CLI cleanups

gemma-cli/src/main/java/ubic/gemma/core/apps/AffyDataFromCelCli.java

@@ -22,10 +22,12 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import org.apache.commons.lang3.StringUtils;
 import ubic.gemma.core.loader.expression.DataUpdater;
 import ubic.gemma.core.loader.expression.geo.model.GeoPlatform;
 import ubic.gemma.core.util.AbstractCLI;
+import ubic.gemma.core.util.CLI;
 import ubic.gemma.model.common.auditAndSecurity.eventType.DataReplacedEvent;
 import ubic.gemma.model.common.auditAndSecurity.eventType.FailedDataReplacedEvent;
 import ubic.gemma.model.common.quantitationtype.QuantitationType;
@@ -60,8 +62,8 @@ private boolean checkForAlreadyDone( BioAssaySet ee ) {
     }
 
     @Override
-    public GemmaCLI.CommandGroup getCommandGroup() {
-        return GemmaCLI.CommandGroup.EXPERIMENT;
+    public CommandGroup getCommandGroup() {
+        return CLI.CommandGroup.EXPERIMENT;
     }
 
     @Override
@@ -75,16 +77,16 @@ public String getShortDesc() {
     }
 
     @Override
-    protected void buildOptions( Options options ) {
-        super.buildOptions( options );
+    protected void buildBatchOptions( Options options ) {
+        super.buildBatchOptions( options );
         options.addOption( Option.builder( AffyDataFromCelCli.APT_FILE_OPT ).longOpt( null ).desc( "File output from apt-probeset-summarize; use if you want to override usual GEO download behaviour; "
                 + "ensure you used the right official CDF/MPS configuration" ).argName( "path" ).hasArg().build() );
         super.addForceOption( options );
 
     }
 
     @Override
-    protected void doWork() throws Exception {
+    protected void doBatchWork() throws Exception {
         DataUpdater serv = this.getBean( DataUpdater.class );
 
         if ( this.expressionExperiments.isEmpty() )
@@ -182,8 +184,8 @@ protected void doWork() throws Exception {
     }
 
     @Override
-    protected void processOptions( CommandLine commandLine ) {
-        super.processOptions( commandLine );
+    protected void processBatchOptions( CommandLine commandLine ) throws ParseException {
+        super.processBatchOptions( commandLine );
         if ( commandLine.hasOption( AffyDataFromCelCli.APT_FILE_OPT ) ) {
             this.aptFile = commandLine.getOptionValue( AffyDataFromCelCli.APT_FILE_OPT );
         }

gemma-cli/src/main/java/ubic/gemma/core/apps/AffyProbeCollapseCli.java

@@ -22,6 +22,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import ubic.gemma.core.analysis.sequence.SequenceManipulation;
 import ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader;
 import ubic.gemma.model.expression.designElement.CompositeSequence;
@@ -60,17 +61,22 @@ public String getCommandName() {
     }
 
     @Override
-    protected void buildOptions( Options options ) {
-        super.buildOptions( options );
+    public String getShortDesc() {
+        return null;
+    }
+
+    @Override
+    protected void buildBatchOptions( Options options ) {
+        super.buildBatchOptions( options );
         options.addOption( Option.builder( "affyProbeFile" )
                 .hasArg()
                 .desc( "Affymetrix probe file to use as input" )
                 .required().build() );
     }
 
     @Override
-    protected void processOptions( CommandLine commandLine ) {
-        super.processOptions( commandLine );
+    protected void processBatchOptions( CommandLine commandLine ) throws ParseException {
+        super.processBatchOptions( commandLine );
         affyProbeFileName = commandLine.getOptionValue( "affyProbeFile" );
     }
 
@@ -80,7 +86,7 @@ protected void processOptions( CommandLine commandLine ) {
      * @see ubic.gemma.core.util.AbstractCLI#doWork(java.lang.String[])
      */
     @Override
-    protected void doWork() throws IOException {
+    protected void doBatchWork() throws IOException {
 
         // parse
         AffyProbeReader apr = new AffyProbeReader();

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignAlternativePopulateCli.java

@@ -22,8 +22,7 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Options;
 import org.apache.commons.lang3.StringUtils;
-import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
-import ubic.gemma.core.util.AbstractCLIContextCLI;
+import ubic.gemma.core.util.AbstractCLI;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
 import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
 
@@ -37,7 +36,7 @@
  *
  * @author paul
  */
-public class ArrayDesignAlternativePopulateCli extends AbstractCLIContextCLI {
+public class ArrayDesignAlternativePopulateCli extends AbstractCLI {
 
     @Override
     public CommandGroup getCommandGroup() {
@@ -60,7 +59,7 @@ protected boolean requireLogin() {
     }
 
     @Override
-    protected void processOptions( CommandLine commandLine ) throws Exception {
+    protected void processOptions( CommandLine commandLine ) {
 
