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63 changes: 63 additions & 0 deletions
63
...-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentAnalysisUtils.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| /* | ||
| * Copyright 2015-2020 OpenCB | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
|
|
||
| package org.opencb.opencga.analysis.alignment; | ||
|
|
||
| import org.opencb.opencga.catalog.exceptions.CatalogException; | ||
| import org.opencb.opencga.catalog.managers.CatalogManager; | ||
| import org.opencb.opencga.core.exceptions.ToolException; | ||
| import org.opencb.opencga.core.models.file.*; | ||
| import org.opencb.opencga.core.response.OpenCGAResult; | ||
|
|
||
| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
| import java.util.Collections; | ||
|
|
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| public class AlignmentAnalysisUtils { | ||
|
|
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| 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()) | ||
| .setPath(Paths.get(jobId).resolve(outPath.getFileName()).toString()); | ||
| OpenCGAResult<File> 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 + "'"); | ||
| } | ||
| File outCatalogFile = fileResult.first(); | ||
|
|
||
| // Updating file: samples, related file | ||
| FileUpdateParams updateParams = new FileUpdateParams() | ||
| .setSampleIds(bamCatalogFile.getSampleIds()) | ||
| .setRelatedFiles(Collections.singletonList(new SmallRelatedFileParams() | ||
| .setFile(bamCatalogFile.getId()) | ||
| .setRelation(FileRelatedFile.Relation.ALIGNMENT))); | ||
| try { | ||
| OpenCGAResult<File> updateResult = catalogManager.getFileManager().update(study, outCatalogFile.getId(), updateParams, null, | ||
| token); | ||
| if (updateResult.getNumUpdated() != 1) { | ||
| catalogManager.getFileManager().unlink(study, outCatalogFile.getId(), token); | ||
| throw new ToolException("It could not update OpenCGA file catalog (" + outCatalogFile.getId() | ||
| + ") from alignment file ID '" + bamCatalogFile.getId() + "'"); | ||
| } | ||
| } catch (CatalogException e) { | ||
| catalogManager.getFileManager().unlink(study, outCatalogFile.getId(), token); | ||
| throw e; | ||
| } | ||
| return outCatalogFile; | ||
| } | ||
| } |
26 changes: 26 additions & 0 deletions
26
opencga-analysis/src/main/java/org/opencb/opencga/analysis/alignment/AlignmentConstants.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| /* | ||
| * Copyright 2015-2020 OpenCB | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0 | ||
| * | ||
| * Unless required by applicable law or agreed to in writing, software | ||
| * distributed under the License is distributed on an "AS IS" BASIS, | ||
| * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | ||
| * See the License for the specific language governing permissions and | ||
| * limitations under the License. | ||
| */ | ||
|
|
||
| package org.opencb.opencga.analysis.alignment; | ||
|
|
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| public class AlignmentConstants { | ||
|
|
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| public static final String BAM_EXTENSION = ".bam"; | ||
| public static final String BAI_EXTENSION = ".bai"; | ||
| public static final String CRAM_EXTENSION = ".cram"; | ||
| public static final String CRAI_EXTENSION = ".crai"; | ||
| public static final String BIGWIG_EXTENSION = ".bw"; | ||
| } |
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