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Let users launch NextFlow from file browser (#470)
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98 changes: 87 additions & 11 deletions
98
nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,44 +1,120 @@ | ||
| package org.labkey.nextflow.pipeline; | ||
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|
||
| import lombok.Getter; | ||
| import org.apache.commons.lang3.StringUtils; | ||
| import org.jetbrains.annotations.NotNull; | ||
| import org.labkey.api.data.Container; | ||
| import org.labkey.api.files.FileContentService; | ||
| import org.labkey.api.pipeline.ParamParser; | ||
| import org.labkey.api.pipeline.PipeRoot; | ||
| import org.labkey.api.pipeline.PipelineJob; | ||
| import org.labkey.api.pipeline.PipelineJobService; | ||
| import org.labkey.api.pipeline.TaskId; | ||
| import org.labkey.api.pipeline.TaskPipeline; | ||
| import org.labkey.api.pipeline.file.AbstractFileAnalysisJob; | ||
| import org.labkey.api.util.FileUtil; | ||
| import org.labkey.api.util.URLHelper; | ||
| import org.labkey.api.util.PageFlowUtil; | ||
| import org.labkey.api.view.ViewBackgroundInfo; | ||
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|
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| import java.io.BufferedWriter; | ||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.io.InputStream; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.util.List; | ||
|
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| public class NextFlowPipelineJob extends PipelineJob | ||
| @Getter | ||
| public class NextFlowPipelineJob extends AbstractFileAnalysisJob | ||
| { | ||
| private Path config; | ||
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| @SuppressWarnings("unused") // For serialization | ||
| protected NextFlowPipelineJob() | ||
| {} | ||
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| public NextFlowPipelineJob(ViewBackgroundInfo info, @NotNull PipeRoot root) | ||
| public static NextFlowPipelineJob create(ViewBackgroundInfo info, @NotNull PipeRoot root, Path templateConfig, List<Path> inputFiles) throws IOException | ||
| { | ||
| super(null, info, root); | ||
| setLogFile(new File(String.valueOf(root.getLogDirectory()), FileUtil.makeFileNameWithTimestamp("NextFlowPipelineJob", "log")).toPath()); | ||
| Path parentDir = inputFiles.get(0).getParent(); | ||
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| String jobName = FileUtil.makeFileNameWithTimestamp("NextFlow"); | ||
| Path jobDir = parentDir.resolve(jobName); | ||
| Path log = jobDir.resolve(jobName + ".log"); | ||
| FileUtil.createDirectory(jobDir); | ||
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| Path config = createConfig(templateConfig, log.getParent(), jobDir, info.getContainer()); | ||
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| return new NextFlowPipelineJob(info, root, config, inputFiles, log); | ||
| } | ||
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| @Override | ||
| public URLHelper getStatusHref() | ||
| public NextFlowPipelineJob(ViewBackgroundInfo info, @NotNull PipeRoot root, Path config, List<Path> inputFiles, Path log) throws IOException | ||
| { | ||
| return null; | ||
| super(new NextFlowProtocol(), NextFlowPipelineProvider.NAME, info, root, config.getFileName().toString(), config, inputFiles, false, false); | ||
| this.config = config; | ||
| setLogFile(log); | ||
| } | ||
|
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||
| @Override | ||
| public ParamParser getInputParameters() | ||
| { | ||
| return PipelineJobService.get().createParamParser(); | ||
| } | ||
|
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| /** Take the template config file and substitute in the values for this job */ | ||
| private static Path createConfig(Path configTemplate, Path parentDir, Path jobDir, Container container) throws IOException | ||
| { | ||
| String template; | ||
| try (InputStream in = Files.newInputStream(configTemplate)) | ||
| { | ||
| template = PageFlowUtil.getStreamContentsAsString(in); | ||
| } | ||
|
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| String webdavUrl = FileContentService.get().getWebDavUrl(parentDir, container, FileContentService.PathType.full); | ||
| webdavUrl = StringUtils.stripEnd(webdavUrl, "/"); | ||
|
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| String substitutedContent = template.replace("${quant_spectra_dir}", "quant_spectra_dir = '" + webdavUrl + "'"); | ||
|
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| Path substitutedFile = jobDir.resolve(configTemplate.getFileName()); | ||
| try (BufferedWriter writer = Files.newBufferedWriter(substitutedFile)) | ||
| { | ||
| writer.write(substitutedContent); | ||
| } | ||
| return substitutedFile; | ||
| } | ||
|
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| @Override | ||
| public String getDescription() | ||
| { | ||
| return "NextFlow Job"; | ||
| return "NextFlow analysis using " + config.getFileName() + " of " + getInputFilePaths().size() + " files"; | ||
| } | ||
|
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| @Override | ||
| public TaskPipeline<?> getTaskPipeline() | ||
| { | ||
| return PipelineJobService.get().getTaskPipeline(new TaskId(NextFlowPipelineJob.class)); | ||
| return PipelineJobService.get().getTaskPipeline(getTaskPipelineId()); | ||
| } | ||
|
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| @Override | ||
| public TaskId getTaskPipelineId() | ||
| { | ||
| return new TaskId(NextFlowPipelineJob.class); | ||
| } | ||
|
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| @Override | ||
| public AbstractFileAnalysisJob createSingleFileJob(File file) | ||
| { | ||
| throw new UnsupportedOperationException(); | ||
| } | ||
|
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| @Override | ||
| public File findInputFile(String name) | ||
| { | ||
| throw new UnsupportedOperationException(); | ||
| } | ||
|
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| @Override | ||
| public File findOutputFile(String name) | ||
| { | ||
| return null; | ||
| } | ||
|
|
||
| } |
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