Merge pull request #1288 from PavlidisLab/feature-single-cell-ui-work

UI work for single-cell
PavlidisLab · Nov 15, 2024 · f45ef66 · f45ef66
2 parents e3e85c4 + 39fe57c
commit f45ef66
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diff --git a/.idea/runConfigurations/Build_static_assets.xml b/.idea/runConfigurations/Build_static_assets.xml
diff --git a/.idea/runConfigurations/Build_static_assets__dev_.xml b/.idea/runConfigurations/Build_static_assets__dev_.xml
diff --git a/.idea/runConfigurations/Deploy__dev_.xml b/.idea/runConfigurations/Deploy__dev_.xml
diff --git a/.idea/runConfigurations/Deploy__staging_.xml b/.idea/runConfigurations/Deploy__staging_.xml
diff --git a/.idea/runConfigurations/Serve_static_assets.xml b/.idea/runConfigurations/Serve_static_assets.xml
diff --git a/.../java/ubic/gemma/persistence/service/common/quantitationtype/QuantitationTypeDaoImpl.java b/.../java/ubic/gemma/persistence/service/common/quantitationtype/QuantitationTypeDaoImpl.java
@@ -30,7 +30,6 @@
 import org.springframework.util.Assert;
 import org.springframework.util.LinkedMultiValueMap;
 import org.springframework.util.MultiValueMap;
-import ubic.gemma.model.common.quantitationtype.GeneralType;
 import ubic.gemma.model.common.quantitationtype.QuantitationType;
 import ubic.gemma.model.common.quantitationtype.QuantitationTypeValueObject;
 import ubic.gemma.model.expression.bioAssayData.*;
@@ -39,10 +38,7 @@
 import ubic.gemma.persistence.service.AbstractCriteriaFilteringVoEnabledDao;
 
 import javax.annotation.Nullable;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
 import java.util.stream.Collectors;
 
 import static ubic.gemma.persistence.util.QueryUtils.optimizeParameterList;

diff --git a/.../java/ubic/gemma/persistence/service/common/quantitationtype/QuantitationTypeService.java b/.../java/ubic/gemma/persistence/service/common/quantitationtype/QuantitationTypeService.java
@@ -30,6 +30,7 @@
 import javax.annotation.Nullable;
 import java.util.Collection;
 import java.util.List;
+import java.util.Map;
 
 /**
  * @author kelsey
@@ -127,6 +128,8 @@ public interface QuantitationTypeService extends BaseService<QuantitationType>,
     @Nullable
     Class<? extends DataVector> getDataVectorType( QuantitationType qt );
 
+    Map<QuantitationType, Class<? extends DataVector>> getDataVectorTypes( Collection<QuantitationType> qts );
+
     /**
      * Infer all the mapped vector types that are subclasses of the given vector type.
      */

diff --git a/...a/ubic/gemma/persistence/service/common/quantitationtype/QuantitationTypeServiceImpl.java b/...a/ubic/gemma/persistence/service/common/quantitationtype/QuantitationTypeServiceImpl.java
@@ -29,10 +29,7 @@
 import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.AbstractFilteringVoEnabledService;
 
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
+import java.util.*;
 
 /**
  * @author keshav
@@ -90,6 +87,18 @@ public Class<? extends DataVector> getDataVectorType( QuantitationType qt ) {
         return quantitationTypeDao.getDataVectorType( qt );
     }
 
+    @Override
+    @Transactional(readOnly = true)
+    public Map<QuantitationType, Class<? extends DataVector>> getDataVectorTypes( Collection<QuantitationType> qts ) {
+        Map<QuantitationType, Class<? extends DataVector>> vectorTypes = new HashMap<>();
+        for ( QuantitationType qt : qts ) {
+            if ( !vectorTypes.containsKey( qt ) ) {
+                vectorTypes.put( qt, getDataVectorType( qt ) );
+            }
+        }
+        return vectorTypes;
+    }
+
     @Override
     // no need for a transaction
     public Collection<Class<? extends DataVector>> getMappedDataVectorType( Class<? extends DataVector> vectorType ) {

