Add a CLI to lint ACls

Relocate H2 init SQL scripts since it's not possible to refer to them
unambiguously in gemma-cli.

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

@@ -0,0 +1,105 @@
+package ubic.gemma.core.apps;
+
+import gemma.gsec.acl.domain.AclObjectIdentity;
+import gemma.gsec.model.Securable;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.hibernate.Session;
+import org.hibernate.SessionFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+import ubic.gemma.core.util.AbstractCLI;
+import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
+import ubic.gemma.model.expression.bioAssay.BioAssay;
+import ubic.gemma.model.expression.biomaterial.BioMaterial;
+import ubic.gemma.model.expression.experiment.*;
+
+import javax.annotation.Nullable;
+import java.util.List;
+
+@Component
+public class AclLinterCli extends AbstractCLI {
+
+    @Autowired
+    private SessionFactory sessionFactory;
+
+    @Override
+    protected void buildOptions( Options options ) {
+
+    }
+
+    @Override
+    protected void processOptions( CommandLine commandLine ) throws ParseException {
+
+    }
+
+    @Override
+    protected void doWork() throws Exception {
+        Session session = sessionFactory.openSession();
+        try {
+            warnEntitiesLackingObjectIdentity( session, ArrayDesign.class );
+            warnEntitiesLackingObjectIdentity( session, ExpressionExperiment.class );
+            warnEntitiesLackingObjectIdentity( session, ExpressionExperimentSubSet.class );
+            warnEntitiesLackingObjectIdentity( session, BioMaterial.class );
+            warnEntitiesLackingObjectIdentity( session, BioAssay.class );
+            warnEntitiesLackingObjectIdentity( session, ExperimentalDesign.class );
+            warnEntitiesLackingObjectIdentity( session, ExperimentalFactor.class );
+            warnEntitiesLackingObjectIdentity( session, FactorValue.class );
+
+            warnEntitiesWhoseParentObjectIsMissing( session, ExpressionExperimentSubSet.class, ExpressionExperiment.class );
+            warnEntitiesWhoseParentObjectIsMissing( session, BioAssay.class, ExpressionExperiment.class );
+            warnEntitiesWhoseParentObjectIsMissing( session, ExperimentalDesign.class, ExpressionExperiment.class );
+            warnEntitiesWhoseParentObjectIsMissing( session, ExperimentalFactor.class, ExpressionExperiment.class );
+            warnEntitiesWhoseParentObjectIsMissing( session, FactorValue.class, ExpressionExperiment.class );
+        } finally {
+            session.close();
+        }
+    }
+
+    private void warnEntitiesLackingObjectIdentity( Session session, Class<? extends Securable> clazz ) {
+        //language=HQL
+        //noinspection unchecked
+        List<? extends Securable> list = session
+                .createQuery( "select e from " + clazz.getName() + " e "
+                        + "where e.id not in ( " + "select aoi.identifier from AclObjectIdentity aoi where aoi.type = :type" + ")" )
+                .setParameter( "type", clazz.getName() )
+                .list();
+        for ( Securable ee : list ) {
+            addErrorObject( ee, String.format( "Object with ID %d lacks an ACL identity of type %s", ee.getId(), clazz.getName() ) );
+        }
+    }
+
+    private void warnEntitiesWhoseParentObjectIsMissing( Session session, Class<? extends Securable> clazz, Class<? extends Securable> parentType ) {
+        //noinspection unchecked
+        List<Object[]> list = session
+                .createQuery( "select e, aoi.parentObject from " + clazz.getName() + " e, AclObjectIdentity aoi "
+                        + "where aoi.identifier = e.id and aoi.type = :type "
+                        + "and aoi.parentObject is not null "
+                        + "and aoi.parentObject.identifier not in (select p.id from " + parentType.getName() + " p)" )
+                .setParameter( "type", clazz.getName() )
+                .list();
+        for ( Object[] ee : list ) {
+            Securable s = ( Securable ) ee[0];
+            AclObjectIdentity parentAoi = ( AclObjectIdentity ) ee[1];
+            addErrorObject( s, String.format( "Parent of object with ID %d does not exist; parent ACL identity is %s", s.getId(), parentAoi ) );
+        }
+    }
+
+    @Nullable
+    @Override
+    public String getCommandName() {
+        return "lintAcls";
+    }
+
+    @Nullable
+    @Override
+    public String getShortDesc() {
+        return null;
+    }
+
+    @Override
+    public GemmaCLI.CommandGroup getCommandGroup() {
+        return GemmaCLI.CommandGroup.SYSTEM;
+    }
+}

