Numerious cleanups for Gemma Web [WIP]

PavlidisLab · Nov 9, 2024 · 75f3dc9 · 75f3dc9
1 parent 076e6e1
commit 75f3dc9
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Showing 76 changed files with 1,727 additions and 1,963 deletions.
diff --git a/...e/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDao.java b/...e/src/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDao.java
@@ -48,10 +48,9 @@ public interface BioMaterialDao extends BaseVoEnabledDao<BioMaterial, BioMateria
     Collection<BioMaterial> findByFactor( ExperimentalFactor experimentalFactor );
 
     /**
-     * @param bioMaterialId biomaterial id
-     * @return the experiment the biomaterial appears in
+     * Obtain all the experiments a biomaterial is used in.
      */
-    ExpressionExperiment getExpressionExperiment( Long bioMaterialId );
+    Collection<ExpressionExperiment> getExpressionExperiments( BioMaterial bm );
 
     /**
      * Thaw the given BioMaterial.

diff --git a/...c/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDaoImpl.java b/...c/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialDaoImpl.java
@@ -160,10 +160,12 @@ public Collection<BioMaterial> findByFactor( ExperimentalFactor experimentalFact
     }
 
     @Override
-    public ExpressionExperiment getExpressionExperiment( Long bioMaterialId ) {
-        return ( ExpressionExperiment ) this.getSessionFactory().getCurrentSession().createQuery(
-                        "select distinct e from ExpressionExperiment e inner join e.bioAssays ba inner join ba.sampleUsed bm where bm.id =:bmid " )
-                .setParameter( "bmid", bioMaterialId ).uniqueResult();
+    public Collection<ExpressionExperiment> getExpressionExperiments( BioMaterial bm ) {
+        //noinspection unchecked
+        return ( List<ExpressionExperiment> ) this.getSessionFactory().getCurrentSession()
+                .createQuery( "select distinct e from ExpressionExperiment e join e.bioAssays ba join ba.sampleUsed bm where bm = :bm " )
+                .setParameter( "bm", bm )
+                .list();
     }
 
     @Override

diff --git a/...c/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialService.java b/...c/main/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialService.java
@@ -29,6 +29,7 @@
 import ubic.gemma.persistence.service.BaseVoEnabledService;
 
 import javax.annotation.CheckReturnValue;
+import javax.annotation.Nullable;
 import java.util.Collection;
 import java.util.Map;
 
@@ -81,8 +82,9 @@ public interface BioMaterialService extends BaseService<BioMaterial>, BaseVoEnab
     @Secured({ "GROUP_USER", "ACL_SECURABLE_EDIT" })
     void update( BioMaterial bioMaterial );
 
-    @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_READ" })
-    ExpressionExperiment getExpressionExperiment( Long id );
+    @Nullable
+    @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_COLLECTION_READ" })
+    Collection<ExpressionExperiment> getExpressionExperiments( BioMaterial bm );
 
     @CheckReturnValue
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "ACL_SECURABLE__READ" })

diff --git a/...in/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialServiceImpl.java b/...in/java/ubic/gemma/persistence/service/expression/biomaterial/BioMaterialServiceImpl.java
@@ -85,8 +85,8 @@ public Collection<BioMaterial> findByFactor( ExperimentalFactor experimentalFact
 
     @Override
     @Transactional(readOnly = true)
-    public ExpressionExperiment getExpressionExperiment( Long id ) {
-        return this.bioMaterialDao.getExpressionExperiment( id );
+    public Collection<ExpressionExperiment> getExpressionExperiments( BioMaterial bm ) {
+        return this.bioMaterialDao.getExpressionExperiments( bm );
     }
 
     @Override

diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDaoImpl.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/genome/gene/GeneSetDaoImpl.java
@@ -91,7 +91,9 @@ public DatabaseBackedGeneSetValueObject loadValueObject( GeneSet geneSet ) {
     @Override
     public DatabaseBackedGeneSetValueObject loadValueObjectById( Long id ) {
         DatabaseBackedGeneSetValueObject vo = loadValueObjectByIdLite( id );
-        fillGeneIds( Collections.singletonList( vo ) );
+        if ( vo != null ) {
+            fillGeneIds( Collections.singletonList( vo ) );
+        }
         return vo;
     }
 