diff --git a/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/bioAssay/BioAssayDao.java b/gemma-core/src/main/java/ubic/gemma/persistence/service/expression/bioAssay/BioAssayDao.java
@@ -22,7 +22,7 @@
 import ubic.gemma.model.expression.bioAssay.BioAssay;
 import ubic.gemma.model.expression.bioAssay.BioAssayValueObject;
 import ubic.gemma.model.expression.bioAssayData.BioAssayDimension;
-import ubic.gemma.persistence.service.BaseVoEnabledDao;
+import ubic.gemma.model.expression.experiment.BioAssaySet;
 import ubic.gemma.persistence.service.FilteringVoEnabledDao;
 
 import java.util.Collection;
@@ -40,5 +40,7 @@ public interface BioAssayDao extends FilteringVoEnabledDao<BioAssay, BioAssayVal
 
     Collection<BioAssay> findByAccession( String accession );
 
+    Collection<BioAssaySet> getBioAssaySets( BioAssay bioAssay );
+
     List<BioAssayValueObject> loadValueObjects( Collection<BioAssay> entities, Map<Long, ArrayDesignValueObject> arrayDesignValueObjects, boolean basic );
 }
diff --git a/...ore/src/main/java/ubic/gemma/persistence/service/expression/bioAssay/BioAssayDaoImpl.java b/...ore/src/main/java/ubic/gemma/persistence/service/expression/bioAssay/BioAssayDaoImpl.java
@@ -26,6 +26,7 @@
 import ubic.gemma.model.expression.bioAssay.BioAssay;
 import ubic.gemma.model.expression.bioAssay.BioAssayValueObject;
 import ubic.gemma.model.expression.bioAssayData.BioAssayDimension;
+import ubic.gemma.model.expression.experiment.BioAssaySet;
 import ubic.gemma.persistence.service.AbstractNoopFilteringVoEnabledDao;
 import ubic.gemma.persistence.util.BusinessKey;
 
@@ -68,6 +69,22 @@ public Collection<BioAssay> findByAccession( String accession ) {
                 .setParameter( "accession", accession ).list();
     }
 
+    @Override
+    public Collection<BioAssaySet> getBioAssaySets( BioAssay bioAssay ) {
+        Collection<BioAssaySet> results = new HashSet<>();
+        //noinspection unchecked
+        results.addAll( getSessionFactory().getCurrentSession()
+                .createQuery( "select distinct bas from ExpressionExperiment bas join bas.bioAssays ba where ba = :ba" )
+                .setParameter( "ba", bioAssay )
+                .list() );
+        //noinspection unchecked
+        results.addAll( getSessionFactory().getCurrentSession()
+                .createQuery( "select distinct bas from ExpressionExperimentSubSet bas join bas.bioAssays ba where ba = :ba" )
+                .setParameter( "ba", bioAssay )
+                .list() );
+        return results;
+    }
+
     /**
      * Method that allows specification of FactorValueBasicValueObject in the bioMaterialVOs
      *

diff --git a/...ore/src/main/java/ubic/gemma/persistence/service/expression/bioAssay/BioAssayService.java b/...ore/src/main/java/ubic/gemma/persistence/service/expression/bioAssay/BioAssayService.java
@@ -25,15 +25,14 @@
 import ubic.gemma.model.expression.bioAssay.BioAssayValueObject;
 import ubic.gemma.model.expression.bioAssayData.BioAssayDimension;
 import ubic.gemma.model.expression.biomaterial.BioMaterial;
-import ubic.gemma.persistence.service.*;
-import ubic.gemma.persistence.util.Filter;
-import ubic.gemma.persistence.util.Sort;
+import ubic.gemma.model.expression.experiment.BioAssaySet;
+import ubic.gemma.persistence.service.BaseService;
+import ubic.gemma.persistence.service.FilteringVoEnabledService;
+import ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService;
 
-import javax.annotation.Nullable;
 import javax.annotation.CheckReturnValue;
 import java.util.Collection;
 import java.util.List;
-import java.util.Set;
 
 /**
  * @author kelsey
@@ -66,6 +65,15 @@ public interface BioAssayService extends BaseService<BioAssay>, FilteringVoEnabl
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_COLLECTION_READ" })
     Collection<BioAssay> findByAccession( String accession );
 
