Write bash script with orphan file pipeline job

Author: bbimber

SequenceAnalysis/resources/queries/pipeline/Job/Sequence Jobs Without Data.qview.xml

@@ -1,14 +1,11 @@
 <customView xmlns="http://labkey.org/data/xml/queryCustomView" containerFilter="CurrentAndSubfolders">
     <columns>
+        <column name="RowId" />
         <column name="Status" />
         <column name="Description" />
-        <column name="ActiveHostName"/>
         <column name="Created" />
         <column name="Provider"/>
-        <column name="totalReadsets"/>
-        <column name="totalAnalyses"/>
-        <column name="totalOutputs"/>
-        <column name="sequenceJobWithoutData"/>
+        <column name="Folder/Path"/>
     </columns>
     <filters>
         <filter column="sequenceJobWithoutData" operator="eq" value="true"/>

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

@@ -18,6 +18,7 @@
 import org.labkey.api.pipeline.AbstractTaskFactorySettings;
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.PipelineJob;
+import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.PipelineJobService;
 import org.labkey.api.pipeline.PipelineService;
 import org.labkey.api.pipeline.PipelineStatusFile;
@@ -33,11 +34,14 @@
 import org.labkey.api.util.PageFlowUtil;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.view.ViewBackgroundInfo;
+import org.labkey.api.writer.PrintWriters;
 import org.labkey.sequenceanalysis.SequenceAnalysisSchema;
 import org.labkey.sequenceanalysis.util.SequenceUtil;
 
 import java.io.File;
 import java.io.FileFilter;
+import java.io.IOException;
+import java.io.PrintWriter;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.sql.ResultSet;
@@ -131,7 +135,7 @@ public boolean isJobComplete(PipelineJob job)
         }
 
         @Override
-        public RecordedActionSet run()
+        public RecordedActionSet run() throws PipelineJobException
         {
             getJob().getLogger().info("## The following sections list any files or pipeline jobs that appear to be orphans, not connected to any imported readsets or sequence outputs:");
 
@@ -205,8 +209,25 @@ public RecordedActionSet run()
             if (!probableDeletes.isEmpty())
             {
                 StringBuilder sb = new StringBuilder();
+                File output = new File(getJob().getLogFile().getParentFile(), "toRemove.sh");
+                try (PrintWriter writer = PrintWriters.getPrintWriter(output))
+                {
+                    writer.println("#!/bin/bash");
+                    writer.println("");
+                    writer.println("set -e");
+                    writer.println("set -x");
+                    writer.println("");
+                    probableDeletes.forEach(f -> writer.println("rm -Rf " + f.getPath()));
+                }
+                catch (IOException e)
+                {
+                    throw new PipelineJobException(e);
+                }
+
                 probableDeletes.forEach(f -> sb.append("\n").append(f.getPath()));
-                getJob().getLogger().info("## The following files can almost certainly be deleted; however, please exercise caution:" + sb.toString());
+                getJob().getLogger().info("## The following files can almost certainly be deleted; however, please exercise caution. Note: the file toRemove.sh has been written and can be executed to remove these:" + sb.toString());
+
+
             }
 
             return new RecordedActionSet();