diff --git a/gemma-rest/src/main/resources/restapidocs/index.jsp b/gemma-rest/src/main/resources/restapidocs/index.jsp
@@ -1,4 +1,5 @@
-<%@ page contentType="text/html;charset=UTF-8" %>
+<%@ page pageEncoding="UTF-8" contentType="text/html;charset=UTF-8" trimDirectiveWhitespaces="true" %>
+<jsp:useBean id="appConfig" scope="application" type="java.util.Map" />
 <!DOCTYPE html>
 <html lang="en">
 <head>

diff --git a/...src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignController.java b/...src/main/java/ubic/gemma/web/controller/expression/arrayDesign/ArrayDesignController.java
@@ -495,9 +495,7 @@ public ModelAndView showArrayDesignByName( @RequestParam("name") String name ) {
 
     private ModelAndView showArrayDesignInternal( ArrayDesign arrayDesign ) {
         return new ModelAndView( "arrayDesign.detail" )
-                .addObject( "arrayDesignId", arrayDesign.getId() )
-                .addObject( "arrayDesignShortName", arrayDesign.getShortName() )
-                .addObject( "arrayDesignName", arrayDesign.getName() );
+                .addObject( "arrayDesign", arrayDesign );
     }
 
     @RequestMapping(value = "/showCompositeSequenceSummary.html", method = { RequestMethod.GET, RequestMethod.HEAD })

diff --git a/...a-web/src/main/java/ubic/gemma/web/controller/expression/bioAssay/BioAssayController.java b/...a-web/src/main/java/ubic/gemma/web/controller/expression/bioAssay/BioAssayController.java
@@ -18,7 +18,6 @@
  */
 package ubic.gemma.web.controller.expression.bioAssay;
 
-import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -38,7 +37,6 @@
 import ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentService;
 import ubic.gemma.web.util.EntityNotFoundException;
 
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.Map;
@@ -66,6 +64,15 @@ public class BioAssayController {
     @Autowired
     private OutlierDetectionService outlierDetectionService;
 
+    @RequestMapping(value = { "/showBioAssay.html", "/" }, method = { RequestMethod.GET, RequestMethod.HEAD })
+    public ModelAndView show( @RequestParam("id") Long id ) {
+        BioAssay bioAssay = bioAssayService.loadOrFail( id, EntityNotFoundException::new );
+        bioAssay = bioAssayService.thaw( bioAssay );
+        return new ModelAndView( "bioAssay.detail" )
+                .addObject( "bioAssay", new BioAssayValueObject( bioAssay, false ) );
+    }
+
+    @SuppressWarnings("unused") // Is used in EEManager.js
     public Collection<BioAssayValueObject> getBioAssays( Long eeId ) {
         ExpressionExperiment ee = eeService.loadAndThawLiteOrFail( eeId,
                 EntityNotFoundException::new, "Could not load experiment with ID=" + eeId );
@@ -94,39 +101,4 @@ public String markOutlier( Collection<Long> ids ) {
     public String unmarkOutlier( Collection<Long> ids ) {
         return taskRunningService.submitTaskCommand( new BioAssayOutlierProcessingTaskCommand( ids, true ) );
     }
-
-    @RequestMapping(value = { "/showBioAssay.html", "/" }, method = { RequestMethod.GET, RequestMethod.HEAD })
-    public ModelAndView show( @RequestParam("id") Long id ) {
-        BioAssay bioAssay = bioAssayService.load( id );
-        if ( bioAssay == null ) {
-            throw new EntityNotFoundException( id + " not found" );
-        }
-        bioAssay = bioAssayService.thaw( bioAssay );
-        return new ModelAndView( "bioAssay.detail" )
-                .addObject( "bioAssay", new BioAssayValueObject( bioAssay, false ) );
-    }
-
-    @RequestMapping(value = "/showAllBioAssays.html", method = { RequestMethod.GET, RequestMethod.HEAD })
-    public ModelAndView showAllBioAssays( @RequestParam(value = "id", required = false) String sId ) {
-        Collection<BioAssay> bioAssays = new ArrayList<>();
-        if ( StringUtils.isBlank( sId ) ) {
-            /*
-             * Probably not desirable ... there are >380,000 of them
-             */
-            bioAssays = bioAssayService.loadAll();
-        } else {
-            String[] idList = StringUtils.split( sId, ',' );
-            for ( String anIdList : idList ) {
-                Long id = Long.parseLong( anIdList );
-                BioAssay bioAssay = bioAssayService.load( id );
-                if ( bioAssay == null ) {
-                    throw new EntityNotFoundException( id + " not found" );
-                }
-                bioAssay = bioAssayService.thaw( bioAssay );
-                bioAssays.add( bioAssay );
-            }
-        }
-        return new ModelAndView( "bioAssays" ).addObject( "bioAssays", bioAssays );
-    }
-
 }
diff --git a/...src/main/java/ubic/gemma/web/controller/expression/biomaterial/BioMaterialController.java b/...src/main/java/ubic/gemma/web/controller/expression/biomaterial/BioMaterialController.java
@@ -161,8 +161,9 @@ public Collection<FactorValueValueObject> getFactorValues( EntityDelegator<BioMa
     public ModelAndView show( @RequestParam("id") Long id ) {
         BioMaterial bioMaterial = bioMaterialService.loadOrFail( id, EntityNotFoundException::new );
         bioMaterial = bioMaterialService.thaw( bioMaterial );
-        return new ModelAndView( "bioMaterial.detail" ).addObject( "bioMaterial", bioMaterial )
-                .addObject( "expressionExperiment", bioMaterialService.getExpressionExperiment( id ) );
+        return new ModelAndView( "bioMaterial.detail" )
+                .addObject( "bioMaterial", bioMaterial )
+                .addObject( "expressionExperiments", bioMaterialService.getExpressionExperiments( bioMaterial ) );
     }
 }
 
