", + "info": {} + } + }, + { + "analysisType": { + "name": "sequencingRead", + "version": 1 + }, + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false + }, + "analysisId": "EGAZ00001254247", + "studyId": "PEME-CA", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA604905", + "specimenId": "SP200947", + "submitterSampleId": "MDT-AP-0432_control", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP200947", + "donorId": "DO232959", + "submitterSpecimenId": "MDT-AP-0432_control_specimen", + "specimenType": "Normal - blood derived" + }, + "donor": { + "donorId": "DO232959", + "submitterDonorId": "MDT-AP-0432", + "studyId": "PEME-CA", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "464116e4-afc9-5879-b567-6f54513a32dc", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "bundle.EGAZ00001254247.xml", + "fileSize": 6352, + "fileType": "XML", + "fileMd5sum": "cad2b396e0f7dc5384a5275f89ccad3a", + "fileAccess": "open", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "6aa8d318-e168-520e-9d1e-cef127ee6b65", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "b2e40ebb719e1754e99be2e752239639.control_MDT-AP-0432_merged.mdup.bam.bai", + "fileSize": 8982928, + "fileType": "BAI", + "fileMd5sum": "227a2a11d660a8a53a7375c6623034e2", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "9ce9358d-c93a-5f83-8032-4addcb84b51a", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "b2e40ebb719e1754e99be2e752239639.control_MDT-AP-0432_merged.mdup.bam", + "fileSize": 77675501639, + "fileType": "BAM", + "fileMd5sum": "b2e40ebb719e1754e99be2e752239639", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "analysisId": "EGAZ00001254247", + "aligned": true, + "libraryStrategy": "WGS", + "info": {} + } + } + ], + "totalAnalyses": 2, + "currentTotalAnalyses": 2 +} diff --git a/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/empty-response.json b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/empty-response.json new file mode 100644 index 00000000..78d7dd61 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/FileCentricIntegrationTest/empty-response.json @@ -0,0 +1,7 @@ +{ + "analyses": + [ + ], + "totalAnalyses": 2, + "currentTotalAnalyses": 0 +} diff --git a/maestro-app/src/test/resources/fixtures/SongStudyDAOTest/PEME-CA.response.json b/maestro-app/src/test/resources/fixtures/SongStudyDAOTest/PEME-CA.response.json new file mode 100644 index 00000000..3ee7af42 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/SongStudyDAOTest/PEME-CA.response.json @@ -0,0 +1,174 @@ +{ + "analyses": + [ + { + "analysisType": { + "name": "sequencingRead", + "version": 1 + }, + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false + }, + "analysisId": "EGAZ00001254368", + "studyId": "PEME-CA", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA604924", + "specimenId": "SP201301", + "submitterSampleId": "MDT-AP-0749_tumor", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP201301", + "donorId": "DO232978", + "submitterSpecimenId": "MDT-AP-0749_tumor_specimen", + "specimenType": "Primary tumour - solid tissue" + }, + "donor": { + "donorId": "DO232978", + "submitterDonorId": "MDT-AP-0749", + "studyId": "PEME-CA", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "41ba4fb3-9428-50b5-af6c-d779cd59b04d", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254368", + "fileName": "bundle.EGAZ00001254368.xml", + "fileSize": 6342, + "fileType": "XML", + "fileMd5sum": "fb157ece007dc31b3d34add273efedcb", + "fileAccess": "open", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "d819f154-2292-56f7-94f3-bbe03fb45bc5", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254368", + "fileName": "29ff9df727803d20834b9997bc17e970.tumor_MDT-AP-0749_merged.mdup.bam.bai", + "fileSize": 