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Merge pull request #299 from LabKey/fb_merge_24.3_to_develop
Merge 24.3 to develop
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110 changes: 110 additions & 0 deletions
110
SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/DockerWrapper.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,110 @@ | ||
| package org.labkey.api.sequenceanalysis.run; | ||
|
|
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| import org.apache.commons.io.FileUtils; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.apache.logging.log4j.Logger; | ||
| import org.labkey.api.pipeline.PipelineJobException; | ||
| import org.labkey.api.sequenceanalysis.pipeline.PipelineOutputTracker; | ||
| import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; | ||
| import org.labkey.api.writer.PrintWriters; | ||
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|
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| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.io.PrintWriter; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
|
|
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| public class DockerWrapper extends AbstractCommandWrapper | ||
| { | ||
| private final String _containerName; | ||
| private File _tmpDir = null; | ||
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| public DockerWrapper(String containerName, Logger log) | ||
| { | ||
| super(log); | ||
| _containerName = containerName; | ||
| } | ||
|
|
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| public void setTmpDir(File tmpDir) | ||
| { | ||
| _tmpDir = tmpDir; | ||
| } | ||
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| public void executeWithDocker(List<String> containerArgs, File workDir, PipelineOutputTracker tracker) throws PipelineJobException | ||
| { | ||
| File localBashScript = new File(workDir, "docker.sh"); | ||
| File dockerBashScript = new File(workDir, "dockerRun.sh"); | ||
| tracker.addIntermediateFile(localBashScript); | ||
| tracker.addIntermediateFile(dockerBashScript); | ||
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| setWorkingDir(workDir); | ||
| try (PrintWriter writer = PrintWriters.getPrintWriter(localBashScript); PrintWriter dockerWriter = PrintWriters.getPrintWriter(dockerBashScript)) | ||
| { | ||
| writer.println("#!/bin/bash"); | ||
| writer.println("set -x"); | ||
| writer.println("WD=`pwd`"); | ||
| writer.println("HOME=`echo ~/`"); | ||
| writer.println("DOCKER='" + SequencePipelineService.get().getDockerCommand() + "'"); | ||
| writer.println("sudo $DOCKER pull " + _containerName); | ||
| writer.println("sudo $DOCKER run --rm=true \\"); | ||
| writer.println("\t-v \"${WD}:/work\" \\"); | ||
| writer.println("\t-v \"${HOME}:/homeDir\" \\"); | ||
| if (_tmpDir != null) | ||
| { | ||
| writer.println("\t-v \"" + _tmpDir.getPath() + ":/tmp\" \\"); | ||
| } | ||
| writer.println("\t--entrypoint /bin/bash \\"); | ||
| writer.println("\t-w /work \\"); | ||
| Integer maxRam = SequencePipelineService.get().getMaxRam(); | ||
| if (maxRam != null) | ||
| { | ||
| writer.println("\t-e SEQUENCEANALYSIS_MAX_RAM=" + maxRam + " \\"); | ||
| writer.println("\t--memory='" + maxRam + "g' \\"); | ||
| } | ||
| writer.println("\t" + _containerName + " \\"); | ||
| writer.println("\t/work/" + dockerBashScript.getName()); | ||
| writer.println("EXIT_CODE=$?"); | ||
| writer.println("echo 'Docker run exit code: '$EXIT_CODE"); | ||
| writer.println("exit $EXIT_CODE"); | ||
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| dockerWriter.println("#!/bin/bash"); | ||
| dockerWriter.println("set -x"); | ||
| dockerWriter.println(StringUtils.join(containerArgs, " ")); | ||
| dockerWriter.println("EXIT_CODE=$?"); | ||
| dockerWriter.println("echo 'Exit code: '$?"); | ||
| dockerWriter.println("exit $EXIT_CODE"); | ||
| } | ||
| catch (IOException e) | ||
| { | ||
| throw new PipelineJobException(e); | ||
| } | ||
|
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| execute(Arrays.asList("/bin/bash", localBashScript.getPath())); | ||
| } | ||
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| public File ensureLocalCopy(File input, File workingDirectory, PipelineOutputTracker output) throws PipelineJobException | ||
| { | ||
| try | ||
| { | ||
| if (workingDirectory.equals(input.getParentFile())) | ||
| { | ||
| return input; | ||
| } | ||
|
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| File local = new File(workingDirectory, input.getName()); | ||
| if (!local.exists()) | ||
| { | ||
| getLogger().debug("Copying file locally: " + input.getPath()); | ||
| FileUtils.copyFile(input, local); | ||
| } | ||
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| output.addIntermediateFile(local); | ||
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| return local; | ||
| } | ||
| catch (IOException e) | ||
| { | ||
| throw new PipelineJobException(e); | ||
| } | ||
| } | ||
| } |
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16 changes: 16 additions & 0 deletions
16
SequenceAnalysis/resources/queries/sequenceanalysis/chain_files/.qview.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| <customView xmlns="http://labkey.org/data/xml/queryCustomView"> | ||
| <columns> | ||
| <!--<column name="rowid" />--> | ||
| <column name="genomeId1" /> | ||
| <column name="genomeId2" /> | ||
| <column name="source" /> | ||
| <column name="version" /> | ||
| <column name="datedisabled" /> | ||
| <column name="chainFile" /> | ||
| </columns> | ||
| <sorts> | ||
| <sort column="genomeId1/name"/> | ||
| <sort column="genomeId2/name"/> | ||
| <sort column="version"/> | ||
| </sorts> | ||
| </customView> |
17 changes: 17 additions & 0 deletions
17
SequenceAnalysis/resources/queries/sequenceanalysis/chain_files/With Filepath.qview.xml
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|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| <customView xmlns="http://labkey.org/data/xml/queryCustomView"> | ||
| <columns> | ||
| <!--<column name="rowid" />--> | ||
| <column name="genomeId1" /> | ||
| <column name="genomeId2" /> | ||
| <column name="source" /> | ||
| <column name="version" /> | ||
| <column name="dateDisabled" /> | ||
| <column name="chainFile" /> | ||
| <column name="chainFile/DataFileUrl" /> | ||
| </columns> | ||
| <sorts> | ||
| <sort column="genomeId1/name"/> | ||
| <sort column="genomeId2/name"/> | ||
| <sort column="version"/> | ||
| </sorts> | ||
| </customView> |
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