diff --git a/.../java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentController.java b/.../java/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentController.java
@@ -97,6 +97,7 @@
 import java.text.NumberFormat;
 import java.util.*;
 import java.util.concurrent.TimeUnit;
+import java.util.stream.Collectors;
 
 import static ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectUtils.getBatchEffectStatistics;
 import static ubic.gemma.core.analysis.preprocess.batcheffects.BatchEffectUtils.getBatchEffectType;
@@ -885,9 +886,9 @@ public ModelAndView showAllLinkSummaries() {
     @RequestMapping(value = { "/showBioAssaysFromExpressionExperiment.html", "/bioAssays" }, method = { RequestMethod.GET, RequestMethod.HEAD })
     public ModelAndView showBioAssays( @RequestParam("id") Long id ) {
         ExpressionExperiment expressionExperiment = getExperimentById( id, true );
-        ModelAndView mv = new ModelAndView( "bioAssays" ).addObject( "bioAssays", bioAssayService.thaw( expressionExperiment.getBioAssays() ) );
+        ModelAndView mv = new ModelAndView( "expressionExperiment.bioAssays" )
+                .addObject( "expressionExperiment", expressionExperiment );
         this.addQCInfo( expressionExperiment, mv );
-        mv.addObject( "expressionExperiment", expressionExperiment );
         return mv;
     }
 
@@ -904,15 +905,9 @@ public ModelAndView showBioMaterials( @RequestParam("id") Long id ) {
             }
         }
 
-        ModelAndView mav = new ModelAndView( "bioMaterials" );
-        if ( ExpressionExperimentController.AJAX ) {
-            mav.addObject( "bioMaterialIdList", bioMaterialService.getBioMaterialIdList( bioMaterials ) );
-        }
-
-        Integer numBioMaterials = bioMaterials.size();
-        mav.addObject( "numBioMaterials", numBioMaterials );
-        mav.addObject( "bioMaterials", bioMaterialService.thaw( bioMaterials ) );
-
+        ModelAndView mav = new ModelAndView( "expressionExperiment.bioMaterials" )
+                .addObject( "expressionExperiment", expressionExperiment )
+                .addObject( "bioMaterials", bioMaterialService.thaw( bioMaterials ) );
         this.addQCInfo( expressionExperiment, mav );
 
         return mav;
@@ -941,7 +936,8 @@ private ModelAndView showExpressionExperiment( ExpressionExperiment ee ) {
         return new ModelAndView( "expressionExperiment.detail" )
                 .addObject( "expressionExperiment", ee )
                 .addObject( "eeId", ee.getId() )
-                .addObject( "eeClass", ee.getClass() );
+                .addObject( "eeClass", ee.getClass() )
+                .addObject( "annotations", expressionExperimentService.getAnnotations( ee ).stream().map( AnnotationValueObject::getTermName ).collect( Collectors.joining( "," ) ) );
     }
 
     /**
@@ -953,8 +949,8 @@ public ModelAndView showSubSet( @RequestParam("id") Long id ) {
         if ( subset == null ) {
             throw new EntityNotFoundException( "No experiment subset with ID " + id + "." );
         }
-        // request.setAttribute( "id", id );
-        return new ModelAndView( "bioAssays" ).addObject( "bioAssays", subset.getBioAssays() );
+        return new ModelAndView( "bioAssaySet" )
+                .addObject( "bioAssaySet", subset );
     }
 
