Release 1.29.0

README.md

@@ -1,7 +1,9 @@
 # Gemma code repository
 
-If you are looking for the public instance of Gemma, you can either access it through the
-[Gemma Website](https://gemma.msl.ubc.ca/), or check out our [RESTful API](https://gemma.msl.ubc.ca/resources/restapidocs/).
+This repository is for the Gemma software system.
+
+If you are looking to access the genomics data in Gemma, please see the
+[Gemma Website](https://gemma.msl.ubc.ca/), the Bioconductor package [Gemma.R](https://doi.org/doi:10.18129/B9.bioc.gemma.R), or our [RESTful API](https://gemma.msl.ubc.ca/resources/restapidocs/).
 
 Please see the end-user documentation at our [GitHub Pages](https://pavlidislab.github.io/Gemma/) for more information
 on how to use Gemma and related tools, and to credits and contact information.

gemma-cli/pom.xml

@@ -0,0 +1,81 @@
+<project xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/POM/4.0.0"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+    <parent>
+        <artifactId>gemma</artifactId>
+        <groupId>gemma</groupId>
+        <version>1.29.0</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+    <artifactId>gemma-cli</artifactId>
+    <name>Gemma CLI</name>
+    <description>Module containing the Gemma CLI.</description>
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>appassembler-maven-plugin</artifactId>
+                <version>2.1.0</version>
+                <configuration>
+                    <repositoryName>lib</repositoryName>
+                    <repositoryLayout>flat</repositoryLayout>
+                    <copyConfigurationDirectory>true</copyConfigurationDirectory>
+                    <platforms>
+                        <platform>unix</platform>
+                    </platforms>
+                    <programs>
+                        <program>
+                            <id>gemma-cli</id>
+                            <mainClass>ubic.gemma.core.apps.GemmaCLI</mainClass>
+                        </program>
+                    </programs>
+                    <!-- this allows Log4j 2 to lookup for Log4j 1.2 configuration -->
+                    <extraJvmArguments>-Dlog4j1.compatibility=true -Djava.awt.headless=true</extraJvmArguments>
+                    <!-- Gemma CLI extensions can be dropped in that folder -->
+                    <endorsedDir>contrib</endorsedDir>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>make-appassembly</id>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>assemble</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <version>3.3.0</version>
+                <configuration>
+                    <descriptors>
+                        <descriptor>src/assembly/appassembler.xml</descriptor>
+                    </descriptors>
+                </configuration>
+            </plugin>
+        </plugins>
+    </build>
+    <dependencies>
+        <dependency>
+            <groupId>gemma</groupId>
+            <artifactId>gemma-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>gemma</groupId>
+            <artifactId>gemma-core</artifactId>
+            <version>${project.version}</version>
+            <type>test-jar</type>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>commons-cli</groupId>
+            <artifactId>commons-cli</artifactId>
+            <version>1.5.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-api</artifactId>
+        </dependency>
+    </dependencies>
+</project>

gemma-cli/src/main/java/ubic/gemma/contrib/apps/README.md

@@ -0,0 +1,5 @@
+# Gemma Contrib Apps
+
+This package can be used by other Java packages to include CLIs.
+
+Standard applications reside in `ubic.pavlab.gemma.core.apps`.

gemma-core/src/main/java/ubic/gemma/core/apps/ArrayDesignProbeMapperCli.java → gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignProbeMapperCli.java

@@ -178,7 +178,6 @@ protected boolean requireLogin() {
      * See 'configure' for how the other options are handled. (non-Javadoc)
      *
      * @see AbstractCLI#processOptions(CommandLine)
-     * @param commandLine
      */
     @Override
     protected void processOptions( CommandLine commandLine ) {

gemma-core/src/main/java/ubic/gemma/core/apps/ArrayDesignSequenceAssociationCli.java → gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignSequenceAssociationCli.java

@@ -150,8 +150,6 @@ protected void doWork() throws Exception {
     }
 
     /**
-     * @param  taxon
-     * @return
      */
     private String[] chooseBLASTdbs( Taxon taxon ) {
         String[] databases = null;

gemma-core/src/main/java/ubic/gemma/core/apps/BioSequenceCleanupCli.java → gemma-cli/src/main/java/ubic/gemma/core/apps/BioSequenceCleanupCli.java

@@ -214,9 +214,6 @@ public String getShortDesc() {
     /**
      * Test whether two sequences are effectively equal (ignore the ID)
      *
-     * @param  one
-     * @param  that
-     * @return
      */
     private boolean equals( BioSequence one, BioSequence that ) {
 
@@ -241,7 +238,6 @@ private boolean equals( BioSequence one, BioSequence that ) {
     }
 
     /**
-     * @param bioSequences
      */
     private void processSequences( Collection<BioSequence> bioSequences ) {
         // ///////////////////////////////
@@ -324,8 +320,6 @@ private void processSequences( Collection<BioSequence> bioSequences ) {
     }
 
     /**
-     * @param keeper
-     * @param toRemove
      */
     private void switchAndDeleteExtra( BioSequence keeper, BioSequence toRemove ) {
 

gemma-core/src/main/java/ubic/gemma/core/apps/BlacklistCli.java → gemma-cli/src/main/java/ubic/gemma/core/apps/BlacklistCli.java

@@ -226,12 +226,7 @@ private void proactivelyBlacklistExperiments( ExternalDatabase geo ) throws Exce
     }
 
