Add step to add study metadata to seurat objects

Author: bbimber

singlecell/resources/chunks/StudyMetadata.R

@@ -0,0 +1,28 @@
+if (!file.exists('/homeDir/.netrc')) {
+    print(list.files('/homeDir'))
+    stop('Unable to find file: /homeDir/.netrc')
+}
+
+invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = '/homeDir/.netrc'))
+Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
+
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    if (studyName == 'PC475') {
+        seuratObj <- Rdiscvr::ApplyPC475Metadata(seuratObj, errorIfUnknownIdsFound = errorIfUnknownIdsFound)
+    } else if (studyName == 'TB') {
+        seuratObj <- Rdiscvr::ApplyTBMetadata(seuratObj, errorIfUnknownIdsFound = errorIfUnknownIdsFound)
+    } else if (studyName == 'Malaria') {
+        seuratObj <- Rdiscvr::ApplyMalariaMetadata(seuratObj, errorIfUnknownIdsFound = errorIfUnknownIdsFound)
+    } else {
+        stop(paste0('Unknown study: ', studyName))
+    }
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -229,6 +229,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new RunEscape.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunCsCore.Provider());
         SequencePipelineService.get().registerPipelineStep(new CustomGSEA.Provider());
+        SequencePipelineService.get().registerPipelineStep(new StudyMetadata.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

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

@@ -0,0 +1,48 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.json.JSONObject;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.Arrays;
+import java.util.List;
+
+public class StudyMetadata extends AbstractRDiscvrStep
+{
+    public StudyMetadata(PipelineContext ctx, StudyMetadata.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("StudyMetadata", "Append Study Metadata", "RDiscvr", "This uses Rdiscvr to append study-specific metadata.", Arrays.asList(
+                    SeuratToolParameter.create("testsToUse", "Tests To Use", "The set of tests to perform.", "ldk-simplecombo", new JSONObject()
+                    {{
+                        put("multiSelect", false);
+                        put("allowBlank", false);
+                        put("storeValues", "PC475;TB;Malaria");
+                        put("delimiter", ";");
+                    }}, null, null, false, false),
+                    SeuratToolParameter.create("errorIfUnknownIdsFound", "Error If Unknown Ids Found", "If true, the job will fail if the seurat object contains ID not present in the metadata", "checkbox", null, true)
+            ), null, null);
+        }
+
+        @Override
+        public StudyMetadata create(PipelineContext ctx)
+        {
+            return new StudyMetadata(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "study";
+    }
+}
+