gemma-cli/src/test/java/ubic/gemma/core/apps/AclLinterCliTest.java

@@ -0,0 +1,36 @@
+package ubic.gemma.core.apps;
+
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.test.context.ContextConfiguration;
+import ubic.gemma.core.util.test.BaseDatabaseTest;
+import ubic.gemma.persistence.util.TestComponent;
+
+import static ubic.gemma.core.util.test.Assertions.assertThat;
+
+@ContextConfiguration
+public class AclLinterCliTest extends BaseDatabaseTest {
+
+    @Configuration
+    @TestComponent
+    static class AclLinterCliTestContextConfiguration extends BaseDatabaseTestContextConfiguration {
+
+        @Bean
+        public AclLinterCli aclLinterCli() {
+            return new AclLinterCli();
+        }
+    }
+
+    @Autowired
+    private AclLinterCli aclLinterCli;
+
+    @Test
+    public void test() {
+        assertThat( aclLinterCli )
+                .withArguments()
+                .hasCommandName( "lintAcls" )
+                .succeeds();
+    }
+}

gemma-cli/src/test/java/ubic/gemma/core/util/test/Assertions.java

@@ -0,0 +1,10 @@
+package ubic.gemma.core.util.test;
+
+import ubic.gemma.core.util.CLI;
+
+public class Assertions {
+
+    public static CliAssert assertThat( CLI cli ) {
+        return new CliAssert( cli );
+    }
+}

gemma-cli/src/test/java/ubic/gemma/core/util/test/CliAssert.java

@@ -0,0 +1,30 @@
+package ubic.gemma.core.util.test;
+
+import org.assertj.core.api.AbstractAssert;
+import ubic.gemma.core.util.CLI;
+
+/**
+ * AssertJ assertions for {@link CLI}.
+ */
+public class CliAssert extends AbstractAssert<CliAssert, CLI> {
+
+    private String[] args = {};
+
+    public CliAssert( CLI cli ) {
+        super( cli, CliAssert.class );
+    }
+
+    public CliAssert withArguments( String... args ) {
+        this.args = args;
+        return myself;
+    }
+
+    public CliAssert hasCommandName( String commandName ) {
+        objects.assertEqual( info, commandName, actual.getCommandName() );
+        return myself;
+    }
+
+    public void succeeds() {
+        objects.assertEqual( info, 0, actual.executeCommand( args ) );
+    }
+}

gemma-core/src/test/java/ubic/gemma/core/util/test/BaseDatabaseTest.java

@@ -123,8 +123,8 @@ public DataSourceInitializer( DataSource dataSource ) {
         @Override
         public void afterPropertiesSet() {
             JdbcTestUtils.executeSqlScript( template, applicationContext.getResource( "/sql/init-acls.sql" ), false );
-            JdbcTestUtils.executeSqlScript( template, applicationContext.getResource( "/sql/init-entities.sql" ), false );
-            JdbcTestUtils.executeSqlScript( template, applicationContext.getResource( "/sql/init-indices.sql" ), false );
+            JdbcTestUtils.executeSqlScript( template, applicationContext.getResource( "/sql/h2/init-entities.sql" ), false );
+            JdbcTestUtils.executeSqlScript( template, applicationContext.getResource( "/sql/h2/init-indices.sql" ), false );
         }
     }
 }