     /**
-     * @param  geo
-     * @param  gbs
-     * @param  blacklistedEntityDao
-     * @param  candidates
      * @return number of actually blacklisted experiments in this batch.
-     * @throws InterruptedException
      */
     private int fetchAndBlacklist( ExternalDatabase geo, GeoBrowser gbs, BlacklistedEntityService blacklistedEntityDao, Collection<String> candidates )
             throws InterruptedException {

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

@@ -0,0 +1,112 @@
+package ubic.gemma.core.apps;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Option;
+import org.apache.commons.cli.Options;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+import ubic.gemma.core.util.AbstractCLI;
+import ubic.gemma.core.util.AbstractSpringAwareCLI;
+import ubic.gemma.model.common.description.ExternalDatabase;
+import ubic.gemma.persistence.service.common.description.ExternalDatabaseService;
+
+import java.net.URL;
+import java.util.Date;
+
+import static java.util.Objects.requireNonNull;
+
+@Component
+public class ExternalDatabaseUpdaterCli extends AbstractSpringAwareCLI {
+
+    private static final String NAME_OPTION = "n",
+            DESCRIPTION_OPTION = "d",
+            RELEASE_OPTION = "release",
+            RELEASE_NOTE_OPTION = "releaseNote",
+            RELEASE_VERSION_OPTION = "releaseVersion",
+            RELEASE_URL_OPTION = "releaseUrl",
+            LAST_UPDATED_OPTION = "lastUpdated";
+
+    @Autowired
+    private ExternalDatabaseService externalDatabaseService;
+
+    private String name;
+    private String description;
+    private boolean release;
+    private String releaseNote;
+    private String releaseVersion;
+    private URL releaseUrl;
+    private Date lastUpdated;
+
+    @Override
+    public String getCommandName() {
+        return "updateExternalDatabase";
+    }
+
+    @Override
+    public GemmaCLI.CommandGroup getCommandGroup() {
+        return GemmaCLI.CommandGroup.SYSTEM;
+    }
+
+    @Override
+    protected boolean requireLogin() {
+        return true;
+    }
+
+    @Override
+    protected void buildOptions( Options options ) {
+        options.addOption( Option.builder( NAME_OPTION )
+                .longOpt( "name" )
+                .hasArg()
+                .optionalArg( false )
+                .desc( "External database name" ).build() );
+        options.addOption( DESCRIPTION_OPTION, "description", true, "New description" );
+        options.addOption( RELEASE_OPTION, "release", false, "Update the release (only affects last modified moment))" );
+        options.addOption( RELEASE_VERSION_OPTION, "release-version", true, "Release version" );
+        options.addOption( Option.builder( RELEASE_URL_OPTION )
+                .longOpt( "release-url" )
+                .hasArg()
+                .desc( "Release URL (optional)" )
+                .type( URL.class ).build() );
+        options.addOption( RELEASE_NOTE_OPTION, "release-note", true, "Note to include in the audit event related to the new release" );
+        options.addOption( Option.builder( LAST_UPDATED_OPTION )
+                .longOpt( "last-updated" )
+                .hasArg()
+                .desc( "Moment the release was performed if known, otherwise the current time will be used." )
+                .type( Date.class ).build() );
+    }
+
+    @Override
+    protected void processOptions( CommandLine commandLine ) throws Exception {
+        name = commandLine.getOptionValue( NAME_OPTION );
+        description = commandLine.getOptionValue( DESCRIPTION_OPTION );
+        release = commandLine.hasOption( RELEASE_OPTION );
+        releaseNote = commandLine.getOptionValue( RELEASE_NOTE_OPTION );
+        releaseVersion = commandLine.getOptionValue( RELEASE_VERSION_OPTION );
+        releaseUrl = ( URL ) commandLine.getParsedOptionValue( RELEASE_URL_OPTION );
+        lastUpdated = ( Date ) commandLine.getParsedOptionValue( LAST_UPDATED_OPTION );
+        if ( lastUpdated == null ) {
+            lastUpdated = new Date();
+        }
+    }
+
+    @Override
+    protected void doWork() throws Exception {
+        ExternalDatabase ed = requireNonNull( externalDatabaseService.findByNameWithAuditTrail( name ),
+                String.format( "No database with name %s.", name ) );
+        if ( description != null ) {
+            ed.setDescription( description );
+        }
+        if ( release || releaseVersion != null ) {
+            if ( releaseVersion != null ) {
+                AbstractCLI.log.info( String.format( "Updating %s release version to %s.", name, releaseVersion ) );
+                externalDatabaseService.updateReleaseDetails( ed, releaseVersion, releaseUrl, releaseNote, lastUpdated );
+            } else {
+                AbstractCLI.log.info( String.format( "Updating %s last updated moment to %s.", name, lastUpdated ) );
+                externalDatabaseService.updateReleaseLastUpdated( ed, releaseNote, lastUpdated );
+            }
+        } else {
+            AbstractCLI.log.info( String.format( "Updating %s. Use the --release flag to update last updated or release infos.", name ) );
+            externalDatabaseService.update( ed ); /* only update description, etc. */
+        }
+    }
+}

gemma-core/src/main/java/ubic/gemma/core/apps/ExternalFileGeneLoaderCLI.java → gemma-cli/src/main/java/ubic/gemma/core/apps/ExternalFileGeneLoaderCLI.java

@@ -45,7 +45,6 @@ public String getShortDesc() {
 
     /**
      * This method is called at the end of processCommandLine
-     * @param commandLine
      */
     @Override
     protected void processOptions( CommandLine commandLine ) {