Revert "Use constructor injection for web services"

This reverts commit 2a9174b.

Autowiring via constructor with CGLIB does not work in Spring 3. That
will require moving to Spring 3.

See #508.

gemma-web/src/main/java/ubic/gemma/web/services/rest/AnalysisResultSetsWebService.java

@@ -51,6 +51,7 @@
 import java.util.Collection;
 import java.util.List;
 import java.util.Map;
+import java.util.stream.Collectors;
 
 /**
  * Endpoint for {@link ubic.gemma.model.analysis.AnalysisResultSet}
@@ -61,18 +62,17 @@ public class AnalysisResultSetsWebService {
 
     private static final String TEXT_TAB_SEPARATED_VALUE_Q9_MEDIA_TYPE = MediaTypeUtils.TEXT_TAB_SEPARATED_VALUES_UTF8 + "; q=0.9";
 
-    private final ExpressionAnalysisResultSetService expressionAnalysisResultSetService;
-    private final ExpressionExperimentService expressionExperimentService;
-    private final DatabaseEntryService databaseEntryService;
-    private final ExpressionAnalysisResultSetFileService expressionAnalysisResultSetFileService;
+    @Autowired
+    private ExpressionAnalysisResultSetService expressionAnalysisResultSetService;
 
     @Autowired
-    public AnalysisResultSetsWebService( ExpressionAnalysisResultSetService expressionAnalysisResultSetService, ExpressionExperimentService expressionExperimentService, DatabaseEntryService databaseEntryService, ExpressionAnalysisResultSetFileService expressionAnalysisResultSetFileService ) {
-        this.expressionAnalysisResultSetService = expressionAnalysisResultSetService;
-        this.expressionExperimentService = expressionExperimentService;
-        this.databaseEntryService = databaseEntryService;
-        this.expressionAnalysisResultSetFileService = expressionAnalysisResultSetFileService;
-    }
+    private ExpressionExperimentService expressionExperimentService;
+
+    @Autowired
+    private DatabaseEntryService databaseEntryService;
+
+    @Autowired
+    private ExpressionAnalysisResultSetFileService expressionAnalysisResultSetFileService;
 
     /**
      * Retrieve all {@link AnalysisResultSet} matching a set of criteria.

gemma-web/src/main/java/ubic/gemma/web/services/rest/AnnotationsWebService.java

@@ -68,11 +68,17 @@ public class AnnotationsWebService {
 
     private static final String URL_PREFIX = "http://";
 
-    private final OntologyService ontologyService;
-    private final SearchService searchService;
-    private final CharacteristicService characteristicService;
-    private final ExpressionExperimentService expressionExperimentService;
-    private final TaxonService taxonService;
+    private OntologyService ontologyService;
+    private SearchService searchService;
+    private CharacteristicService characteristicService;
+    private ExpressionExperimentService expressionExperimentService;
+    private TaxonService taxonService;
+
+    /**
+     * Required by spring
+     */
+    public AnnotationsWebService() {
+    }
 
     /**
      * Constructor for service autowiring

gemma-web/src/main/java/ubic/gemma/web/services/rest/DatasetsWebService.java

@@ -81,18 +81,24 @@ public class DatasetsWebService {
     private static final String ERROR_DATA_FILE_NOT_AVAILABLE = "Data file for experiment %s can not be created.";
     private static final String ERROR_DESIGN_FILE_NOT_AVAILABLE = "Design file for experiment %s can not be created.";
 
-    private final ExpressionExperimentService service;
-    private final ExpressionExperimentService expressionExperimentService;
-    private final ExpressionDataFileService expressionDataFileService;
-    private final ArrayDesignService arrayDesignService;
-    private final BioAssayService bioAssayService;
-    private final ProcessedExpressionDataVectorService processedExpressionDataVectorService;
-    private final GeneService geneService;
-    private final SVDService svdService;
-    private final DifferentialExpressionAnalysisService differentialExpressionAnalysisService;
-    private final AuditEventService auditEventService;
-    private final OutlierDetectionService outlierDetectionService;
-    private final QuantitationTypeService quantitationTypeService;
+    private ExpressionExperimentService service;
+    private ExpressionExperimentService expressionExperimentService;
+    private ExpressionDataFileService expressionDataFileService;
+    private ArrayDesignService arrayDesignService;
+    private BioAssayService bioAssayService;
+    private ProcessedExpressionDataVectorService processedExpressionDataVectorService;
+    private GeneService geneService;
+    private SVDService svdService;
+    private DifferentialExpressionAnalysisService differentialExpressionAnalysisService;
+    private AuditEventService auditEventService;
+    private OutlierDetectionService outlierDetectionService;
+    private QuantitationTypeService quantitationTypeService;
+
+    /**
+     * Required by spring
+     */
+    public DatasetsWebService() {
+    }
 
     /**
      * Constructor for service autowiring

gemma-web/src/main/java/ubic/gemma/web/services/rest/GeneWebService.java

@@ -53,11 +53,17 @@
 @Path("/genes")
 public class GeneWebService {
 
-    private final GeneService geneService;
-    private final GeneOntologyService geneOntologyService;
-    private final CompositeSequenceService compositeSequenceService;
-    private final PhenotypeAssociationManagerService phenotypeAssociationManagerService;
-    private final GeneCoexpressionSearchService geneCoexpressionSearchService;
+    private GeneService geneService;
+    private GeneOntologyService geneOntologyService;
+    private CompositeSequenceService compositeSequenceService;
+    private PhenotypeAssociationManagerService phenotypeAssociationManagerService;
+    private GeneCoexpressionSearchService geneCoexpressionSearchService;
+
+    /**
+     * Required by spring
+     */
+    public GeneWebService() {
+    }
 
