Allow using any supported identifier when linting ACLs

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

@@ -3,11 +3,12 @@
 import lombok.AllArgsConstructor;
 import lombok.Getter;
 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.springframework.beans.factory.annotation.Autowired;
 import ubic.gemma.cli.util.AbstractAuthenticatedCLI;
+import ubic.gemma.cli.util.EntityLocator;
+import ubic.gemma.cli.util.EntityOptionsUtils;
 import ubic.gemma.cli.util.OptionsUtils;
 import ubic.gemma.core.security.authorization.acl.AclLinterConfig;
 import ubic.gemma.core.security.authorization.acl.AclLinterService;
@@ -68,9 +69,12 @@ private enum SecurableType {
     @Autowired
     private AclLinterService aclLinterService;
 
+    @Autowired
+    private EntityLocator entityLocator;
+
     private Class<? extends Securable> clazz;
 
-    private Long identifier;
+    private String identifier;
 
     private boolean lintPermissions;
 
@@ -82,8 +86,8 @@ private enum SecurableType {
     @Override
     protected void buildOptions( Options options ) {
         OptionsUtils.addEnumOption( options, "type", "type", "Type of securable entities to lint.", SecurableType.class );
-        options.addOption( Option.builder( "identifier" ).longOpt( "identifier" ).hasArg().type( Long.class )
-                .desc( "Identifier of the securable entity to lint. Requires the -type,--type option to be set." ).get() );
+        EntityOptionsUtils.addEntityOption( options, "identifier", "identifier",
+                "Identifier of the securable entity to lint. Requires the -type,--type option to be set." );
         options.addOption( "lintPermissions", "lint-permissions", false, "Lint permissions." );
         options.addOption( "applyFixes", "apply-fixes", false, "Apply fixes to ACLs" );
     }
@@ -92,7 +96,7 @@ protected void buildOptions( Options options ) {
     protected void processOptions( CommandLine commandLine ) throws ParseException {
         SecurableType st = OptionsUtils.getEnumOptionValue( commandLine, "type" );
         this.clazz = st != null ? st.getClazz() : null;
-        this.identifier = getParsedOptionValue( commandLine, "identifier",
+        this.identifier = getOptionValue( commandLine, "identifier",
                 requires( toBeSet( "type" ) ) );
         this.lintPermissions = commandLine.hasOption( "lintPermissions" );
         this.applyFixes = commandLine.hasOption( "applyFixes" );
@@ -111,7 +115,9 @@ protected void doAuthenticatedWork() throws Exception {
                 .build();
         Collection<AclLinterService.LintResult> results;
         if ( identifier != null ) {
-            results = aclLinterService.lintAcls( clazz, identifier, config );
+            Securable entity = entityLocator.locateEntity( clazz, identifier, true );
+            assert entity.getId() != null;
+            results = aclLinterService.lintAcls( clazz, entity.getId(), config );
         } else if ( clazz != null ) {
             results = aclLinterService.lintAcls( clazz, config );
         } else {

gemma-cli/src/main/java/ubic/gemma/cli/util/EntityLocator.java

@@ -1,6 +1,7 @@
 package ubic.gemma.cli.util;
 
 import ubic.gemma.model.analysis.expression.diff.DifferentialExpressionAnalysis;
+import ubic.gemma.model.common.Identifiable;
 import ubic.gemma.model.common.protocol.Protocol;
 import ubic.gemma.model.common.quantitationtype.QuantitationType;
 import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
@@ -16,11 +17,13 @@
 import java.util.Map;
 
 /**
- * Locate various entities using identifiers supplied by the CLI.
+ * Locate various entities using identifiers.
  * @author poirigui
  */
 public interface EntityLocator {
 
+    <T extends Identifiable> T locateEntity( Class<T> clazz, String identifier, boolean useReferencesIfPossible );
+
     Taxon locateTaxon( String identifier );
 
     ArrayDesign locateArrayDesign( String identifier );

gemma-cli/src/main/java/ubic/gemma/cli/util/EntityLocatorImpl.java

@@ -3,6 +3,7 @@
 import lombok.extern.apachecommons.CommonsLog;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.Pair;
+import org.hibernate.SessionFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 import org.springframework.util.Assert;
@@ -52,6 +53,38 @@ public class EntityLocatorImpl implements EntityLocator {
     private SingleCellExpressionExperimentService singleCellExpressionExperimentService;
     @Autowired
     private DifferentialExpressionAnalysisService differentialExpressionAnalysisService;
+    @Autowired
+    private SessionFactory sessionFactory;
+
+    @Override
+    @SuppressWarnings("unchecked")
+    public <T extends Identifiable> T locateEntity( Class<T> clazz, String identifier, boolean useReferencesIfPossible ) {
+        // if a match by ID is possible, prefer it so we can apply useReferencesIfPossible for anything
+        try {
+            Long id = Long.parseLong( identifier );
+            if ( useReferencesIfPossible ) {
+                return ( T ) sessionFactory.getCurrentSession().load( clazz, id );
+            } else {
+                return ( T ) requireNonNull( sessionFactory.getCurrentSession().get( clazz, id ),
+                        "No " + clazz.getSimpleName() + " found with ID " + id + "." );
+            }
+        } catch ( NumberFormatException e ) {
+            // ignore
+        }
+        // this is a non-ID lookup, so delegate to the appropriate locator
+        if ( Taxon.class.isAssignableFrom( clazz ) ) {
+            return ( T ) locateTaxon( identifier );
+        } else if ( Protocol.class.isAssignableFrom( clazz ) ) {
+            return ( T ) locateProtocol( identifier );
+        } else if ( ArrayDesign.class.isAssignableFrom( clazz ) ) {
+            return ( T ) locateArrayDesign( identifier );
+        } else if ( ExpressionExperiment.class.isAssignableFrom( clazz ) ) {
+            return ( T ) locateExpressionExperiment( identifier, useReferencesIfPossible );
+        } else {
+            // all the other locator in this class require an experiment context, so we cannot support them here.
+            throw new UnsupportedOperationException( "Cannot locate an entity of type " + clazz.getSimpleName() + "." );
+        }
+    }
 
     @Override
     public Taxon locateTaxon( String identifier ) {

gemma-cli/src/main/java/ubic/gemma/cli/util/EntityOptionsUtils.java

@@ -2,6 +2,7 @@
 
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
+import org.apache.commons.lang3.Strings;
 import ubic.gemma.cli.completion.CompletionType;
 import ubic.gemma.cli.completion.CompletionUtils;
 
@@ -11,6 +12,19 @@
  */
 public class EntityOptionsUtils {
 
+
+    /**
+     * @see EntityLocator#locateEntity(Class, String, boolean)
+     */
+    public static void addEntityOption( Options options, String optionName, String longOpt, String description ) {
+        options.addOption( Option.builder( optionName )
+                .longOpt( longOpt )
+                .hasArg()
+                .argName( "ID, short name, name, NCBI ID, common name, scientific name, alternate name" )
+                .desc( Strings.CS.appendIfMissing( description, "." ) + " Entity ID, short name, name, NCBI ID, common name, scientific name, alternate name" )
+                .get() );
+    }
+
     /**
      * Add an option for supplying a dataset.
      */