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Write failed and successful annotations to additional files
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62 changes: 62 additions & 0 deletions
62
...eline/src/main/java/org/cbioportal/annotation/pipeline/DefaultFlatFileHeaderCallback.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| /* | ||
| * Copyright (c) 2016 Memorial Sloan-Kettering Cancer Center. | ||
| * | ||
| * This library is distributed in the hope that it will be useful, but WITHOUT | ||
| * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS | ||
| * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder | ||
| * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no | ||
| * obligations to provide maintenance, support, updates, enhancements or | ||
| * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be | ||
| * liable to any party for direct, indirect, special, incidental or | ||
| * consequential damages, including lost profits, arising out of the use of this | ||
| * software and its documentation, even if Memorial Sloan-Kettering Cancer | ||
| * Center has been advised of the possibility of such damage. | ||
| */ | ||
|
|
||
| /* | ||
| * This file is part of cBioPortal CMO-Pipelines. | ||
| * | ||
| * cBioPortal is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as | ||
| * published by the Free Software Foundation, either version 3 of the | ||
| * License. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Affero General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Affero General Public License | ||
| * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
|
|
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| package org.cbioportal.annotation.pipeline; | ||
|
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| import org.apache.commons.lang.StringUtils; | ||
| import org.springframework.batch.item.file.FlatFileHeaderCallback; | ||
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|
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| import java.io.IOException; | ||
| import java.io.Writer; | ||
| import java.util.List; | ||
|
|
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| /** | ||
| * @author Mete Ozguz | ||
| */ | ||
| public class DefaultFlatFileHeaderCallback implements FlatFileHeaderCallback { | ||
| private final List<String> header; | ||
| private final List<String> commentLines; | ||
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| public DefaultFlatFileHeaderCallback(List<String> header, List<String> commentLines) { | ||
| this.header = header; | ||
| this.commentLines = commentLines; | ||
| } | ||
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| @Override | ||
| public void writeHeader(Writer writer) throws IOException { | ||
| // first write out the comment lines, then write the actual header | ||
| for (String comment : commentLines) { | ||
| writer.write(comment + "\n"); | ||
| } | ||
| writer.write(StringUtils.join(header, "\t")); | ||
| } | ||
| } |
32 changes: 32 additions & 0 deletions
32
...Pipeline/src/main/java/org/cbioportal/annotation/pipeline/DefaultLineCallbackHandler.java
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103 changes: 103 additions & 0 deletions
103
...Pipeline/src/main/java/org/cbioportal/annotation/pipeline/FailedMutationRecordWriter.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,103 @@ | ||
| /* | ||
| * Copyright (c) 2016 Memorial Sloan-Kettering Cancer Center. | ||
| * | ||
| * This library is distributed in the hope that it will be useful, but WITHOUT | ||
| * ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS | ||
| * FOR A PARTICULAR PURPOSE. The software and documentation provided hereunder | ||
| * is on an "as is" basis, and Memorial Sloan-Kettering Cancer Center has no | ||
| * obligations to provide maintenance, support, updates, enhancements or | ||
| * modifications. In no event shall Memorial Sloan-Kettering Cancer Center be | ||
| * liable to any party for direct, indirect, special, incidental or | ||
| * consequential damages, including lost profits, arising out of the use of this | ||
| * software and its documentation, even if Memorial Sloan-Kettering Cancer | ||
| * Center has been advised of the possibility of such damage. | ||
| */ | ||
|
|
||
| /* | ||
| * This file is part of cBioPortal CMO-Pipelines. | ||
| * | ||
| * cBioPortal is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU Affero General Public License as | ||
| * published by the Free Software Foundation, either version 3 of the | ||
| * License. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Affero General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Affero General Public License | ||
| * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
|
|
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| package org.cbioportal.annotation.pipeline; | ||
|
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| import org.springframework.batch.item.ExecutionContext; | ||
| import org.springframework.batch.item.ItemStreamException; | ||
| import org.springframework.batch.item.ItemStreamWriter; | ||
| import org.springframework.batch.item.file.FlatFileItemWriter; | ||
| import org.springframework.batch.item.file.transform.PassThroughLineAggregator; | ||
| import org.springframework.beans.factory.annotation.Value; | ||
| import org.springframework.core.io.FileSystemResource; | ||
|
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| import java.nio.file.Path; | ||
| import java.nio.file.Paths; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
|
|
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| /** | ||
| * @author Mete Ozguz | ||
| */ | ||
| public class FailedMutationRecordWriter implements ItemStreamWriter<String> { | ||
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| @Value("#{jobParameters[failedOutputFilename]}") | ||
| private String failedOutputFilename; | ||
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| @Value("#{stepExecutionContext['commentLines']}") | ||
| private List<String> commentLines; | ||
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| @Value("#{stepExecutionContext['mutation_header']}") | ||
| private List<String> header; | ||
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| @Value("#{stepExecutionContext['failedRecordsCount']}") | ||
| private Integer failedRecordsCount; | ||
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| private FlatFileItemWriter<String> flatFileItemWriter = new FlatFileItemWriter<>(); | ||
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| // Set up the writer and print the json from CVR to a file | ||
| @Override | ||
| public void open(ExecutionContext ec) throws ItemStreamException { | ||
| if (failedOutputFilename != null && !failedOutputFilename.isEmpty() && failedRecordsCount > 0) { | ||
| Path stagingFile = Paths.get(failedOutputFilename); | ||
| PassThroughLineAggregator aggr = new PassThroughLineAggregator(); | ||
| flatFileItemWriter.setLineAggregator(aggr); | ||
| flatFileItemWriter.setResource(new FileSystemResource(stagingFile.toString())); | ||
| flatFileItemWriter.setHeaderCallback(new DefaultFlatFileHeaderCallback(header, commentLines)); | ||
| flatFileItemWriter.open(ec); | ||
| } | ||
| } | ||
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| @Override | ||
| public void update(ExecutionContext ec) throws ItemStreamException { | ||
| } | ||
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| @Override | ||
| public void close() throws ItemStreamException { | ||
| if (failedOutputFilename != null && !failedOutputFilename.isEmpty() && failedRecordsCount > 0) { | ||
| flatFileItemWriter.close(); | ||
| } | ||
| } | ||
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| @Override | ||
| public void write(List<? extends String> items) throws Exception { | ||
| if (failedOutputFilename != null && !failedOutputFilename.isEmpty() && failedRecordsCount > 0) { | ||
| List<String> failedItems = new ArrayList<>(); | ||
| for (String item : items) { | ||
| if (item.contains("\tFAILED")) { | ||
| failedItems.add(item); | ||
| } | ||
| } | ||
| flatFileItemWriter.write(failedItems); | ||
| } | ||
| } | ||
| } |
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