Improve flexibility for running CellTypist

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/VariantProcessingRemoteMergeTask.java

@@ -191,7 +191,7 @@ private File runDefaultVariantMerge(TaskFileManagerImpl manager, RecordedAction
 
                 if (subsetVcfIdx.exists())
                 {
-                    getJob().getLogger().debug("Index exists, will not re-submit the VCF: " + subsetVcf.getName());
+                    getJob().getLogger().debug("Index exists, will not re-subset the VCF: " + subsetVcf.getName());
                 }
                 else
                 {

cluster/resources/web/cluster/window/Buttons.js

@@ -44,6 +44,16 @@ Cluster.Utils = new function() {
             }
 
             window.location = LABKEY.ActionURL.buildURL('cluster', 'forcePipelineCancel', null, {jobIds: checked.join(',')});
-        }
+        },
+
+        replaceJobStore: function (dataRegionName) {
+            const checked = LABKEY.DataRegions[dataRegionName].getChecked();
+            if (!checked.length){
+                Ext4.Msg.alert('Error', 'No rows selected');
+                return;
+            }
+
+            window.location = LABKEY.ActionURL.buildURL('cluster', 'replaceJobStore', null, {jobIds: checked.join(',')});
+        },
     };
 };

cluster/src/org/labkey/cluster/ClusterModule.java

@@ -41,6 +41,7 @@
 import org.labkey.cluster.pipeline.TestCase;
 import org.labkey.cluster.query.ForceCancelJobsButton;
 import org.labkey.cluster.query.RecoverCompletedJobsButton;
+import org.labkey.cluster.query.ReplaceJobStoreButton;
 import org.labkey.cluster.query.ViewClusterSubmissionsButton;
 import org.labkey.cluster.query.ViewJavaLogButton;
 
@@ -103,6 +104,7 @@ public void doStartupAfterSpringConfig(ModuleContext moduleContext)
         LDKService.get().registerQueryButton(new ViewClusterSubmissionsButton(), "pipeline", "job");
         LDKService.get().registerQueryButton(new RecoverCompletedJobsButton(), "pipeline", "job");
         LDKService.get().registerQueryButton(new ForceCancelJobsButton(), "pipeline", "job");
+        LDKService.get().registerQueryButton(new ReplaceJobStoreButton(), "pipeline", "job");
     }
 
     @Override

cluster/src/org/labkey/cluster/query/RecoverCompletedJobsButton.java

@@ -25,6 +25,6 @@ public RecoverCompletedJobsButton()
     @Override
     public boolean isAvailable(TableInfo ti)
     {
-        return super.isAvailable(ti) || ContainerManager.getRoot().equals(ti.getUserSchema().getContainer());
+        return ti.getUserSchema().getUser().isInSiteAdminGroup() && (super.isAvailable(ti) || ContainerManager.getRoot().equals(ti.getUserSchema().getContainer()));
     }
 }

cluster/src/org/labkey/cluster/query/ReplaceJobStoreButton.java

@@ -0,0 +1,30 @@
+package org.labkey.cluster.query;
+
+import org.labkey.api.data.ContainerManager;
+import org.labkey.api.data.TableInfo;
+import org.labkey.api.ldk.table.SimpleButtonConfigFactory;
+import org.labkey.api.module.ModuleLoader;
+import org.labkey.api.security.permissions.AdminPermission;
+import org.labkey.api.view.template.ClientDependency;
+import org.labkey.cluster.ClusterModule;
+
+import java.util.Arrays;
+
+public class ReplaceJobStoreButton extends SimpleButtonConfigFactory
+{
+    public ReplaceJobStoreButton()
+    {
+        super(ModuleLoader.getInstance().getModule(ClusterModule.class), "Replace JobStore from JSON", "Cluster.Utils.replaceJobStore(dataRegionName);", Arrays.asList(
+                ClientDependency.supplierFromPath("Ext4"),
+                ClientDependency.supplierFromPath("cluster/window/Buttons.js")
+        ));
+
+        setPermission(AdminPermission.class);
+    }
+
+    @Override
+    public boolean isAvailable(TableInfo ti)
+    {
+        return ti.getUserSchema().getUser().isInSiteAdminGroup() && (super.isAvailable(ti) || ContainerManager.getRoot().equals(ti.getUserSchema().getContainer()));
+    }
+}

singlecell/resources/chunks/RunCelltypist.R

@@ -2,7 +2,9 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- RIRA::RunCellTypist(seuratObj, convertAmbiguousToNA = convertAmbiguousToNA, columnPrefix = columnPrefix, pThreshold = pThreshold, minProp = minProp)
+    for (mn in modelNames) {
+        seuratObj <- RIRA::RunCellTypist(seuratObj, modelName = paste0(mn, '.pkl'), convertAmbiguousToNA = convertAmbiguousToNA, columnPrefix = paste0('celltypist.', mn, '.'), pThreshold = pThreshold, minProp = minProp, maxAllowableClasses = maxAllowableClasses)
+    }
 
     saveData(seuratObj, datasetId)
 }

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

@@ -20,14 +20,19 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         public Provider()
         {
             super("RunCelltypist", "Run Celltypist (Built-In Model)", "Celltypist", "This will run Celltypist with the Immune_All_Low.pkl model.", Arrays.asList(
+                    SeuratToolParameter.create( "modelNames", "Model(s)", "The build-in model(s) to use.", "ldk-simplecombo", new JSONObject(){{
+                        put("storeValues", "Immune_All_Low;Immune_All_High;Human_Lung_Atlas;Healthy_COVID19_PBMC");
+                        put("allowBlank", false);
+                        put("multiSelect", true);
+                    }}, "Immune_All_Low.pkl", null, true, true).delimiter(";"),
                     SeuratToolParameter.create("convertAmbiguousToNA", "Convert Ambiguous To NA", "If true, any values for majority_voting with commas (indicating they are ambiguous) will be converted to NA", "checkbox", new JSONObject()
                     {{
                         put("checked", false);
                     }}, false),
-                    SeuratToolParameter.create("columnPrefix", "Column Prefix", "If provided, this string will be added to the beginning of all output column names.", "textfield", new JSONObject()
+                    SeuratToolParameter.create("maxAllowableClasses", "Max Allowable Classes", "Celltypist can assign a cell to many classes, creating extremely long labels. Any cell with more than this number of labels will be set to NA", "ldk-integerfield", new JSONObject()
                     {{
-
-                    }}, null),
+                        put("minValue", 0);
+                    }}, 5),
                     SeuratToolParameter.create("pThreshold", "pThreshold", "This is passed to the --p-thres argument.", "ldk-numberfield", new JSONObject()
                     {{
                         put("minValue", 0);