From f9da105214a2f2f6504f29dd5ee8ea321cc0b855 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?= Date: Mon, 19 Feb 2024 10:30:23 +0100 Subject: [PATCH] analysis: implement overwrite for alignment index and coverage; and generate clients, #TASK-5679, #TASK-5662 --- .../alignment/AlignmentAnalysisUtils.java | 11 +- .../alignment/AlignmentCoverageAnalysis.java | 51 ++++---- .../alignment/AlignmentIndexOperation.java | 31 ++++- .../alignment/AlignmentStorageManager.java | 3 +- .../executors/AlignmentCommandExecutor.java | 123 +----------------- .../options/AlignmentCommandOptions.java | 28 ++-- .../app/cli/main/OpenCgaCompleter.java | 2 +- .../app/cli/main/OpencgaCliOptionsParser.java | 2 +- .../AnalysisAlignmentCommandExecutor.java | 6 +- .../AnalysisAlignmentCommandOptions.java | 24 ++-- opencga-client/src/main/R/R/Admin-methods.R | 2 +- .../src/main/R/R/Alignment-methods.R | 6 +- opencga-client/src/main/R/R/AllGenerics.R | 22 ++-- .../src/main/R/R/Clinical-methods.R | 4 +- opencga-client/src/main/R/R/Cohort-methods.R | 4 +- opencga-client/src/main/R/R/Family-methods.R | 4 +- opencga-client/src/main/R/R/File-methods.R | 4 +- opencga-client/src/main/R/R/GA4GH-methods.R | 2 +- .../src/main/R/R/Individual-methods.R | 4 +- opencga-client/src/main/R/R/Job-methods.R | 4 +- opencga-client/src/main/R/R/Meta-methods.R | 2 +- .../src/main/R/R/Operation-methods.R | 2 +- opencga-client/src/main/R/R/Panel-methods.R | 4 +- opencga-client/src/main/R/R/Project-methods.R | 4 +- opencga-client/src/main/R/R/Sample-methods.R | 4 +- opencga-client/src/main/R/R/Study-methods.R | 4 +- opencga-client/src/main/R/R/User-methods.R | 4 +- opencga-client/src/main/R/R/Variant-methods.R | 2 +- .../client/rest/clients/AdminClient.java | 2 +- .../client/rest/clients/AlignmentClient.java | 6 +- .../rest/clients/ClinicalAnalysisClient.java | 2 +- .../client/rest/clients/CohortClient.java | 2 +- .../rest/clients/DiseasePanelClient.java | 2 +- .../client/rest/clients/FamilyClient.java | 2 +- .../client/rest/clients/FileClient.java | 2 +- .../client/rest/clients/GA4GHClient.java | 2 +- .../client/rest/clients/IndividualClient.java | 2 +- .../client/rest/clients/JobClient.java | 2 +- .../client/rest/clients/MetaClient.java | 2 +- .../client/rest/clients/ProjectClient.java | 2 +- .../client/rest/clients/SampleClient.java | 2 +- .../client/rest/clients/StudyClient.java | 2 +- .../client/rest/clients/UserClient.java | 2 +- .../client/rest/clients/VariantClient.java | 2 +- .../rest/clients/VariantOperationClient.java | 2 +- opencga-client/src/main/javascript/Admin.js | 2 +- .../src/main/javascript/Alignment.js | 6 +- .../src/main/javascript/ClinicalAnalysis.js | 2 +- opencga-client/src/main/javascript/Cohort.js | 2 +- .../src/main/javascript/DiseasePanel.js | 2 +- opencga-client/src/main/javascript/Family.js | 2 +- opencga-client/src/main/javascript/File.js | 2 +- opencga-client/src/main/javascript/GA4GH.js | 2 +- .../src/main/javascript/Individual.js | 2 +- opencga-client/src/main/javascript/Job.js | 2 +- opencga-client/src/main/javascript/Meta.js | 2 +- opencga-client/src/main/javascript/Project.js | 2 +- opencga-client/src/main/javascript/Sample.js | 2 +- opencga-client/src/main/javascript/Study.js | 2 +- opencga-client/src/main/javascript/User.js | 2 +- opencga-client/src/main/javascript/Variant.js | 2 +- .../src/main/javascript/VariantOperation.js | 2 +- .../pyopencga/rest_clients/admin_client.py | 2 +- .../rest_clients/alignment_client.py | 8 +- .../rest_clients/clinical_analysis_client.py | 2 +- .../pyopencga/rest_clients/cohort_client.py | 2 +- .../rest_clients/disease_panel_client.py | 2 +- .../pyopencga/rest_clients/family_client.py | 2 +- .../pyopencga/rest_clients/file_client.py | 2 +- .../pyopencga/rest_clients/ga4gh_client.py | 2 +- .../rest_clients/individual_client.py | 2 +- .../pyopencga/rest_clients/job_client.py | 2 +- .../pyopencga/rest_clients/meta_client.py | 2 +- .../pyopencga/rest_clients/project_client.py | 2 +- .../pyopencga/rest_clients/sample_client.py | 2 +- .../pyopencga/rest_clients/study_client.py | 2 +- .../pyopencga/rest_clients/user_client.py | 2 +- .../pyopencga/rest_clients/variant_client.py | 2 +- .../rest_clients/variant_operation_client.py | 2 +- .../opencga/core/api/FieldConstants.java | 9 +- .../opencga/core/api/ParamConstants.java | 2 - .../alignment/AlignmentIndexParams.java | 21 +-- .../models/alignment/CoverageIndexParams.java | 46 ++++--- .../rest/analysis/AlignmentWebService.java | 4 +- 84 files changed, 246 insertions(+), 315 deletions(-) diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentAnalysisUtils.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentAnalysisUtils.java index cbd21b3df58..c1933c0e65d 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentAnalysisUtils.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentAnalysisUtils.java @@ -28,14 +28,13 @@ public class AlignmentAnalysisUtils { - public static File linkAndUpdate(File bamCatalogFile, Path outPath, String study, CatalogManager catalogManager, String token) + public static File linkAndUpdate(File bamCatalogFile, Path outPath, String jobId, String study, CatalogManager catalogManager, String token) throws CatalogException, ToolException { // Link BW file and update sample info - FileLinkParams fileLinkParams = new FileLinkParams().setUri(outPath.toString()); - if (Paths.get(bamCatalogFile.getPath()).getParent() != null) { - fileLinkParams.setPath(Paths.get(bamCatalogFile.getPath()).getParent().resolve(outPath.getFileName()).toString()); - } - OpenCGAResult fileResult = catalogManager.getFileManager().link(study, fileLinkParams, false, token); + FileLinkParams fileLinkParams = new FileLinkParams() + .setUri(outPath.toString()) + .setPath(Paths.get(jobId).resolve(outPath.getFileName()).toString()); + OpenCGAResult fileResult = catalogManager.getFileManager().link(study, fileLinkParams, true, token); if (fileResult.getNumResults() != 1) { throw new ToolException("It could not link OpenCGA file catalog file for '" + outPath + "'"); } diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentCoverageAnalysis.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentCoverageAnalysis.java index 27e809f25c9..eedabbda00f 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentCoverageAnalysis.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentCoverageAnalysis.java @@ -26,7 +26,6 @@ import org.opencb.opencga.core.models.common.InternalStatus; import org.opencb.opencga.core.models.file.File; import org.opencb.opencga.core.models.file.FileInternalCoverageIndex; -import org.opencb.opencga.core.response.OpenCGAResult; import org.opencb.opencga.core.tools.annotations.Tool; import org.opencb.opencga.core.tools.annotations.ToolParams; @@ -43,7 +42,7 @@ public class AlignmentCoverageAnalysis extends OpenCgaToolScopeStudy { public static final String ID = "coverage-index-run"; - public static final String DESCRIPTION = "Compute the coverage from a given alignment file, e.g., create a " + public static final String DESCRIPTION = "Compute the coverage from a given BAM alignment file, e.g., create a " + AlignmentConstants.BIGWIG_EXTENSION + " file from a " + AlignmentConstants.BAM_EXTENSION + " file"; @ToolParams @@ -63,37 +62,36 @@ protected void check() throws Exception { // Checking BAM file ID try { - bamCatalogFile = catalogManager.getFileManager().get(getStudy(), coverageParams.getBamFileId(), QueryOptions.empty(), + bamCatalogFile = catalogManager.getFileManager().get(getStudy(), coverageParams.getFileId(), QueryOptions.empty(), getToken()).first(); if (bamCatalogFile == null) { - throw new ToolException("Could not find BAM file from ID '" + coverageParams.getBamFileId() + "'"); + throw new ToolException("Could not find BAM file from ID '" + coverageParams.getFileId() + "'"); } } catch (Exception e) { - throw new ToolException("Could not get BAM file from ID " + coverageParams.getBamFileId()); + throw new ToolException("Could not get BAM file from ID " + coverageParams.getFileId()); } // Check if the input file is .bam if (!bamCatalogFile.getName().endsWith(AlignmentConstants.BAM_EXTENSION)) { - throw new ToolException("Invalid input alignment file '" + coverageParams.getBamFileId() + "' (" + bamCatalogFile.getName() + throw new ToolException("Invalid input alignment file '" + coverageParams.getFileId() + "' (" + bamCatalogFile.getName() + "): it must be in BAM format"); } // Getting BAI file - String baiFileId = coverageParams.getBaiFileId(); + String baiFileId; + try { + baiFileId = bamCatalogFile.getInternal().getAlignment().getIndex().getFileId(); + } catch (Exception e) { + throw new ToolException("Could not get internal alignment index file Id from BAM file ID '" + bamCatalogFile.getId() + "'"); + } if (StringUtils.isEmpty(baiFileId)) { - // BAI