     /**
      * Constructor for service autowiring

gemma-web/src/main/java/ubic/gemma/web/services/rest/PhenotypeWebService.java

@@ -42,7 +42,13 @@
 @Path("/phenotypes")
 public class PhenotypeWebService {
 
-    private final PhenotypeAssociationManagerService phenotypeAssociationManagerService;
+    private PhenotypeAssociationManagerService phenotypeAssociationManagerService;
+
+    /**
+     * Required by spring
+     */
+    public PhenotypeWebService() {
+    }
 
     /**
      * Constructor for service autowiring

gemma-web/src/main/java/ubic/gemma/web/services/rest/PlatformsWebService.java

@@ -58,11 +58,17 @@ public class PlatformsWebService {
     private static final Log log = LogFactory.getLog( PlatformsWebService.class.getName() );
     private static final String ERROR_ANNOTATION_FILE_NOT_AVAILABLE = "Annotation file for platform %s does not exist or can not be accessed.";
 
-    private final GeneService geneService;
-    private final ArrayDesignService arrayDesignService;
-    private final ExpressionExperimentService expressionExperimentService;
-    private final CompositeSequenceService compositeSequenceService;
-    private final ArrayDesignAnnotationService annotationFileService;
+    private GeneService geneService;
+    private ArrayDesignService arrayDesignService;
+    private ExpressionExperimentService expressionExperimentService;
+    private CompositeSequenceService compositeSequenceService;
+    private ArrayDesignAnnotationService annotationFileService;
+
+    /**
+     * Required by spring
+     */
+    public PlatformsWebService() {
+    }
 
     /**
      * Constructor for service autowiring

gemma-web/src/main/java/ubic/gemma/web/services/rest/RootWebService.java

@@ -5,12 +5,14 @@
 import io.swagger.v3.oas.annotations.enums.SecuritySchemeType;
 import io.swagger.v3.oas.annotations.security.SecurityScheme;
 import io.swagger.v3.oas.models.OpenAPI;
+import lombok.Getter;
 import lombok.Value;
 import lombok.extern.apachecommons.CommonsLog;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Service;
 import org.springframework.web.servlet.support.ServletUriComponentsBuilder;
+import org.springframework.web.util.UriComponentsBuilder;
 import ubic.gemma.core.security.authentication.UserManager;
 import ubic.gemma.model.common.auditAndSecurity.User;
 import ubic.gemma.model.common.description.ExternalDatabaseValueObject;
@@ -56,14 +58,11 @@ public class RootWebService {
      */
     private static final String[] EXTERNAL_DATABASE_NAMES = Settings.getStringArray( "gemma.externalDatabases.featured" );
 
-    private final ExternalDatabaseService externalDatabaseService;
-    private final UserManager userManager;
+    @Autowired
+    private ExternalDatabaseService externalDatabaseService;
 
     @Autowired
-    public RootWebService( ExternalDatabaseService externalDatabaseService, UserManager userManager ) {
-        this.externalDatabaseService = externalDatabaseService;
-        this.userManager = userManager;
-    }
+    private UserManager userManager;
 
     /**
      * Returns an object with API information.

gemma-web/src/main/java/ubic/gemma/web/services/rest/SearchWebService.java

@@ -65,16 +65,12 @@ public class SearchWebService {
      */
     public static final int MAX_SEARCH_RESULTS = 1000;
 
-    private final SearchService searchService;
-    private final TaxonService taxonService;
-    private final ArrayDesignService arrayDesignService;
-
     @Autowired
-    public SearchWebService( SearchService searchService, TaxonService taxonService, ArrayDesignService arrayDesignService ) {
-        this.searchService = searchService;
-        this.taxonService = taxonService;
-        this.arrayDesignService = arrayDesignService;
-    }
+    private SearchService searchService;
+    @Autowired
+    private TaxonService taxonService;
+    @Autowired
+    private ArrayDesignService arrayDesignService;
 
     /**
      * Search everything subject to taxon and platform constraints.

gemma-web/src/main/java/ubic/gemma/web/services/rest/TaxaWebService.java

@@ -61,11 +61,17 @@
 public class TaxaWebService {
 
     protected static final Log log = LogFactory.getLog( TaxaWebService.class.getName() );
-    private final TaxonService taxonService;
-    private final GeneService geneService;
-    private final ExpressionExperimentService expressionExperimentService;
-    private final PhenotypeAssociationManagerService phenotypeAssociationManagerService;
-    private final ChromosomeService chromosomeService;
+    private TaxonService taxonService;
+    private GeneService geneService;
+    private ExpressionExperimentService expressionExperimentService;
+    private PhenotypeAssociationManagerService phenotypeAssociationManagerService;
+    private ChromosomeService chromosomeService;
+
+    /**
+     * Required by spring
+     */
+    public TaxaWebService() {
+    }
 
     /**
      * Constructor for service autowiring

gemma-web/src/test/java/ubic/gemma/web/services/rest/SearchWebServiceTest.java

@@ -40,8 +40,8 @@ public class SearchWebServiceTest extends AbstractJUnit4SpringContextTests {
     public static class SearchWebServiceTestContextConfiguration {
 
         @Bean
-        public SearchWebService searchWebService( SearchService searchService, TaxonService taxonService, ArrayDesignService arrayDesignService ) {
-            return new SearchWebService( searchService, taxonService, arrayDesignService );
+        public SearchWebService searchWebService() {
+            return new SearchWebService();
         }
 
         @Bean