     /**

diff --git a/...va/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentSetController.java b/...va/ubic/gemma/web/controller/expression/experiment/ExpressionExperimentSetController.java
@@ -27,6 +27,7 @@
 import org.springframework.stereotype.Controller;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.servlet.ModelAndView;
 import ubic.gemma.model.analysis.expression.ExpressionExperimentSet;
 import ubic.gemma.model.expression.experiment.ExpressionExperimentDetailsValueObject;
@@ -39,7 +40,6 @@
 import ubic.gemma.web.persistence.SessionListManager;
 import ubic.gemma.web.util.EntityNotFoundException;
 
-import javax.servlet.http.HttpServletRequest;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
@@ -343,22 +343,17 @@ public Collection<ExpressionExperimentSetValueObject> removeUserAndSessionGroups
     }
 
     @RequestMapping(value = "/showExpressionExperimentSet.html", method = { RequestMethod.GET, RequestMethod.HEAD })
-    public ModelAndView showExpressionExperimentSet( HttpServletRequest request ) {
-
-        ModelAndView mav = new ModelAndView( "expressionExperimentSet.detail" );
-        StopWatch timer = new StopWatch();
-        timer.start();
-
-        ExpressionExperimentSetValueObject eesvo = this.getExpressionExperimentSetFromRequest( request );
-
-        mav.addObject( "eeSetId", eesvo.getId() );
-        mav.addObject( "eeSetName", eesvo.getName() );
-
+    public ModelAndView showExpressionExperimentSet( @RequestParam("id") Long id ) {
+        StopWatch timer = StopWatch.createStarted();
+        ExpressionExperimentSetValueObject eesvo = expressionExperimentSetService.loadValueObjectById( id );
+        if ( eesvo == null ) {
+            throw new EntityNotFoundException( "No experiment set with ID " + id );
+        }
         if ( timer.getTime() > 200 ) {
             log.info( "Show experiment set was slow: id=" + eesvo.getId() + " " + timer.getTime() + "ms" );
         }
-
-        return mav;
+        return new ModelAndView( "expressionExperimentSet.detail" )
+                .addObject( "eeSet", eesvo );
     }
 
     /**
@@ -454,31 +449,6 @@ private ExpressionExperimentSet create( ExpressionExperimentSetValueObject obj )
         return expressionExperimentSetValueObjectHelper.create( obj );
     }
 
-    /**
-     * @throws IllegalArgumentException if a matching EE can't be loaded
-     */
-    private ExpressionExperimentSetValueObject getExpressionExperimentSetFromRequest( HttpServletRequest request ) {
-
-        ExpressionExperimentSetValueObject set;
-        Long id;
-
-        if ( request.getParameter( "id" ) != null ) {
-            try {
-                id = Long.parseLong( request.getParameter( "id" ) );
-            } catch ( NumberFormatException e ) {
-                throw new IllegalArgumentException( "You must provide a valid numerical identifier" );
-            }
-            set = expressionExperimentSetService.loadValueObjectById( id );
-
-            if ( set == null ) {
-                throw new EntityNotFoundException( "Unable to access experiment set with id=" + id );
-            }
-        } else {
-            throw new IllegalArgumentException( "You must provide an id" );
-        }
-        return set;
-    }
-
     /**
      * Delete a EEset from the system.
      *

diff --git a/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneController.java b/gemma-web/src/main/java/ubic/gemma/web/controller/genome/gene/GeneController.java
@@ -145,15 +145,8 @@ public ModelAndView show( HttpServletRequest request ) {
         Long id = geneVO.getId();
 
         assert id != null;
-        ModelAndView mav = new ModelAndView( "gene.detail" );
-        mav.addObject( "geneId", id );
-        mav.addObject( "geneOfficialSymbol", geneVO.getOfficialSymbol() );
-        mav.addObject( "geneOfficialName", geneVO.getOfficialName() );
-        mav.addObject( "geneNcbiId", geneVO.getNcbiId() );
-        mav.addObject( "geneTaxonCommonName", geneVO.getTaxonCommonName() );
-        mav.addObject( "geneTaxonId", geneVO.getTaxonId() );
-
-        return mav;
+        return new ModelAndView( "gene.detail" )
+                .addObject( "gene", geneVO );
     }
 
     @RequestMapping(value = "/downloadGeneList.html", method = { RequestMethod.GET, RequestMethod.HEAD })