file ID was not provided, looking for it - logger.info("BAI file ID was not provided, getting it from the internal alignment index of the BAM file ID {}", - bamCatalogFile.getId()); - try { - baiFileId = bamCatalogFile.getInternal().getAlignment().getIndex().getFileId(); - } catch (Exception e) { - throw new ToolException("Could not get internal alignment index file Id from BAM file ID '" + bamCatalogFile.getId()); - } + throw new ToolException("Could not find the alignment index file for the BAM file ID '" + bamCatalogFile.getId() + "'. Please," + + " create the alignment index file before computing the coverage"); } try { baiCatalogFile = catalogManager.getFileManager().get(getStudy(), baiFileId, QueryOptions.empty(), getToken()).first(); if (baiCatalogFile == null) { - throw new ToolException("Could not find BAI file from ID '" + coverageParams.getBaiFileId() + "'"); + throw new ToolException("Could not find BAI file from ID '" + baiFileId + "'"); } } catch (Exception e) { throw new ToolException("Could not get BAI file from file ID " + baiFileId); @@ -114,6 +112,18 @@ protected void check() throws Exception { coverageParams.setWindowSize(Integer.parseInt(COVERAGE_WINDOW_SIZE_DEFAULT)); logger.info("Window size is set to {}", coverageParams.getWindowSize()); } + + // Check overwrite + String bwFileId; + try { + bwFileId = bamCatalogFile.getInternal().getAlignment().getCoverage().getFileId(); + } catch (Exception e) { + bwFileId = null; + } + if (StringUtils.isNotEmpty(bwFileId) && !coverageParams.isOverwrite()) { + throw new ToolException("Coverage file ID '" + bwFileId + "' already exists for file ID '" + bamCatalogFile.getId() + + "'. To overwrite the BIGWIG file use the flag --overwrite"); + } } @Override @@ -189,17 +199,12 @@ protected void run() throws Exception { } // Link generated BIGWIG file and update samples info - File bwCatalogFile = AlignmentAnalysisUtils.linkAndUpdate(bamCatalogFile, bwPath, study, catalogManager, token); + File bwCatalogFile = AlignmentAnalysisUtils.linkAndUpdate(bamCatalogFile, bwPath, getJobId(), study, catalogManager, token); // Update BAM file internal in order to set the coverage index (BIGWIG) FileInternalCoverageIndex fileCoverageIndex = new FileInternalCoverageIndex(new InternalStatus(InternalStatus.READY), bwCatalogFile.getId(), "deeptools bamCoverage", coverageParams.getWindowSize()); - OpenCGAResult openCGAResult = catalogManager.getFileManager().updateFileInternalCoverageIndex(bamCatalogFile, - fileCoverageIndex, token); - if (openCGAResult.getNumUpdated() != 1) { - throw new ToolException("It could not update OpenCGA file catalog (alignment index " + bamCatalogFile.getId() + ") with" - + " the coverage index (BIGWIG) file '" + bwCatalogFile.getId() + "'"); - } + catalogManager.getFileManager().updateFileInternalCoverageIndex(bamCatalogFile, fileCoverageIndex, token); }); } } diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentIndexOperation.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentIndexOperation.java index 38d89cf2b5c..44d9bd900a1 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentIndexOperation.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentIndexOperation.java @@ -16,6 +16,7 @@ package org.opencb.opencga.analysis.alignment; +import org.apache.commons.lang3.StringUtils; import org.opencb.biodata.tools.alignment.BamManager; import org.opencb.commons.datastore.core.QueryOptions; import org.opencb.opencga.analysis.tools.OpenCgaTool; @@ -23,7 +24,8 @@ import org.opencb.opencga.core.exceptions.ToolException; import org.opencb.opencga.core.models.common.Enums; import org.opencb.opencga.core.models.common.InternalStatus; -import org.opencb.opencga.core.models.file.*; +import org.opencb.opencga.core.models.file.File; +import org.opencb.opencga.core.models.file.FileInternalAlignmentIndex; import org.opencb.opencga.core.response.OpenCGAResult; import org.opencb.opencga.core.tools.annotations.Tool; @@ -35,10 +37,12 @@ public class AlignmentIndexOperation extends OpenCgaTool { public static final String ID = "alignment-index-run"; - public static final String DESCRIPTION = "Index a given alignment file, e.g., create a .bai file from a .bam file"; + public static final String DESCRIPTION = "Index a given alignment file BAM/CRAM, e.g., create a " + AlignmentConstants.BAI_EXTENSION + + " file from a " + AlignmentConstants.BAM_EXTENSION + " file"; private String study; private String inputFile; + private boolean overwrite = false; private File inputCatalogFile; private Path inputPath; @@ -67,6 +71,18 @@ protected void check() throws Exception { throw new ToolException("Invalid input alignment file '" + inputFile + "': it must be in BAM or CRAM format"); } + // Check overwrite + String baiFileId; + try { + baiFileId = inputCatalogFile.getInternal().getAlignment().getIndex().getFileId(); + } catch (Exception e) { + baiFileId = null; + } + if (StringUtils.isNotEmpty(baiFileId) && !overwrite) { + throw new ToolException("Alignment index file ID '" + baiFileId + "' already exists for file ID '" + inputCatalogFile.getId() + + "'. To overwrite the alignment index file use the flag --overwrite"); + } + outputPath = getOutDir().resolve(filename + (filename.endsWith(AlignmentConstants.BAM_EXTENSION) ? AlignmentConstants.BAI_EXTENSION : AlignmentConstants.CRAI_EXTENSION)); } @@ -103,7 +119,7 @@ protected void run() throws Exception { } // Link generated BAI file and update samples info, related file - File baiCatalogFile = AlignmentAnalysisUtils.linkAndUpdate(inputCatalogFile, outputPath, study, catalogManager, token); + File baiCatalogFile = AlignmentAnalysisUtils.linkAndUpdate(inputCatalogFile, outputPath, getJobId(), study, catalogManager, token); // Update BAM file internal in order to set the alignment index (BAI) FileInternalAlignmentIndex fileAlignmentIndex = new FileInternalAlignmentIndex(new InternalStatus(InternalStatus.READY), @@ -129,4 +145,13 @@ public AlignmentIndexOperation setInputFile(String inputFile) { this.inputFile = inputFile; return this; } + + public boolean isOverwrite() { + return overwrite; + } + + public AlignmentIndexOperation setOverwrite(boolean overwrite) { + this.overwrite = overwrite; + return this; + } } diff --git a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java index 2aa314a9fd5..fd8a0cebad5 100644 --- a/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java +++ b/opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentStorageManager.java @@ -91,7 +91,7 @@ public AlignmentStorageManager(CatalogManager catalogManager, StorageEngineFacto // INDEX //------------------------------------------------------------------------- - public void index(String study, String inputFile, String outdir, String token) throws ToolException { + public void index(String study, String inputFile, boolean overwrite, String outdir, String token) throws ToolException { ObjectMap params = new ObjectMap(); AlignmentIndexOperation indexOperation = new AlignmentIndexOperation(); @@ -99,6 +99,7 @@ public void index(String study, String inputFile, String outdir, String token) t indexOperation.setStudy(study); indexOperation.setInputFile(inputFile); + indexOperation.setOverwrite(overwrite); indexOperation.start(); } diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/AlignmentCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/AlignmentCommandExecutor.java index 07ed1b36c1f..6afb5b6805a 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/AlignmentCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/executors/AlignmentCommandExecutor.java @@ -50,7 +50,6 @@ public class AlignmentCommandExecutor extends InternalCommandExecutor { private AlignmentCommandOptions alignmentCommandOptions; private String jobId; -// private AlignmentStorageEngine alignmentStorageManager; public AlignmentCommandExecutor(AlignmentCommandOptions options) { super(options.analysisCommonOptions); @@ -76,18 +75,6 @@ public void execute() throws Exception { case "gene-coveratge-stats-run": geneCoverageStatsRun(); break; -// case "stats-run": -// statsRun(); -// break; -// case "flagstats-run": -// flagStatsRun(); -// break; -// case "fastqcmetrics-run": -// fastQcMetricsRun(); -// break; -// case "hsmetrics-run": -// hsMetricsRun(); -// break; case "coverage-index-run": coverageRun(); break; @@ -119,38 +106,12 @@ public void execute() throws Exception { private void indexRun() throws Exception { AlignmentCommandOptions.IndexAlignmentCommandOptions cliOptions = alignmentCommandOptions.indexAlignmentCommandOptions; - AlignmentStorageManager alignmentManager = new AlignmentStorageManager(catalogManager, storageEngineFactory, alignmentCommandOptions.internalJobOptions.jobId); + AlignmentStorageManager alignmentManager = new