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Add step to re-process Seurat prototypes
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‎singlecell/resources/chunks/UpdateSeuratPrototype.R‎

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if (!file.exists('/homeDir/.netrc')) {
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print(list.files('/homeDir'))
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stop('Unable to find file: /homeDir/.netrc')
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}
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invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = '/homeDir/.netrc'))
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Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
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for (datasetId in names(seuratObjects)) {
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printName(datasetId)
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seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
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if (reapplyMetadata) {
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seuratObj <- Rdiscvr::QueryAndApplyCdnaMetadata(seuratObj)
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}
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if (runRira) {
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seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
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seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
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seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
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}
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if (applyTCR) {
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seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = allowMissingTcr)
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}
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if (runTNKClassification) {
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# ClassifyTNKByExpression will fail without this, so ignore allowMissingTcr
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if (!'HasCDR3Data' %in% names(seuratObj@meta.data)) {
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seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj)
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}
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seuratObj <- Rdiscvr::ClassifyTNKByExpression(seuratObj)
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}
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saveData(seuratObj, datasetId)
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# Cleanup
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rm(seuratObj)
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gc()
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}

‎singlecell/src/org/labkey/singlecell/SingleCellModule.java‎

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SequencePipelineService.get().registerPipelineStep(new RunCsCore.Provider());
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SequencePipelineService.get().registerPipelineStep(new CustomGSEA.Provider());
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SequencePipelineService.get().registerPipelineStep(new StudyMetadata.Provider());
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SequencePipelineService.get().registerPipelineStep(new UpdateSeuratPrototype.Provider());
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SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
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}

‎singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java‎

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package org.labkey.singlecell.pipeline.singlecell;
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import org.apache.commons.io.FileUtils;
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import org.json.JSONObject;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.sequenceanalysis.SequenceOutputFile;
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import org.labkey.api.sequenceanalysis.model.Readset;
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import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
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import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
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import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
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import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
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import org.labkey.api.singlecell.pipeline.SingleCellStep;
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import org.labkey.api.util.FileUtil;
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import org.labkey.api.writer.PrintWriters;
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import org.labkey.singlecell.analysis.AbstractSingleCellHandler;
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import java.io.File;
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import java.io.IOException;
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import java.io.PrintWriter;
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import java.nio.file.Files;
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import java.util.Arrays;
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import java.util.List;
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import static org.labkey.singlecell.analysis.AbstractSingleCellHandler.SEURAT_PROTOTYPE;
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public class UpdateSeuratPrototype extends AbstractRDiscvrStep
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{
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public UpdateSeuratPrototype(PipelineContext ctx, UpdateSeuratPrototype.Provider provider)
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{
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super(provider, ctx);
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}
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public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
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{
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public Provider()
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{
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super("UpdateSeuratPrototype", "Update Seurat Prototype", "CellMembrane/Rdiscvr", "This will re-process an existing seurat prototype object and overwrite the original", Arrays.asList(
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SeuratToolParameter.create("reapplyMetadata", "Reapply Metadata", "If checked, metadata will be re-applied", "checkbox", null, true),
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SeuratToolParameter.create("runRira", "Run RIRA", "If checked, RIRA classification will be re-run", "checkbox", null, true),
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SeuratToolParameter.create("runTNKClassification", "Run T/NK Classification", "If checked, T/NK expression-based classification will be re-run", "checkbox", null, true),
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SeuratToolParameter.create("applyTCR", "Append TCR Data", "If checked, TCR data will be applied. This will fail if", "checkbox", null, true),
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SeuratToolParameter.create("allowMissingTcr", "Allow Missing TCR Data", "Unless checked, an error will be thrown if any sample lacks TCR data", "checkbox", new JSONObject()
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{{
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put("checked", false);
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}}, false),
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SeuratToolParameter.create("keepOriginal", "Keep Copy of Original File", "If checked, the original file will be copied with the file extension '.bk'", "checkbox", new JSONObject()
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{{
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put("checked", false);
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}}, false)
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), null, null);
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}
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@Override
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public UpdateSeuratPrototype create(PipelineContext ctx)
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{
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return new UpdateSeuratPrototype(ctx, this);
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}
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}
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@Override
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public void init(SequenceOutputHandler.JobContext ctx, List<SequenceOutputFile> inputFiles) throws PipelineJobException
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{
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if (inputFiles.size() > 1)
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{
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throw new PipelineJobException("Seurat prototype step expects this job to have a single input. Consider selecting the option to run jobs individually instead of merged");
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}
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if (inputFiles.get(0).getReadset() == null)
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{
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throw new PipelineJobException("Seurat prototype step expects all inputs to have a readset ID.");
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}
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if (!SEURAT_PROTOTYPE.equals(inputFiles.get(0).getCategory()))
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{
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throw new PipelineJobException("Expected the input to be a seurat prototype, found: " + inputFiles.get(0).getCategory());
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}
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if (ctx.getSequenceSupport().getCachedGenomes().size() > 1)
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{
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throw new PipelineJobException("Expected seurat prototype step to use a single genome");
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}
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Readset rs = ctx.getSequenceSupport().getCachedReadset(inputFiles.get(0).getReadset());
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if (!ctx.getJob().getContainer().getId().equalsIgnoreCase(rs.getContainer()))
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{
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throw new PipelineJobException("Seurat prototype jobs must be submitted to the same folder as the source readset");
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}
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}
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@Override
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public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWrapper> inputObjects, String outputPrefix) throws PipelineJobException
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{
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Output output = super.execute(ctx, inputObjects, outputPrefix);
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if (ctx.getSequenceSupport().getCachedGenomes().size() > 1)
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{
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throw new PipelineJobException("Expected seurat prototype step to use a single genome");
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}
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if (output.getSeuratObjects().size() != 1)
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{
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throw new PipelineJobException("Expected a single output object, found: " + output.getSeuratObjects().size());
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}
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SeuratObjectWrapper inputRDS = inputObjects.get(0);
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SeuratObjectWrapper wrapper = output.getSeuratObjects().get(0);
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if (wrapper.getReadsetId() == null)
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{
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throw new PipelineJobException("Missing readset Id: " + wrapper.getDatasetId());
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}
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File toReplace = inputRDS.getSequenceOutputFile().getFile();
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if (!toReplace.exists())
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{
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throw new PipelineJobException("Missing file: " + toReplace);
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}
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try
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{
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ctx.getLogger().info("Replacing existing prototype: " + toReplace.getPath());
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if (ctx.getParams().optBoolean("keepOriginal", false))
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{
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File backup = new File(toReplace.getPath() + ".orig");
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if (backup.exists())
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{
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backup.delete();
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}
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FileUtils.moveFile(toReplace, backup);
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}
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if (toReplace.exists())
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{
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toReplace.delete();
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}
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FileUtils.moveFile(wrapper.getFile(), toReplace);
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}
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catch (IOException e)
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{
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throw new PipelineJobException(e);
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}
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return output;
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}
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}

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