     }
 

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignAnnotationFileCli.java

@@ -31,17 +31,18 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import org.apache.commons.lang3.StringUtils;
 
 import ubic.gemma.core.analysis.service.ArrayDesignAnnotationService;
-import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
 import ubic.gemma.core.genome.gene.service.GeneService;
 import ubic.gemma.core.ontology.providers.GeneOntologyService;
 import ubic.gemma.core.util.AbstractCLI;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
 import ubic.gemma.model.expression.arrayDesign.TechnologyType;
 import ubic.gemma.model.genome.Gene;
 import ubic.gemma.model.genome.Taxon;
+import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
 import ubic.gemma.persistence.service.genome.taxon.TaxonService;
 
 /**
@@ -81,9 +82,8 @@ public CommandGroup getCommandGroup() {
     }
 
     @Override
-    protected void buildOptions( Options options ) {
-        super.buildOptions( options );
-
+    protected void buildBatchOptions( Options options ) {
+        super.buildBatchOptions( options );
         Option fileLoading = Option.builder( "l" ).desc( ArrayDesignAnnotationFileCli.FILE_LOAD_DESC ).hasArg()
                 .argName( "file of short names" ).build();
 
@@ -106,9 +106,9 @@ protected void buildOptions( Options options ) {
     }
 
     @Override
-    protected void processOptions( CommandLine commandLine ) {
-
-        if ( autoSeek ) {
+    protected void processBatchOptions( CommandLine commandLine ) throws ParseException {
+        super.processBatchOptions( commandLine );
+        if ( isAutoSeek() ) {
             throw new IllegalArgumentException( "This CLI doesn't support the auto option" );
         }
 
@@ -145,8 +145,6 @@ protected void processOptions( CommandLine commandLine ) {
         if ( commandLine.hasOption( 'o' ) )
             this.overWrite = true;
 
-        super.processOptions( commandLine );
-
         this.arrayDesignAnnotationService = this.getBean( ArrayDesignAnnotationService.class );
         this.goService = this.getBean( GeneOntologyService.class );
     }
@@ -162,7 +160,7 @@ public String getCommandName() {
     }
 
     @Override
-    protected void doWork() throws Exception {
+    protected void doBatchWork() throws Exception {
         this.taxonService = this.getBean( TaxonService.class );
 
         this.waitForGeneOntologyReady();
@@ -334,7 +332,8 @@ private void processFromListInFile() throws IOException {
                     continue;
                 }
 
-                ArrayDesign arrayDesign = this.locateArrayDesign( accession, getArrayDesignService() );
+                ArrayDesignService arrayDesignService = getArrayDesignService();
+                ArrayDesign arrayDesign = arrayDesignService.findByNameOrByShortName( accession );
 
                 try {
                     this.processAD( arrayDesign );

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignAuditTrailCleanupCli.java

@@ -47,13 +47,18 @@ public String getCommandName() {
         return "adATcleanup";
     }
 
+    @Override
+    public String getShortDesc() {
+        return null;
+    }
+
     /*
      * (non-Javadoc)
      *
      * @see ubic.gemma.core.util.AbstractCLI#doWork(java.lang.String[])
      */
     @Override
-    protected void doWork() throws Exception {
+    protected void doBatchWork() throws Exception {
         for ( ArrayDesign arrayDesign : this.getArrayDesignsToProcess() ) {
             arrayDesign = getArrayDesignService().thawLite( arrayDesign );
 

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignBioSequenceDetachCli.java

@@ -21,8 +21,8 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
 import ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent;
-import ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
 import ubic.gemma.model.expression.designElement.CompositeSequence;
 import ubic.gemma.model.genome.biosequence.BioSequence;
@@ -51,23 +51,22 @@ public String getCommandName() {
     }
 
     @Override
-    protected void buildOptions( Options options ) {
-        super.buildOptions( options );
-
+    protected void buildBatchOptions( Options options ) {
+        super.buildBatchOptions( options );
         Option fileOption = Option.builder( "delete" )
                 .desc( "Delete sequences instead of detaching them - use with care" ).build();
 
         options.addOption( fileOption );
     }
 
     @Override
-    protected void processOptions( CommandLine commandLine ) {
-        super.processOptions( commandLine );
+    protected void processBatchOptions( CommandLine commandLine ) throws ParseException {
+        super.processBatchOptions( commandLine );
         this.delete = commandLine.hasOption( "delete" );
     }
 