AlignmentStorageManager(catalogManager, storageEngineFactory, + alignmentCommandOptions.internalJobOptions.jobId); - alignmentManager.index(cliOptions.study, cliOptions.file, cliOptions.outdir, cliOptions.commonOptions.token); + alignmentManager.index(cliOptions.study, cliOptions.file, cliOptions.overwrite, cliOptions.outdir, cliOptions.commonOptions.token); } - -// private void query() throws InterruptedException, CatalogException, IOException { -// ObjectMap objectMap = new ObjectMap(); -// objectMap.putIfNotNull("sid", alignmentCommandOptions.queryAlignmentCommandOptions.commonOptions.token); -// objectMap.putIfNotNull("study", alignmentCommandOptions.queryAlignmentCommandOptions.study); -// objectMap.putIfNotNull(AlignmentDBAdaptor.QueryParams.REGION.key(), alignmentCommandOptions.queryAlignmentCommandOptions.region); -// objectMap.putIfNotNull(AlignmentDBAdaptor.QueryParams.MIN_MAPQ.key(), -// alignmentCommandOptions.queryAlignmentCommandOptions.minMappingQuality); -// objectMap.putIfNotNull(AlignmentDBAdaptor.QueryParams.CONTAINED.key(), -// alignmentCommandOptions.queryAlignmentCommandOptions.contained); -// objectMap.putIfNotNull(AlignmentDBAdaptor.QueryParams.MD_FIELD.key(), -// alignmentCommandOptions.queryAlignmentCommandOptions.mdField); -// objectMap.putIfNotNull(AlignmentDBAdaptor.QueryParams.BIN_QUALITIES.key(), -// alignmentCommandOptions.queryAlignmentCommandOptions.binQualities); -// objectMap.putIfNotNull(QueryOptions.LIMIT, alignmentCommandOptions.queryAlignmentCommandOptions.limit); -// objectMap.putIfNotNull(QueryOptions.SKIP, alignmentCommandOptions.queryAlignmentCommandOptions.skip); -// objectMap.putIfNotNull(QueryOptions.COUNT, alignmentCommandOptions.queryAlignmentCommandOptions.count); -// -// OpenCGAClient openCGAClient = new OpenCGAClient(clientConfiguration); -// RestResponse alignments = openCGAClient.getAlignmentClient() -// .query(alignmentCommandOptions.queryAlignmentCommandOptions.fileId, objectMap); -// -// for (ReadAlignment readAlignment : alignments.allResults()) { -// System.out.println(readAlignment); -// } -// } - private void qcRun() throws ToolException { AlignmentCommandOptions.QcAlignmentCommandOptions cliOptions = alignmentCommandOptions.qcAlignmentCommandOptions; @@ -179,64 +140,13 @@ private void geneCoverageStatsRun() throws ToolException { toolRunner.execute(AlignmentGeneCoverageStatsAnalysis.class, params, Paths.get(cliOptions.outdir), jobId, token); } -// private void statsRun() throws ToolException { -// AlignmentCommandOptions.StatsAlignmentCommandOptions cliOptions = alignmentCommandOptions.statsAlignmentCommandOptions; -// -// ObjectMap params = new AlignmentStatsParams( -// cliOptions.file, -// cliOptions.outdir -// ).toObjectMap(cliOptions.commonOptions.params) -// .append(ParamConstants.STUDY_PARAM, cliOptions.study); -// -// toolRunner.execute(AlignmentStatsAnalysis.class, params, Paths.get(cliOptions.outdir), jobId, token); -// } -// -// private void flagStatsRun() throws ToolException { -// AlignmentCommandOptions.FlagStatsAlignmentCommandOptions cliOptions = alignmentCommandOptions.flagStatsAlignmentCommandOptions; -// -// ObjectMap params = new AlignmentFlagStatsParams( -// cliOptions.file, -// cliOptions.outdir -// ).toObjectMap(cliOptions.commonOptions.params) -// .append(ParamConstants.STUDY_PARAM, cliOptions.study); -// -// toolRunner.execute(AlignmentFlagStatsAnalysis.class, params, Paths.get(cliOptions.outdir), jobId, token); -// } -// -// private void fastQcMetricsRun() throws ToolException { -// AlignmentCommandOptions.FastQcMetricsAlignmentCommandOptions cliOptions = alignmentCommandOptions -// .fastQcMetricsAlignmentCommandOptions; -// -// ObjectMap params = new AlignmentFastQcMetricsParams( -// cliOptions.file, -// cliOptions.outdir -// ).toObjectMap(cliOptions.commonOptions.params) -// .append(ParamConstants.STUDY_PARAM, cliOptions.study); -// -// toolRunner.execute(AlignmentFastQcMetricsAnalysis.class, params, Paths.get(cliOptions.outdir), jobId, token); -// } -// -// private void hsMetricsRun() throws ToolException { -// AlignmentCommandOptions.HsMetricsAlignmentCommandOptions cliOptions = alignmentCommandOptions.hsMetricsAlignmentCommandOptions; -// -// ObjectMap params = new AlignmentHsMetricsParams( -// cliOptions.bamFile, -// cliOptions.bedFile, -// cliOptions.dictFile, -// cliOptions.outdir -// ).toObjectMap(cliOptions.commonOptions.params) -// .append(ParamConstants.STUDY_PARAM, cliOptions.study); -// -// toolRunner.execute(AlignmentHsMetricsAnalysis.class, params, Paths.get(cliOptions.outdir), jobId, token); -// } - private void coverageRun() throws ToolException { AlignmentCommandOptions.CoverageAlignmentCommandOptions cliOptions = alignmentCommandOptions.coverageAlignmentCommandOptions; ObjectMap params = new CoverageIndexParams( cliOptions.bamFileId, - cliOptions.baiFileId, - cliOptions.windowSize + cliOptions.windowSize, + cliOptions.overwrite ).toObjectMap(cliOptions.commonOptions.params).append(ParamConstants.STUDY_PARAM, cliOptions.study); toolRunner.execute(AlignmentCoverageAnalysis.class, params, Paths.get(cliOptions.outdir), jobId, token); @@ -323,27 +233,4 @@ private void picard() throws Exception { toolRunner.execute(PicardWrapperAnalysis.class, params, Paths.get(cliOptions.outdir), jobId, token); } - - //------------------------------------------------------------------------- - // M I S C E L A N E O U S M E T H O D S - //------------------------------------------------------------------------- - - private void addParam(Map map, String key, Object value) { - if (value == null) { - return; - } - - if (value instanceof String) { - if (!((String) value).isEmpty()) { - map.put(key, (String) value); - } - } else if (value instanceof Integer) { - map.put(key, Integer.toString((int) value)); - } else if (value instanceof Boolean) { - map.put(key, Boolean.toString((boolean) value)); - } else { - throw new UnsupportedOperationException(); - } - } - } diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/AlignmentCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/AlignmentCommandOptions.java index 628988b9302..b0d4f6bb39b 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/AlignmentCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/internal/options/AlignmentCommandOptions.java @@ -17,6 +17,8 @@ package org.opencb.opencga.app.cli.internal.options; import com.beust.jcommander.*; +import org.opencb.opencga.analysis.alignment.AlignmentCoverageAnalysis; +import org.opencb.opencga.analysis.alignment.AlignmentIndexOperation; import org.opencb.opencga.analysis.wrappers.bwa.BwaWrapperAnalysis; import org.opencb.opencga.analysis.wrappers.deeptools.DeeptoolsWrapperAnalysis; import org.opencb.opencga.analysis.wrappers.fastqc.FastqcWrapperAnalysis; @@ -24,6 +26,7 @@ import org.opencb.opencga.analysis.wrappers.samtools.SamtoolsWrapperAnalysis; import org.opencb.opencga.app.cli.GeneralCliOptions; import org.opencb.opencga.app.cli.internal.InternalCliOptionsParser; +import org.opencb.opencga.core.api.FieldConstants; import java.util.HashMap; import java.util.Map; @@ -40,10 +43,6 @@ public class AlignmentCommandOptions { public QueryAlignmentCommandOptions queryAlignmentCommandOptions; public QcAlignmentCommandOptions qcAlignmentCommandOptions; public GeneCoverageStatsAlignmentCommandOptions geneCoverageStatsAlignmentCommandOptions; -// public StatsAlignmentCommandOptions statsAlignmentCommandOptions; -// public FlagStatsAlignmentCommandOptions flagStatsAlignmentCommandOptions; -// public FastQcMetricsAlignmentCommandOptions fastQcMetricsAlignmentCommandOptions; -// public HsMetricsAlignmentCommandOptions hsMetricsAlignmentCommandOptions; public CoverageAlignmentCommandOptions coverageAlignmentCommandOptions; public CoverageQueryAlignmentCommandOptions coverageQueryAlignmentCommandOptions; public CoverageRatioAlignmentCommandOptions coverageRatioAlignmentCommandOptions; @@ -76,10 +75,6 @@ public AlignmentCommandOptions(GeneralCliOptions.CommonCommandOptions analysisCo this.queryAlignmentCommandOptions = new QueryAlignmentCommandOptions(); this.qcAlignmentCommandOptions = new QcAlignmentCommandOptions(); this.geneCoverageStatsAlignmentCommandOptions = new GeneCoverageStatsAlignmentCommandOptions(); -// this.statsAlignmentCommandOptions = new StatsAlignmentCommandOptions(); -// this.flagStatsAlignmentCommandOptions = new FlagStatsAlignmentCommandOptions(); -// this.fastQcMetricsAlignmentCommandOptions = new FastQcMetricsAlignmentCommandOptions(); -// this.hsMetricsAlignmentCommandOptions = new HsMetricsAlignmentCommandOptions(); this.coverageAlignmentCommandOptions = new CoverageAlignmentCommandOptions(); this.coverageQueryAlignmentCommandOptions = new CoverageQueryAlignmentCommandOptions(); this.coverageRatioAlignmentCommandOptions = new CoverageRatioAlignmentCommandOptions(); @@ -92,7 +87,7 @@ public AlignmentCommandOptions(GeneralCliOptions.CommonCommandOptions analysisCo this.picardCommandOptions = new PicardCommandOptions(); } - @Parameters(commandNames = {"index"}, commandDescription = ALIGNMENT_INDEX_DESCRIPTION) + @Parameters(commandNames = {"index"}, commandDescription = AlignmentIndexOperation.DESCRIPTION) public class IndexAlignmentCommandOptions extends GeneralCliOptions.StudyOption { @ParametersDelegate @@ -104,9 +99,12 @@ public class IndexAlignmentCommandOptions extends GeneralCliOptions.StudyOption @ParametersDelegate public Object internalJobOptions = internalJobOptionsObject; - @Parameter(names = {"--file"}, description = FILE_ID_DESCRIPTION, required = true, arity = 1) + @Parameter(names = {"--file-id"}, description = FieldConstants.ALIGNMENT_BAM_FILE_ID_DESCRIPTION, required = true, arity = 1) public String file; + @Parameter(names = {"--overwrite"}, description = FieldConstants.ALIGNMENT_OVERWRITE_DESCRIPTION, arity = 0) + public boolean overwrite; + @Parameter(names = {"-o", "--outdir"}, description = OUTPUT_DIRECTORY_DESCRIPTION) public String outdir; } @@ -320,7 +318,7 @@ public class GeneCoverageStatsAlignmentCommandOptions extends GeneralCliOptions. public String outdir; } - @Parameters(commandNames = {"coverage-index-run"}, commandDescription = ALIGNMENT_COVERAGE_DESCRIPTION) + @Parameters(commandNames = {"coverage-index-run"}, commandDescription = AlignmentCoverageAnalysis.DESCRIPTION) public class CoverageAlignmentCommandOptions extends GeneralCliOptions.StudyOption { @ParametersDelegate @@ -332,15 +330,15 @@ public class CoverageAlignmentCommandOptions extends GeneralCliOptions.StudyOpti @ParametersDelegate public Object internalJobOptions = internalJobOptionsObject; - @Parameter(names = {"--bam-file-id"}, description = "BAM file ID", required = true, arity = 1) + @Parameter(names = {"--file-id"}, description = FieldConstants.ALIGNMENT_BAM_FILE_ID_DESCRIPTION, required = true, arity = 1) public String bamFileId; - @Parameter(names = {"--bai-file-id"}, description = "BAI file ID; if not provided, it will search the most recent one", arity = 1) - public String baiFileId; - @Parameter(names = {"--window-size"}, description = COVERAGE_WINDOW_SIZE_DESCRIPTION, arity = 1) public int windowSize = 1; + @Parameter(names = {"--overwrite"}, description = FieldConstants.ALIGNMENT_OVERWRITE_DESCRIPTION, arity = 0) + public boolean overwrite; + @Parameter(names = {"-o", "--outdir"}, description = OUTPUT_DIRECTORY_DESCRIPTION) public String outdir; } diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java index 48db1bde2fd..91c83dd3458 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpenCgaCompleter.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2024-02-14 OpenCB +* Copyright 2015-2024-02-19 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java index af1660a9e33..34091c6c743 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/OpencgaCliOptionsParser.java @@ -1,5 +1,5 @@ /* -* Copyright 2015-2024-02-14 OpenCB +* Copyright 2015-2024-02-19 OpenCB * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java index 217b7421f32..bf253173991 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/executors/AnalysisAlignmentCommandExecutor.java @@ -178,9 +178,9 @@ private RestResponse runCoverageIndex() throws Exception { .readValue(new java.io.File(commandOptions.jsonFile), CoverageIndexParams.class); } else { ObjectMap beanParams = new ObjectMap(); - putNestedIfNotEmpty(beanParams, "bamFileId",commandOptions.bamFileId, true); - putNestedIfNotEmpty(beanParams, "baiFileId",commandOptions.baiFileId, true); + putNestedIfNotEmpty(beanParams, "fileId",commandOptions.fileId, true); putNestedIfNotNull(beanParams, "windowSize",commandOptions.windowSize, true); + putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true); coverageIndexParams = JacksonUtils.getDefaultObjectMapper().copy() .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, true) @@ -387,7 +387,7 @@ private RestResponse runIndex() throws Exception { .readValue(new java.io.File(commandOptions.jsonFile), AlignmentIndexParams.class); } else { ObjectMap beanParams = new ObjectMap(); - putNestedIfNotEmpty(beanParams, "file",commandOptions.file, true); + putNestedIfNotEmpty(beanParams, "fileId",commandOptions.fileId, true); putNestedIfNotNull(beanParams, "overwrite",commandOptions.overwrite, true); alignmentIndexParams = JacksonUtils.getDefaultObjectMapper().copy() diff --git a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisAlignmentCommandOptions.java b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisAlignmentCommandOptions.java index cb5e4f77e45..19dbef7dfc4 100644 --- a/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisAlignmentCommandOptions.java +++ b/opencga-app/src/main/java/org/opencb/opencga/app/cli/main/options/AnalysisAlignmentCommandOptions.java @@ -115,7 +115,7 @@ public class RunBwaCommandOptions { } - @Parameters(commandNames = {"coverage-index-run"}, commandDescription ="Compute coverage for a list of alignment files") + @Parameters(commandNames = {"coverage-index-run"}, commandDescription ="Compute the coverage from a given BAM alignment file, e.g., create a .bw file from a .bam file") public class RunCoverageIndexCommandOptions { @ParametersDelegate @@ -142,14 +142,14 @@ public class RunCoverageIndexCommandOptions { @Parameter(names = {"--job-tags"}, description = "Job tags", required = false, arity = 1) public String jobTags; - @Parameter(names = {"--bam-file-id"}, description = "The body web service bamFileId parameter", required = false, arity = 1) - public String bamFileId; + @Parameter(names = {"--file-id"}, description = "Alignment file ID (in format BAM or CRAM)", required = false, arity = 1) + public String fileId; - @Parameter(names = {"--bai-file-id"}, description = "The body web service baiFileId parameter", required = false, arity = 1) - public String baiFileId; + @Parameter(names = {"--window-size"}, description = "Size of the bins, in bases, for the output of the BIGWIG file", required = false, arity = 1) + public Integer windowSize = 50; - @Parameter(names = {"--window-size"}, description = "The body web service windowSize parameter", required = false, arity = 1) - public Integer windowSize; + @Parameter(names = {"--overwrite"}, description = "Overwrite file", required = false, help = true, arity = 0) + public boolean overwrite = false; } @@ -360,7 +360,7 @@ public class RunFastqcCommandOptions { } - @Parameters(commandNames = {"index-run"}, commandDescription ="Index alignment file") + @Parameters(commandNames = {"index-run"}, commandDescription ="Index a given alignment file BAM/CRAM, e.g., create a .bai file from a .bam file") public class RunIndexCommandOptions { @ParametersDelegate @@ -387,10 +387,10 @@ public class RunIndexCommandOptions { @Parameter(names = {"--job-tags"}, description = "Job tags", required = false, arity = 1) public String jobTags; - @Parameter(names = {"--file"}, description = "The body web service file parameter", required = false, arity = 1) - public String file; + @Parameter(names = {"--file-id"}, description = "Alignment file ID (in format BAM or CRAM)", required = false, arity = 1) + public String fileId; - @Parameter(names = {"--overwrite"}, description = "The body web service overwrite parameter", required = false, help = true, arity = 0) + @Parameter(names = {"--overwrite"}, description = "Overwrite file", required = false, help = true, arity = 0) public boolean overwrite = false; } @@ -580,7 +580,5 @@ public class RunSamtoolsCommandOptions { @DynamicParameter(names = {"--samtools-params"}, description = "The body web service samtoolsParams parameter. Use: --samtools-params key=value", required = false) public java.util.Map samtoolsParams = new HashMap<>(); //Dynamic parameters must be initialized; - } - } \ No newline at end of file diff --git a/opencga-client/src/main/R/R/Admin-methods.R b/opencga-client/src/main/R/R/Admin-methods.R index c3041969f51..e572676578b 100644 --- a/opencga-client/src/main/R/R/Admin-methods.R +++ b/opencga-client/src/main/R/R/Admin-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Alignment-methods.R b/opencga-client/src/main/R/R/Alignment-methods.R index 53cd5d9802c..adf29a2a38c 100644 --- a/opencga-client/src/main/R/R/Alignment-methods.R +++ b/opencga-client/src/main/R/R/Alignment-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -55,7 +55,7 @@ setMethod("alignmentClient", "OpencgaR", function(OpencgaR, endpointName, params subcategoryId=NULL, action="run", params=params, httpMethod="POST", as.queryParam=NULL, ...), #' @section Endpoint /{apiVersion}/analysis/alignment/coverage/index/run: - #' Compute coverage for a list of alignment files. + #' Compute the coverage from a given BAM