add background traits to solr

goci-core/goci-repository/src/main/java/uk/ac/ebi/spot/goci/repository/DiseaseTraitRepository.java

@@ -61,4 +61,12 @@ Page<DiseaseTrait> findByStudiesPublicationIdPubmedId(
             "group by dt.id order by count(dt.id) desc")
     List<Map.Entry> getDiseaseTraitCounts();
 
+    //findByStudiesIdAndStudiesHousekeepingCatalogPublishDateIsNotNullAndStudiesHousekeepingCatalogUnpublishDateIsNull
+    @RestResource(exported = false)
+    @Query("select t from DiseaseTrait t join t.studies s join s.housekeeping h  where h.catalogPublishDate is null " +
+            "and h.catalogUnpublishDate is not null and s.id = :studyId")
+    List<DiseaseTrait> findBackgroundTraitByStudyId(
+            Long studyId);
+
+
 }

goci-core/goci-repository/src/main/java/uk/ac/ebi/spot/goci/repository/EfoTraitRepository.java

@@ -62,5 +62,11 @@ Page<EfoTrait> findByStudiesIdAndStudiesHousekeepingCatalogPublishDateIsNotNullA
     @RestResource(exported = false)
     Page<EfoTrait> findByStudiesPublicationIdPubmedId(String pumbedId, Pageable pageable);
 
+    //findByStudiesIdAndStudiesHousekeepingCatalogPublishDateIsNotNullAndStudiesHousekeepingCatalogUnpublishDateIsNull
+    @RestResource(exported = false)
+    @Query("select t from EfoTrait t join t.studies s join s.housekeeping h  where h.catalogPublishDate is null " +
+            "and h.catalogUnpublishDate is not null and s.id = :studyId")
+    List<EfoTrait> findMappedBackgroundTraitByStudyId(
+            Long studyId);
 }
 

goci-core/goci-service/src/main/java/uk/ac/ebi/spot/goci/service/AssociationService.java

@@ -187,6 +187,8 @@ public void loadAssociatedData(Association association) {
         int traitCount = association.getEfoTraits().size();
         //Study study = studyService.fetchOne(association.getStudy());
         Study study = association.getStudy();
+        study.getBackgroundTrait().getTrait();
+        study.getMappedBackgroundTraits().size();
         AtomicInteger reportedGeneCount = new AtomicInteger();
         Collection<SingleNucleotidePolymorphism> snps = new HashSet<>();
         Collection<SingleNucleotidePolymorphism> proxySnps = new HashSet<>();

goci-core/goci-service/src/main/java/uk/ac/ebi/spot/goci/service/StudyService.java

@@ -214,6 +214,12 @@ public void loadAssociatedData(Study study) {
         int efoTraitCount = study.getEfoTraits().size();
         int associationCount = study.getAssociations().size();
         int ancestryCount = study.getAncestries().size();
+        if(study.getBackgroundTrait() != null) {
+            study.getBackgroundTrait().getTrait();
+        }
+        if(study.getMappedBackgroundTraits() != null) {
+            study.getMappedBackgroundTraits().size();
+        }
 
         study.getAncestries().forEach(
                 ancestry -> {
@@ -272,6 +278,8 @@ public void deepLoadAssociatedData(Study study) {
         int associationCount = study.getAssociations().size();
 //        int snpCount = study.getSingleNucleotidePolymorphisms().size();
         int platformCount = study.getPlatforms().size();
+        study.getMappedBackgroundTraits().size();
+        study.getBackgroundTrait().getTrait();
 
         int ancestryCount = study.getAncestries().size();
 
@@ -329,6 +337,8 @@ public void deepLoadAssociatedData(Study study) {
             for (Association association : study.getAssociations()) {
                 int lociCount = association.getLoci().size();
                 int associationEfoTraitCount = association.getEfoTraits().size();
+                study.getBackgroundTrait().getTrait();
+                study.getMappedBackgroundTraits().size();
                 getLog().trace("Association '" + association.getId() + "' is linked to " + lociCount + " loci and " +
                                        associationEfoTraitCount + "efo traits.");
                 for (Locus locus : association.getLoci()) {

goci-core/goci-service/src/main/java/uk/ac/ebi/spot/goci/service/TraitService.java