+    /**
+     * @see BioMaterialService#findSubBioMaterials(BioMaterial, boolean)
+     */
+    @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_COLLECTION_READ" })
+    Collection<BioAssay> findSubBioAssays( BioAssay bioAssay, boolean direct );
+
+    @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_COLLECTION_READ" })
+    Collection<BioAssay> findSiblings( BioAssay bioAssay );
+
     @Override
     @Secured({ "GROUP_USER", "AFTER_ACL_READ" })
     BioAssay findOrCreate( BioAssay bioAssay );
@@ -94,6 +102,12 @@ public interface BioAssayService extends BaseService<BioAssay>, FilteringVoEnabl
     @Secured({ "GROUP_USER", "ACL_SECURABLE_EDIT" })
     void update( BioAssay bioAssay );
 
+    /**
+     * Obtain all the {@link BioAssaySet} that contain the given {@link BioAssay}.
+     */
+    @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY", "AFTER_ACL_COLLECTION_READ" })
+    Collection<BioAssaySet> getBioAssaySets( BioAssay bioAssay );
+
     /**
      * Removes the association between a specific bioMaterial and a bioAssay.
      *

diff --git a/...src/main/java/ubic/gemma/persistence/service/expression/bioAssay/BioAssayServiceImpl.java b/...src/main/java/ubic/gemma/persistence/service/expression/bioAssay/BioAssayServiceImpl.java
@@ -23,9 +23,11 @@
 import ubic.gemma.model.expression.bioAssay.BioAssayValueObject;
 import ubic.gemma.model.expression.bioAssayData.BioAssayDimension;
 import ubic.gemma.model.expression.biomaterial.BioMaterial;
+import ubic.gemma.model.expression.experiment.BioAssaySet;
 import ubic.gemma.persistence.service.AbstractFilteringVoEnabledService;
 import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignDao;
 import ubic.gemma.persistence.service.expression.biomaterial.BioMaterialDao;
+import ubic.gemma.persistence.service.expression.biomaterial.BioMaterialService;
 
 import java.util.*;
 import java.util.function.Function;
@@ -81,6 +83,29 @@ public Collection<BioAssay> findByAccession( String accession ) {
         return this.bioAssayDao.findByAccession( accession );
     }
 
+    @Autowired
+    private BioMaterialService bioMaterialService;
+
+    @Override
+    @Transactional(readOnly = true)
+    public Collection<BioAssay> findSubBioAssays( BioAssay bioAssay, boolean direct ) {
+        Collection<BioMaterial> bms = bioMaterialService.findSubBioMaterials( bioAssay.getSampleUsed(), direct );
+        return bms.stream().map( BioMaterial::getBioAssaysUsedIn ).flatMap( Collection::stream ).collect( Collectors.toSet() );
+    }
+
+    @Override
+    @Transactional(readOnly = true)
+    public Collection<BioAssay> findSiblings( BioAssay bioAssay ) {
+        Collection<BioMaterial> bms = bioMaterialService.findSiblings( bioAssay.getSampleUsed() );
+        return bms.stream().map( BioMaterial::getBioAssaysUsedIn ).flatMap( Collection::stream ).collect( Collectors.toSet() );
+    }
+
+    @Override
+    @Transactional(readOnly = true)
+    public Collection<BioAssaySet> getBioAssaySets( BioAssay bioAssay ) {
+        return bioAssayDao.getBioAssaySets( bioAssay );
+    }
+
     /**
      * @see BioAssayService#removeBioMaterialAssociation(BioAssay, ubic.gemma.model.expression.biomaterial.BioMaterial)
      */

diff --git a/...ain/java/ubic/gemma/persistence/service/expression/bioAssayData/BioAssayDimensionDao.java b/...ain/java/ubic/gemma/persistence/service/expression/bioAssayData/BioAssayDimensionDao.java
@@ -18,19 +18,23 @@
  */
 package ubic.gemma.persistence.service.expression.bioAssayData;
 
-import ubic.gemma.model.common.quantitationtype.QuantitationType;
+import ubic.gemma.model.expression.bioAssay.BioAssay;
 import ubic.gemma.model.expression.bioAssayData.BioAssayDimension;
 import ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject;
-import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.BaseVoEnabledDao;
 