alignment file, e.g., create a .bw file from a .bam file. #' @param study study. #' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. #' @param jobDependsOn Comma separated list of existing job IDs the job will depend on. @@ -143,7 +143,7 @@ setMethod("alignmentClient", "OpencgaR", function(OpencgaR, endpointName, params subcategoryId=NULL, action="run", params=params, httpMethod="POST", as.queryParam=NULL, ...), #' @section Endpoint /{apiVersion}/analysis/alignment/index/run: - #' Index alignment file. + #' Index a given alignment file BAM/CRAM, e.g., create a .bai file from a .bam file. #' @param study study. #' @param jobId Job ID. It must be a unique string within the study. An ID will be autogenerated automatically if not provided. #' @param jobDependsOn Comma separated list of existing job IDs the job will depend on. diff --git a/opencga-client/src/main/R/R/AllGenerics.R b/opencga-client/src/main/R/R/AllGenerics.R index f9fdb51fe6f..ff9ada80c02 100644 --- a/opencga-client/src/main/R/R/AllGenerics.R +++ b/opencga-client/src/main/R/R/AllGenerics.R @@ -1,51 +1,51 @@ # ############################################################################## ## UserClient -setGeneric("userClient", function(OpencgaR, user, users, filterId, endpointName, params=NULL, ...) +setGeneric("userClient", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) standardGeneric("userClient")) # ############################################################################## ## ProjectClient -setGeneric("projectClient", function(OpencgaR, project, projects, endpointName, params=NULL, ...) +setGeneric("projectClient", function(OpencgaR, projects, project, endpointName, params=NULL, ...) standardGeneric("projectClient")) # ############################################################################## ## StudyClient -setGeneric("studyClient", function(OpencgaR, group, variableSet, studies, templateId, study, members, endpointName, params=NULL, ...) +setGeneric("studyClient", function(OpencgaR, templateId, variableSet, studies, members, study, group, endpointName, params=NULL, ...) standardGeneric("studyClient")) # ############################################################################## ## FileClient -setGeneric("fileClient", function(OpencgaR, folder, annotationSet, file, files, members, endpointName, params=NULL, ...) +setGeneric("fileClient", function(OpencgaR, annotationSet, files, folder, file, members, endpointName, params=NULL, ...) standardGeneric("fileClient")) # ############################################################################## ## JobClient -setGeneric("jobClient", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) +setGeneric("jobClient", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) standardGeneric("jobClient")) # ############################################################################## ## SampleClient -setGeneric("sampleClient", function(OpencgaR, samples, annotationSet, members, sample, endpointName, params=NULL, ...) +setGeneric("sampleClient", function(OpencgaR, members, sample, annotationSet, samples, endpointName, params=NULL, ...) standardGeneric("sampleClient")) # ############################################################################## ## IndividualClient -setGeneric("individualClient", function(OpencgaR, individuals, members, annotationSet, individual, endpointName, params=NULL, ...) +setGeneric("individualClient", function(OpencgaR, members, individual, annotationSet, individuals, endpointName, params=NULL, ...) standardGeneric("individualClient")) # ############################################################################## ## FamilyClient -setGeneric("familyClient", function(OpencgaR, families, family, members, annotationSet, endpointName, params=NULL, ...) +setGeneric("familyClient", function(OpencgaR, members, annotationSet, family, families, endpointName, params=NULL, ...) standardGeneric("familyClient")) # ############################################################################## ## CohortClient -setGeneric("cohortClient", function(OpencgaR, cohort, members, annotationSet, cohorts, endpointName, params=NULL, ...) +setGeneric("cohortClient", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) standardGeneric("cohortClient")) # ############################################################################## ## PanelClient -setGeneric("panelClient", function(OpencgaR, panels, members, endpointName, params=NULL, ...) +setGeneric("panelClient", function(OpencgaR, members, panels, endpointName, params=NULL, ...) standardGeneric("panelClient")) # ############################################################################## @@ -60,7 +60,7 @@ setGeneric("variantClient", function(OpencgaR, endpointName, params=NULL, ...) # ############################################################################## ## ClinicalClient -setGeneric("clinicalClient", function(OpencgaR, interpretation, clinicalAnalysis, interpretations, annotationSet, clinicalAnalyses, members, endpointName, params=NULL, ...) +setGeneric("clinicalClient", function(OpencgaR, clinicalAnalyses, interpretation, annotationSet, interpretations, members, clinicalAnalysis, endpointName, params=NULL, ...) standardGeneric("clinicalClient")) # ############################################################################## diff --git a/opencga-client/src/main/R/R/Clinical-methods.R b/opencga-client/src/main/R/R/Clinical-methods.R index ecd04d6d74d..cefe09aaac0 100644 --- a/opencga-client/src/main/R/R/Clinical-methods.R +++ b/opencga-client/src/main/R/R/Clinical-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -61,7 +61,7 @@ #' [*]: Required parameter #' @export -setMethod("clinicalClient", "OpencgaR", function(OpencgaR, interpretation, clinicalAnalysis, interpretations, annotationSet, clinicalAnalyses, members, endpointName, params=NULL, ...) { +setMethod("clinicalClient", "OpencgaR", function(OpencgaR, clinicalAnalyses, interpretation, annotationSet, interpretations, members, clinicalAnalysis, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/analysis/clinical/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Cohort-methods.R b/opencga-client/src/main/R/R/Cohort-methods.R index b4cbb071860..b2083be84d3 100644 --- a/opencga-client/src/main/R/R/Cohort-methods.R +++ b/opencga-client/src/main/R/R/Cohort-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("cohortClient", "OpencgaR", function(OpencgaR, cohort, members, annotationSet, cohorts, endpointName, params=NULL, ...) { +setMethod("cohortClient", "OpencgaR", function(OpencgaR, members, annotationSet, cohort, cohorts, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/cohorts/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Family-methods.R b/opencga-client/src/main/R/R/Family-methods.R index 9f965314e0f..78128f35c38 100644 --- a/opencga-client/src/main/R/R/Family-methods.R +++ b/opencga-client/src/main/R/R/Family-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("familyClient", "OpencgaR", function(OpencgaR, families, family, members, annotationSet, endpointName, params=NULL, ...) { +setMethod("familyClient", "OpencgaR", function(OpencgaR, members, annotationSet, family, families, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/families/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/File-methods.R b/opencga-client/src/main/R/R/File-methods.R index fd0ad7f691c..adb97b96505 100644 --- a/opencga-client/src/main/R/R/File-methods.R +++ b/opencga-client/src/main/R/R/File-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -54,7 +54,7 @@ #' [*]: Required parameter #' @export -setMethod("fileClient", "OpencgaR", function(OpencgaR, folder, annotationSet, file, files, members, endpointName, params=NULL, ...) { +setMethod("fileClient", "OpencgaR", function(OpencgaR, annotationSet, files, folder, file, members, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/files/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/GA4GH-methods.R b/opencga-client/src/main/R/R/GA4GH-methods.R index d9d2c5689e4..77ad34ad5a3 100644 --- a/opencga-client/src/main/R/R/GA4GH-methods.R +++ b/opencga-client/src/main/R/R/GA4GH-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Individual-methods.R b/opencga-client/src/main/R/R/Individual-methods.R index 72d5e0839dc..cb0e74109de 100644 --- a/opencga-client/src/main/R/R/Individual-methods.R +++ b/opencga-client/src/main/R/R/Individual-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("individualClient", "OpencgaR", function(OpencgaR, individuals, members, annotationSet, individual, endpointName, params=NULL, ...) { +setMethod("individualClient", "OpencgaR", function(OpencgaR, members, individual, annotationSet, individuals, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/individuals/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Job-methods.R