     @Override
-    protected void doWork() throws Exception {
+    protected void doBatchWork() throws Exception {
         BioSequenceService bioSequenceService = this.getBean( BioSequenceService.class );
 
         if ( this.getArrayDesignsToProcess().isEmpty() ) {

gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignBlatCli.java

@@ -21,25 +21,20 @@
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
-import org.springframework.security.core.context.SecurityContext;
-import org.springframework.security.core.context.SecurityContextHolder;
-import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
+import org.apache.commons.cli.ParseException;
 import ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService;
 import ubic.gemma.core.loader.genome.BlatResultParser;
 import ubic.gemma.core.util.AbstractCLI;
 import ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceAnalysisEvent;
-import ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
 import ubic.gemma.model.genome.Taxon;
 import ubic.gemma.model.genome.sequenceAnalysis.BlatResult;
 import ubic.gemma.persistence.service.genome.taxon.TaxonService;
 
 import java.io.File;
 import java.io.IOException;
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Date;
-import java.util.concurrent.*;
 
 /**
  * Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB. You must
@@ -60,11 +55,9 @@ public CommandGroup getCommandGroup() {
         return CommandGroup.PLATFORM;
     }
 
-    @SuppressWarnings("static-access")
     @Override
-    protected void buildOptions( Options options ) {
-        super.buildOptions( options );
-
+    protected void buildBatchOptions( Options options ) {
+        super.buildBatchOptions( options );
         Option blatResultOption = Option.builder( "b" ).hasArg().argName( "PSL file" ).desc(
                         "Blat result file in PSL format (if supplied, BLAT will not be run; will not work with settings that indicate "
                                 + "multiple platforms to run); -t option overrides" )
@@ -75,6 +68,7 @@ protected void buildOptions( Options options ) {
                 .desc(
                         "Threshold (0-1.0) for acceptance of BLAT alignments [Default = " + this.blatScoreThreshold + "]" )
                 .longOpt( "scoreThresh" )
+                .type( Number.class )
                 .build();
 
         options.addOption( Option.builder( "sensitive" ).desc( "Run on more sensitive server, if available" ).build() );
@@ -92,9 +86,8 @@ protected void buildOptions( Options options ) {
     }
 
     @Override
-    protected void processOptions( CommandLine commandLine ) {
-        super.processOptions( commandLine );
-
+    protected void processBatchOptions( CommandLine commandLine ) throws ParseException {
+        super.processBatchOptions( commandLine );
         if ( commandLine.hasOption( "sensitive" ) ) {
             this.sensitive = true;
         }
@@ -108,7 +101,7 @@ protected void processOptions( CommandLine commandLine ) {
 //        }
 
         if ( commandLine.hasOption( 's' ) ) {
-            this.blatScoreThreshold = this.getDoubleOptionValue( commandLine, 's' );
+            this.blatScoreThreshold = ( ( Number ) commandLine.getParsedOptionValue( 's' ) ).doubleValue();
         }
 
         TaxonService taxonService = this.getBean( TaxonService.class );
@@ -131,7 +124,7 @@ public String getCommandName() {
     }
 
     @Override
-    protected void doWork() throws Exception {
+    protected void doBatchWork() throws Exception {
         final Date skipIfLastRunLaterThan = this.getLimitingDate();
 
         if ( !this.getArrayDesignsToProcess().isEmpty() ) {
@@ -185,13 +178,10 @@ protected void doWork() throws Exception {
                     + allArrayDesigns.size() + " items]" );
 
             // split over multiple threads so we can multiplex. Put the array designs in a queue.
-            Collection<Callable<Void>> arrayDesigns = new ArrayList<>( allArrayDesigns.size() );
             for ( ArrayDesign arrayDesign : allArrayDesigns ) {
-                arrayDesigns.add( new ProcessArrayDesign( arrayDesign, skipIfLastRunLaterThan ) );
+                getExecutorService().submit( new ProcessArrayDesign( arrayDesign, skipIfLastRunLaterThan ) );
             }
 
-            executeBatchTasks( arrayDesigns );
-
         } else {
             throw new RuntimeException();
         }
@@ -264,7 +254,7 @@ private void updateMergedOrSubsumed( ArrayDesign design ) {
     /*
      * Here is our task runner.
      */
-    private class ProcessArrayDesign implements Callable<Void> {
+    private class ProcessArrayDesign implements Runnable {
 
         private ArrayDesign arrayDesign;
         private Date skipIfLastRunLaterThan;
@@ -275,14 +265,13 @@ private ProcessArrayDesign( ArrayDesign arrayDesign, Date skipIfLastRunLaterThan
         }
 
         @Override
-        public Void call() {
+        public void run() {
             if ( !ArrayDesignBlatCli.this.shouldRun( skipIfLastRunLaterThan, arrayDesign, ArrayDesignSequenceAnalysisEvent.class ) ) {
-                return null;
+                return;
             }
             arrayDesign = getArrayDesignService().thaw( arrayDesign );
             ArrayDesignBlatCli.this.processArrayDesign( arrayDesign );
             addSuccessObject( arrayDesign, "Processed " + arrayDesign.getShortName() );
-            return null;
         }
     }
 }