-import javax.annotation.Nullable;
+import java.util.Collection;
 
 /**
  * @see ubic.gemma.model.expression.bioAssayData.BioAssayDimension
  */
 public interface BioAssayDimensionDao extends BaseVoEnabledDao<BioAssayDimension, BioAssayDimensionValueObject> {
 
+    /**
+     * Find all the dimensions that contains all the given assays.
+     */
+    Collection<BioAssayDimension> findByBioAssayContainsAll( Collection<BioAssay> bioAssays );
+
     void thawLite( BioAssayDimension bioAssayDimension );
 
     void thaw( BioAssayDimension bioAssayDimension );

diff --git a/...java/ubic/gemma/persistence/service/expression/bioAssayData/BioAssayDimensionDaoImpl.java b/...java/ubic/gemma/persistence/service/expression/bioAssayData/BioAssayDimensionDaoImpl.java
@@ -27,20 +27,19 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Repository;
 import org.springframework.util.Assert;
-import ubic.gemma.model.common.quantitationtype.QuantitationType;
 import ubic.gemma.model.expression.bioAssay.BioAssay;
 import ubic.gemma.model.expression.bioAssayData.BioAssayDimension;
 import ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject;
-import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.model.expression.experiment.FactorValue;
 import ubic.gemma.persistence.service.AbstractVoEnabledDao;
 
-import javax.annotation.Nullable;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
 
 import static ubic.gemma.persistence.service.expression.biomaterial.BioMaterialUtils.visitBioMaterials;
+import static ubic.gemma.persistence.util.QueryUtils.optimizeIdentifiableParameterList;
 
 /**
  * <p>
@@ -107,6 +106,19 @@ public BioAssayDimension find( BioAssayDimension bioAssayDimension ) {
         return null;
     }
 
+    @Override
+    public Collection<BioAssayDimension> findByBioAssayContainsAll( Collection<BioAssay> bioAssays ) {
+        if ( bioAssays.isEmpty() ) {
+            return Collections.emptySet();
+        }
+        //noinspection unchecked
+        return getSessionFactory().getCurrentSession()
+                .createQuery( "select bad from BioAssayDimension bad join bad.bioAssays ba where ba in :bas group by bad having count(ba) = :numBas" )
+                .setParameterList( "bas", optimizeIdentifiableParameterList( bioAssays ) )
+                .setParameter( "numBas", bioAssays.stream().distinct().count() )
+                .list();
+    }
+
     @Override
     public void thawLite( final BioAssayDimension bioAssayDimension ) {
         Hibernate.initialize( bioAssayDimension );

diff --git a/...java/ubic/gemma/persistence/service/expression/bioAssayData/BioAssayDimensionService.java b/...java/ubic/gemma/persistence/service/expression/bioAssayData/BioAssayDimensionService.java
@@ -19,13 +19,14 @@
 package ubic.gemma.persistence.service.expression.bioAssayData;
 
 import org.springframework.security.access.annotation.Secured;
-import ubic.gemma.model.common.quantitationtype.QuantitationType;
+import ubic.gemma.model.expression.bioAssay.BioAssay;
 import ubic.gemma.model.expression.bioAssayData.BioAssayDimension;
 import ubic.gemma.model.expression.bioAssayData.BioAssayDimensionValueObject;
-import ubic.gemma.model.expression.experiment.ExpressionExperiment;
 import ubic.gemma.persistence.service.BaseImmutableService;
 import ubic.gemma.persistence.service.BaseVoEnabledService;
 
+import java.util.Collection;
+
 /**
  * @author Paul
  */
@@ -40,6 +41,9 @@ public interface BioAssayDimensionService
     @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY" })
     BioAssayDimension create( BioAssayDimension bioAssayDimension );
 
+    @Secured({ "IS_AUTHENTICATED_ANONYMOUSLY" })
+    Collection<BioAssayDimension> findByBioAssayContainsAll( Collection<BioAssay> bioAssays );
+
     @Override
     @Secured({ "GROUP_USER" })
     void remove( BioAssayDimension bioAssayDimension );