b/opencga-client/src/main/R/R/Job-methods.R index edfb52fbaff..1c664f80e8d 100644 --- a/opencga-client/src/main/R/R/Job-methods.R +++ b/opencga-client/src/main/R/R/Job-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -40,7 +40,7 @@ #' [*]: Required parameter #' @export -setMethod("jobClient", "OpencgaR", function(OpencgaR, job, members, jobs, endpointName, params=NULL, ...) { +setMethod("jobClient", "OpencgaR", function(OpencgaR, members, jobs, job, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/jobs/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Meta-methods.R b/opencga-client/src/main/R/R/Meta-methods.R index 730500d7b4a..4d913eb7009 100644 --- a/opencga-client/src/main/R/R/Meta-methods.R +++ b/opencga-client/src/main/R/R/Meta-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Operation-methods.R b/opencga-client/src/main/R/R/Operation-methods.R index 11e89656de2..8c4cf77b9c0 100644 --- a/opencga-client/src/main/R/R/Operation-methods.R +++ b/opencga-client/src/main/R/R/Operation-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/R/R/Panel-methods.R b/opencga-client/src/main/R/R/Panel-methods.R index 3d1c5bfb8d3..ff584f8fb1e 100644 --- a/opencga-client/src/main/R/R/Panel-methods.R +++ b/opencga-client/src/main/R/R/Panel-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -36,7 +36,7 @@ #' [*]: Required parameter #' @export -setMethod("panelClient", "OpencgaR", function(OpencgaR, panels, members, endpointName, params=NULL, ...) { +setMethod("panelClient", "OpencgaR", function(OpencgaR, members, panels, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/panels/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Project-methods.R b/opencga-client/src/main/R/R/Project-methods.R index ebbcb80dd92..564515f7f66 100644 --- a/opencga-client/src/main/R/R/Project-methods.R +++ b/opencga-client/src/main/R/R/Project-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -34,7 +34,7 @@ #' [*]: Required parameter #' @export -setMethod("projectClient", "OpencgaR", function(OpencgaR, project, projects, endpointName, params=NULL, ...) { +setMethod("projectClient", "OpencgaR", function(OpencgaR, projects, project, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/projects/create: diff --git a/opencga-client/src/main/R/R/Sample-methods.R b/opencga-client/src/main/R/R/Sample-methods.R index c5f0bbd3357..03b6788fbb6 100644 --- a/opencga-client/src/main/R/R/Sample-methods.R +++ b/opencga-client/src/main/R/R/Sample-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -39,7 +39,7 @@ #' [*]: Required parameter #' @export -setMethod("sampleClient", "OpencgaR", function(OpencgaR, samples, annotationSet, members, sample, endpointName, params=NULL, ...) { +setMethod("sampleClient", "OpencgaR", function(OpencgaR, members, sample, annotationSet, samples, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/samples/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/Study-methods.R b/opencga-client/src/main/R/R/Study-methods.R index c86c0da79b1..87fb4b00209 100644 --- a/opencga-client/src/main/R/R/Study-methods.R +++ b/opencga-client/src/main/R/R/Study-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -46,7 +46,7 @@ #' [*]: Required parameter #' @export -setMethod("studyClient", "OpencgaR", function(OpencgaR, group, variableSet, studies, templateId, study, members, endpointName, params=NULL, ...) { +setMethod("studyClient", "OpencgaR", function(OpencgaR, templateId, variableSet, studies, members, study, group, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/studies/acl/{members}/update: diff --git a/opencga-client/src/main/R/R/User-methods.R b/opencga-client/src/main/R/R/User-methods.R index fb403c674e6..a88d0a01cdc 100644 --- a/opencga-client/src/main/R/R/User-methods.R +++ b/opencga-client/src/main/R/R/User-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. @@ -38,7 +38,7 @@ #' [*]: Required parameter #' @export -setMethod("userClient", "OpencgaR", function(OpencgaR, user, users, filterId, endpointName, params=NULL, ...) { +setMethod("userClient", "OpencgaR", function(OpencgaR, user, filterId, users, endpointName, params=NULL, ...) { switch(endpointName, #' @section Endpoint /{apiVersion}/users/login: diff --git a/opencga-client/src/main/R/R/Variant-methods.R b/opencga-client/src/main/R/R/Variant-methods.R index d114e5d4882..bf160b91166 100644 --- a/opencga-client/src/main/R/R/Variant-methods.R +++ b/opencga-client/src/main/R/R/Variant-methods.R @@ -2,7 +2,7 @@ # WARNING: AUTOGENERATED CODE # # This code was generated by a tool. -# Autogenerated on: 2024-02-14 +# Autogenerated on: 2024-02-19 # # Manual changes to this file may cause unexpected behavior in your application. # Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java index d4fcd4b1d60..744d3f7e9e9 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AdminClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java index c6c8c84fd8b..e54fa6c1382 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/AlignmentClient.java @@ -40,7 +40,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -77,7 +77,7 @@ public RestResponse runBwa(BwaWrapperParams data, ObjectMap params) throws } /** - * Compute coverage for a list of alignment files. + * Compute the coverage from a given BAM alignment file, e.g., create a .bw file from a .bam file. * @param data Coverage computation parameters. * @param params Map containing any of the following optional parameters. * study: study. @@ -214,7 +214,7 @@ public RestResponse runFastqc(FastqcWrapperParams data, ObjectMap params) t } /** - * Index alignment file. + * Index a given alignment file BAM/CRAM, e.g., create a .bai file from a .bam file. * @param data Alignment index params. * @param params Map containing any of the following optional parameters. * study: study. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java index e4858049e0b..d1880093243 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ClinicalAnalysisClient.java @@ -54,7 +54,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java index f136be11310..5353610096a 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/CohortClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java index 497e02f5445..e53672f2de6 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/DiseasePanelClient.java @@ -35,7 +35,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java index 437d6e65255..488f65ca967 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FamilyClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java index 66ae008ab7c..3302dc2b444 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/FileClient.java @@ -43,7 +43,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java index 5d007b409bd..b60696ce807 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/GA4GHClient.java @@ -27,7 +27,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java index 67bb7feb715..3e90a072c20 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/IndividualClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java index c4fb407be93..24f479f78a1 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/JobClient.java @@ -37,7 +37,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java index 4f1873c571c..1fa28045d78 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/MetaClient.java @@ -28,7 +28,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java index 19b3144a06d..8bc22703b5a 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/ProjectClient.java @@ -32,7 +32,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java index f1e5b7ac798..4ce697cc525 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/SampleClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java index 4a9b4550de8..31c1656eb3c 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/StudyClient.java @@ -45,7 +45,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java index bbf582a2cc6..bcb01480219 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/UserClient.java @@ -36,7 +36,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java index c7f91a4730a..7bac1c031ac 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantClient.java @@ -62,7 +62,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java index 92f5dd6772d..607280de631 100644 --- a/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java +++ b/opencga-client/src/main/java/org/opencb/opencga/client/rest/clients/VariantOperationClient.java @@ -50,7 +50,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. -* Autogenerated on: 2024-02-14 +* Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Admin.js b/opencga-client/src/main/javascript/Admin.js index 30fe2d2b09b..75a59ef7fc5 100644 --- a/opencga-client/src/main/javascript/Admin.js +++ b/opencga-client/src/main/javascript/Admin.