8939816, + "fileType": "BAI", + "fileMd5sum": "e2a83668aa4cfe4f4048e75212d44f19", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "43d29864-6756-51f0-bb2a-ba7cff860778", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254368", + "fileName": "29ff9df727803d20834b9997bc17e970.tumor_MDT-AP-0749_merged.mdup.bam", + "fileSize": 88906416144, + "fileType": "BAM", + "fileMd5sum": "29ff9df727803d20834b9997bc17e970", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "analysisId": "EGAZ00001254368", + "aligned": true, + "libraryStrategy": "WGS", + "info": {} + } + }, + { + "analysisType": { + "name": "sequencingRead", + "version": 1 + }, + "info": { + "dcc_project_code": "PEME-CA", + "isPcawg": false + }, + "analysisId": "EGAZ00001254247", + "studyId": "PEME-CA", + "analysisState": "PUBLISHED", + "updatedAt": "2020-12-02T17:18:32.353334", + "firstPublishedAt": "2020-12-02T17:18:32.353334", + "publishedAt": "2020-12-02T17:18:32.353334", + "samples": [ + { + "info": {}, + "sampleId": "SA604905", + "specimenId": "SP200947", + "submitterSampleId": "MDT-AP-0432_control", + "sampleType": "DNA", + "specimen": { + "info": {}, + "specimenId": "SP200947", + "donorId": "DO232959", + "submitterSpecimenId": "MDT-AP-0432_control_specimen", + "specimenType": "Normal - blood derived" + }, + "donor": { + "donorId": "DO232959", + "submitterDonorId": "MDT-AP-0432", + "studyId": "PEME-CA", + "gender": "Female", + "info": {} + } + } + ], + "files": [ + { + "info": {}, + "objectId": "464116e4-afc9-5879-b567-6f54513a32dc", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "bundle.EGAZ00001254247.xml", + "fileSize": 6352, + "fileType": "XML", + "fileMd5sum": "cad2b396e0f7dc5384a5275f89ccad3a", + "fileAccess": "open", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "6aa8d318-e168-520e-9d1e-cef127ee6b65", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "b2e40ebb719e1754e99be2e752239639.control_MDT-AP-0432_merged.mdup.bam.bai", + "fileSize": 8982928, + "fileType": "BAI", + "fileMd5sum": "227a2a11d660a8a53a7375c6623034e2", + "fileAccess": "controlled", + "dataType": "AlignedReads" + }, + { + "info": {}, + "objectId": "9ce9358d-c93a-5f83-8032-4addcb84b51a", + "studyId": "PEME-CA", + "analysisId": "EGAZ00001254247", + "fileName": "b2e40ebb719e1754e99be2e752239639.control_MDT-AP-0432_merged.mdup.bam", + "fileSize": 77675501639, + "fileType": "BAM", + "fileMd5sum": "b2e40ebb719e1754e99be2e752239639", + "fileAccess": "controlled", + "dataType": "AlignedReads" + } + ], + "experiment": { + "analysisId": "EGAZ00001254247", + "aligned": true, + "libraryStrategy": "WGS", + "info": {} + } + } + ], + "totalAnalyses": 2, + "currentTotalAnalyses": 2 +} + diff --git a/maestro-app/src/test/resources/fixtures/SongStudyDAOTest/empty-response.json b/maestro-app/src/test/resources/fixtures/SongStudyDAOTest/empty-response.json new file mode 100644 index 00000000..08241128 --- /dev/null +++ b/maestro-app/src/test/resources/fixtures/SongStudyDAOTest/empty-response.json @@ -0,0 +1,8 @@ +{ + "analyses": + [ + ], + "totalAnalyses": 2, + "currentTotalAnalyses": 0 +} + diff --git a/maestro-domain/src/main/java/bio/overture/maestro/domain/entities/metadata/study/GetAnalysisResponse.java b/maestro-domain/src/main/java/bio/overture/maestro/domain/entities/metadata/study/GetAnalysisResponse.java new file mode 100644 index 00000000..e7ee8372 --- /dev/null +++ b/maestro-domain/src/main/java/bio/overture/maestro/domain/entities/metadata/study/GetAnalysisResponse.java @@ -0,0 +1,16 @@ +package bio.overture.maestro.domain.entities.metadata.study; + +import java.util.List; +import lombok.*; + +@Getter +@Builder +@ToString +@NoArgsConstructor +@AllArgsConstructor +@EqualsAndHashCode +public class GetAnalysisResponse { + private List analyses; + private Integer totalAnalyses; + private Integer currentTotalAnalyses; +}