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Alignment.js b/opencga-client/src/main/javascript/Alignment.js index 764a51d164d..d21eda0ba06 100644 --- a/opencga-client/src/main/javascript/Alignment.js +++ b/opencga-client/src/main/javascript/Alignment.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. @@ -47,7 +47,7 @@ export default class Alignment extends OpenCGAParentClass { return this._post("analysis", null, "alignment/bwa", null, "run", data, params); } - /** Compute coverage for a list of alignment files + /** Compute the coverage from a given BAM alignment file, e.g., create a .bw file from a .bam file * @param {Object} data - Coverage computation parameters. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - study. @@ -157,7 +157,7 @@ export default class Alignment extends OpenCGAParentClass { return this._post("analysis", null, "alignment/fastqc", null, "run", data, params); } - /** Index alignment file + /** Index a given alignment file BAM/CRAM, e.g., create a .bai file from a .bam file * @param {Object} data - Alignment index params. * @param {Object} [params] - The Object containing the following optional parameters: * @param {String} [params.study] - study. diff --git a/opencga-client/src/main/javascript/ClinicalAnalysis.js b/opencga-client/src/main/javascript/ClinicalAnalysis.js index 1556652d3d3..df74e1b9ab5 100644 --- a/opencga-client/src/main/javascript/ClinicalAnalysis.js +++ b/opencga-client/src/main/javascript/ClinicalAnalysis.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Cohort.js b/opencga-client/src/main/javascript/Cohort.js index 97ef19dcbdf..d94234c929a 100644 --- a/opencga-client/src/main/javascript/Cohort.js +++ b/opencga-client/src/main/javascript/Cohort.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/DiseasePanel.js b/opencga-client/src/main/javascript/DiseasePanel.js index 52601203a30..d4aedcc7593 100644 --- a/opencga-client/src/main/javascript/DiseasePanel.js +++ b/opencga-client/src/main/javascript/DiseasePanel.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Family.js b/opencga-client/src/main/javascript/Family.js index 608c23c087d..b22fff636d3 100644 --- a/opencga-client/src/main/javascript/Family.js +++ b/opencga-client/src/main/javascript/Family.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/File.js b/opencga-client/src/main/javascript/File.js index f09d5c4562f..c9c141c6643 100644 --- a/opencga-client/src/main/javascript/File.js +++ b/opencga-client/src/main/javascript/File.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/GA4GH.js b/opencga-client/src/main/javascript/GA4GH.js index b656c0bd696..08b158d10cc 100644 --- a/opencga-client/src/main/javascript/GA4GH.js +++ b/opencga-client/src/main/javascript/GA4GH.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Individual.js b/opencga-client/src/main/javascript/Individual.js index d8bd896ae88..cf05cba4f63 100644 --- a/opencga-client/src/main/javascript/Individual.js +++ b/opencga-client/src/main/javascript/Individual.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Job.js b/opencga-client/src/main/javascript/Job.js index 9489c82bc7a..c880b14248b 100644 --- a/opencga-client/src/main/javascript/Job.js +++ b/opencga-client/src/main/javascript/Job.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Meta.js b/opencga-client/src/main/javascript/Meta.js index b5636ff6a5e..81da6d19dc9 100644 --- a/opencga-client/src/main/javascript/Meta.js +++ b/opencga-client/src/main/javascript/Meta.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Project.js b/opencga-client/src/main/javascript/Project.js index bde7382c84d..f74ca2c10c0 100644 --- a/opencga-client/src/main/javascript/Project.js +++ b/opencga-client/src/main/javascript/Project.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Sample.js b/opencga-client/src/main/javascript/Sample.js index 990f3b3b04e..cf7c00bb3a6 100644 --- a/opencga-client/src/main/javascript/Sample.js +++ b/opencga-client/src/main/javascript/Sample.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Study.js b/opencga-client/src/main/javascript/Study.js index 7d443653ad9..78447e0b2f7 100644 --- a/opencga-client/src/main/javascript/Study.js +++ b/opencga-client/src/main/javascript/Study.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/User.js b/opencga-client/src/main/javascript/User.js index 2093a3aadb4..9ae25a5c05b 100644 --- a/opencga-client/src/main/javascript/User.js +++ b/opencga-client/src/main/javascript/User.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/Variant.js b/opencga-client/src/main/javascript/Variant.js index c98bccd6bf5..25ed20c87b9 100644 --- a/opencga-client/src/main/javascript/Variant.js +++ b/opencga-client/src/main/javascript/Variant.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/javascript/VariantOperation.js b/opencga-client/src/main/javascript/VariantOperation.js index ad54d4104cf..1e228bf7db0 100644 --- a/opencga-client/src/main/javascript/VariantOperation.js +++ b/opencga-client/src/main/javascript/VariantOperation.js @@ -12,7 +12,7 @@ * WARNING: AUTOGENERATED CODE * * This code was generated by a tool. - * Autogenerated on: 2024-02-14 + * Autogenerated on: 2024-02-19 * * Manual changes to this file may cause unexpected behavior in your application. * Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py index 4a60e9c7e2f..a0cfae24658 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/admin_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py index 98b40a3f711..ea10373b0b6 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/alignment_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. @@ -41,7 +41,8 @@ def run_bwa(self, data=None, **options): def run_coverage_index(self, data=None, **options): """ - Compute coverage for a list of alignment files. + Compute the coverage from a given BAM alignment file, e.g., create a + .bw file from a .bam file. PATH: /{apiVersion}/analysis/alignment/coverage/index/run :param dict data: Coverage computation parameters. (REQUIRED) @@ -189,7 +190,8 @@ def run_fastqc(self, data=None, **options): def run_index(self, data=None, **options): """ - Index alignment file. + Index a given alignment file BAM/CRAM, e.g., create a .bai file from a + .bam file. PATH: /{apiVersion}/analysis/alignment/index/run :param dict data: Alignment index params. (REQUIRED) diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py index 1e4a73902cc..4fd0ca988e7 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/clinical_analysis_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py index 50af2a865a2..a0a55bbb6fb 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/cohort_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py index e234b2ff148..074a68209e4 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/disease_panel_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py index 4fd32087258..17415f3700a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/family_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py index 22e58ba63be..c75893ad88b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/file_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py index b15c6e8bd76..af0f87f3b18 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/ga4gh_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py index 3b393328993..d0eacbe900b 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/individual_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py index 1d5369c4639..2d24508ccc7 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/job_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py index 1506926345b..f5109a6a05a 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/meta_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py index 338e65d466c..9e1fe1e15e6 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/project_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py index e83e98d3be2..c7a5b17d0b7 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/sample_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py index 17fda942ec7..1c39642a26d 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/study_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py index f991cf25dae..ba9777bbca9 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/user_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py index 57cd7a1a9cf..b5c6b37f774 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py index b48bb9d8ad4..d5072623fe7 100644 --- a/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py +++ b/opencga-client/src/main/python/pyopencga/rest_clients/variant_operation_client.py @@ -2,7 +2,7 @@ WARNING: AUTOGENERATED CODE This code was generated by a tool. - Autogenerated on: 2024-02-14 + Autogenerated on: 2024-02-19 Manual changes to this file may cause unexpected behavior in your application. Manual changes to this file will be overwritten if the code is regenerated. diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java index d5476e10f60..d534f86fb69 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/FieldConstants.java @@ -1,5 +1,7 @@ package org.opencb.opencga.core.api; +import com.fasterxml.jackson.annotation.JsonProperty; +import org.opencb.commons.annotations.DataField; import org.opencb.opencga.core.models.alignment.AlignmentQcParams; import org.opencb.opencga.core.models.variant.MutationalSignatureAnalysisParams; import org.opencb.opencga.core.models.variant.SampleQcAnalysisParams; @@ -485,7 +487,12 @@ public class FieldConstants { public static final String VARIANT_STATS_DESCRIPTION_DESCRIPTION = "Variant stats description."; public static final String VARIANT_STATS_QUERY_DESCRIPTION = "Variant stats query in JSON format."; - // Alignment QC analysis (asample-qc-run) + // Alignment index and coverage + public static final String ALIGNMENT_BAM_FILE_ID_DESCRIPTION = "Alignment file ID (in format BAM or CRAM)"; + public static final String ALIGNMENT_WINDOW_SIZE_DESCRIPTION = "Size of the bins, in bases, for the output of the BIGWIG file"; + public static final String ALIGNMENT_OVERWRITE_DESCRIPTION = "Overwrite file"; + + // Alignment QC analysis (alignment-qc-run) public static final String ALIGNMENT_QC_BAM_FILE_DESCRIPTION = "ID for the BAM file to process."; public static final String ALIGNMENT_QC_SKIP_DESCRIPTION = "To skip any alignment QC metrics use the following keywords (separated by" + " commas): " + AlignmentQcParams.STATS_SKIP_VALUE + ", " + AlignmentQcParams.FLAGSTATS_SKIP_VALUE + ", " diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java index ebcfa07153c..db500c868c9 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/api/ParamConstants.java @@ -580,9 +580,7 @@ public class ParamConstants { public static final String INDEX_AUXILIAR_COLLECTION_DESCRIPTION = "Index auxiliar collection to improve performance assuming RGA is " + "completely indexed."; public static final String INDEX_AUXILIAR_COLLECTION = "auxiliarIndex"; - public static final String ALIGNMENT_INDEX_DESCRIPTION = "Index alignment file"; public static final String ALIGNMENT_QUERY_DESCRIPTION = "Search over indexed alignments"; - public static final String ALIGNMENT_COVERAGE_DESCRIPTION = "Compute coverage for a given alignemnt file"; public static final String ALIGNMENT_COVERAGE_QUERY_DESCRIPTION = "Query the coverage of an alignment file for regions or genes"; public static final String ALIGNMENT_COVERAGE_RATIO_DESCRIPTION = "Compute coverage ratio from file #1 vs file #2, (e.g. somatic vs " + "germline)"; diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/AlignmentIndexParams.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/AlignmentIndexParams.java index b4e4dc87607..c0b96832957 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/AlignmentIndexParams.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/AlignmentIndexParams.java @@ -1,36 +1,41 @@ package org.opencb.opencga.core.models.alignment; +import org.opencb.commons.annotations.DataField; +import org.opencb.opencga.core.api.FieldConstants; import org.opencb.opencga.core.tools.ToolParams; public class AlignmentIndexParams extends ToolParams { public static final String DESCRIPTION = "Alignment index params"; - private String file; + @DataField(id = "fileId", description = FieldConstants.ALIGNMENT_BAM_FILE_ID_DESCRIPTION) + private String fileId; + + @DataField(id = "overwrite", description = FieldConstants.ALIGNMENT_OVERWRITE_DESCRIPTION) private boolean overwrite; public AlignmentIndexParams() { } - public AlignmentIndexParams(String file, boolean overwrite) { - this.file = file; + public AlignmentIndexParams(String fileId, boolean overwrite) { + this.fileId = fileId; this.overwrite = overwrite; } @Override public String toString() { final StringBuilder sb = new StringBuilder("AlignmentIndexParams{"); - sb.append("file='").append(file).append('\''); + sb.append("fileId='").append(fileId).append('\''); sb.append(", overwrite=").append(overwrite); sb.append('}'); return sb.toString(); } - public String getFile() { - return file; + public String getFileId() { + return fileId; } - public AlignmentIndexParams setFile(String file) { - this.file = file; + public AlignmentIndexParams setFileId(String fileId) { + this.fileId = fileId; return this; } diff --git a/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/CoverageIndexParams.java b/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/CoverageIndexParams.java index f655829625d..655e498db0a 100644 --- a/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/CoverageIndexParams.java +++ b/opencga-core/src/main/java/org/opencb/opencga/core/models/alignment/CoverageIndexParams.java @@ -2,60 +2,66 @@ import com.fasterxml.jackson.annotation.JsonProperty; +import org.opencb.commons.annotations.DataField; +import org.opencb.opencga.core.api.FieldConstants; import org.opencb.opencga.core.tools.ToolParams; public class CoverageIndexParams extends ToolParams { public static final String DESCRIPTION = "Coverage computation parameters"; - private String bamFileId; - private String baiFileId; + @DataField(id = "fileId", description = FieldConstants.ALIGNMENT_BAM_FILE_ID_DESCRIPTION) + private String fileId; - @JsonProperty(defaultValue = "1") + @JsonProperty(defaultValue = "50") + @DataField(id = "windowSize", defaultValue = "50", description = FieldConstants.ALIGNMENT_WINDOW_SIZE_DESCRIPTION) private int windowSize; + @DataField(id = "overwrite", description = FieldConstants.ALIGNMENT_OVERWRITE_DESCRIPTION) + private boolean overwrite; + public CoverageIndexParams() { } - public CoverageIndexParams(String bamFileId, String baiFileId, int windowSize) { - this.bamFileId = bamFileId; - this.baiFileId = baiFileId; + public CoverageIndexParams(String fileId, int windowSize, boolean overwrite) { + this.fileId = fileId; this.windowSize = windowSize; + this.overwrite = overwrite; } @Override public String toString() { final StringBuilder sb = new StringBuilder("CoverageIndexParams{"); - sb.append("bamFileId='").append(bamFileId).append('\''); - sb.append(", baiFileId='").append(baiFileId).append('\''); + sb.append("fileId='").append(fileId).append('\''); sb.append(", windowSize=").append(windowSize); + sb.append(", overwrite=").append(overwrite); sb.append('}'); return sb.toString(); } - public String getBamFileId() { - return bamFileId; + public String getFileId() { + return fileId; } - public CoverageIndexParams setBamFileId(String bamFileId) { - this.bamFileId = bamFileId; + public CoverageIndexParams setFileId(String fileId) { + this.fileId = fileId; return this; } - public String getBaiFileId() { - return baiFileId; + public int getWindowSize() { + return windowSize; } - public CoverageIndexParams setBaiFileId(String baiFileId) { - this.baiFileId = baiFileId; + public CoverageIndexParams setWindowSize(int windowSize) { + this.windowSize = windowSize; return this; } - public int getWindowSize() { - return windowSize; + public boolean isOverwrite() { + return overwrite; } - public CoverageIndexParams setWindowSize(int windowSize) { - this.windowSize = windowSize; + public CoverageIndexParams setOverwrite(boolean overwrite) { + this.overwrite = overwrite; return this; } } diff --git a/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/AlignmentWebService.java b/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/AlignmentWebService.java index 99fa4402fc9..fc2dfa52ea2 100644 --- a/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/AlignmentWebService.java +++ b/opencga-server/src/main/java/org/opencb/opencga/server/rest/analysis/AlignmentWebService.java @@ -76,7 +76,7 @@ public AlignmentWebService(String apiVersion, @Context UriInfo uriInfo, @Context @POST @Path("/index/run") - @ApiOperation(value = ALIGNMENT_INDEX_DESCRIPTION, response = Job.class) + @ApiOperation(value = AlignmentIndexOperation.DESCRIPTION, response = Job.class) public Response indexRun( @ApiParam(value = ParamConstants.STUDY_PARAM) @QueryParam(ParamConstants.STUDY_PARAM) String study, @ApiParam(value = ParamConstants.JOB_ID_CREATION_DESCRIPTION) @QueryParam(ParamConstants.JOB_ID) String jobName, @@ -170,7 +170,7 @@ public Response query(@ApiParam(value = FILE_ID_DESCRIPTION, required = true) @Q @POST @Path("/coverage/index/run") - @ApiOperation(value = "Compute coverage for a list of alignment files", response = Job.class) + @ApiOperation(value = AlignmentCoverageAnalysis.DESCRIPTION, response = Job.class) public Response coverageRun( @ApiParam(value = ParamConstants.STUDY_PARAM) @QueryParam(ParamConstants.STUDY_PARAM) String study, @ApiParam(value = ParamConstants.JOB_ID_CREATION_DESCRIPTION) @QueryParam(ParamConstants.JOB_ID) String jobName,