@@ -34,11 +34,20 @@ public Collection<DiseaseTrait> findReportedTraitByStudyId(Long studyId) {
                 studyId);
     }
 
+    public Collection<DiseaseTrait> findBackgroundTraitByStudyId(Long studyId) {
+        return diseaseTraitRepository.findBackgroundTraitByStudyId(
+                studyId);
+    }
+
     public Collection<DiseaseTrait> findReportedTraitByAssociationId(Long associationId) {
         return diseaseTraitRepository.findByStudiesAssociationsIdAndStudiesHousekeepingCatalogPublishDateIsNotNullAndStudiesHousekeepingCatalogUnpublishDateIsNull(
                 associationId);
     }
 
+    public Collection<EfoTrait> findMappedBackgroundTraitByStudyId(Long studyId) {
+        return efoTraitRepository.findMappedBackgroundTraitByStudyId(studyId);
+    }
+
     public Collection<EfoTrait> findMappedTraitByStudyId(Long studyId) {
         return efoTraitRepository.findByStudiesIdAndStudiesHousekeepingCatalogPublishDateIsNotNullAndStudiesHousekeepingCatalogUnpublishDateIsNull(
                 studyId);

goci-interfaces/goci-solr/src/main/resources/solr/solr/gwas/conf/schema.xml

@@ -184,10 +184,13 @@
 
     <!-- diseasetrait -->
     <field name="traitName" type="text_general" indexed="true" stored="true" multiValued="true" />
+    <field name="backgroundTraitName" type="text_general" indexed="true" stored="true" multiValued="true" />
 
     <!-- efotrait -->
     <field name="mappedLabel" type="text_general" indexed="true" stored="true" multiValued="true" />
     <field name="mappedUri" type="text_general" indexed="true" stored="true" multiValued="true" />
+    <field name="backgroundEfoLabel" type="text_general" indexed="true" stored="true" multiValued="true" />
+    <field name="backgroundEfoUri" type="text_general" indexed="true" stored="true" multiValued="true" />
 
     <!-- ontology expanded info -->
     <field name="trait" type="text_general" indexed="true" stored="true" multiValued="true" />
@@ -397,8 +400,11 @@
     <copyField source="study_additionalAncestryDescription" dest="text" />
     <copyField source="study_accessionId" dest="text" />
     <copyField source="traitName" dest="text" />
+    <copyField source="backgroundTraitName" dest="text" />
     <copyField source="mappedLabel" dest="text" />
     <copyField source="mappedUri" dest="text" />
+    <copyField source="backgroundEfoLabel" dest="text" />
+    <copyField source="backgroundEfoUri" dest="text" />
     <copyField source="trait" dest="text" />
     <copyField source="traitUri" dest="text" />
     <copyField source="shortForm" dest="text" />

goci-tools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/model/AssociationDocument.java

@@ -105,6 +105,13 @@ public class AssociationDocument extends OntologyEnabledDocument<Association> {
     @Field("mappedLabel") private Collection<String> mappedLabels;
     @Field("mappedUri") private Collection<String> mappedUris;
 
+    // embedded DiseaseTrait info
+    @Field("backgroundTraitName") private Collection<String> backgroundTraitNames;
+
+    // embedded EfoTrait info
+    @Field("backgroundEfoLabel") private Collection<String> backgroundEfoLabels;
+    @Field("backgroundEfoUri") private Collection<String> backgroundEfoUris;
+
     public AssociationDocument(Association association) {
         super(association);
         this.riskFrequency = association.getRiskFrequency();
@@ -152,6 +159,11 @@ public AssociationDocument(Association association) {
         this.mappedLabels = new LinkedHashSet<>();
         this.mappedUris = new LinkedHashSet<>();
 
+        this.backgroundTraitNames = new LinkedHashSet<>();
+
+        this.backgroundEfoLabels = new LinkedHashSet<>();
+        this.backgroundEfoUris = new LinkedHashSet<>();
+
         this.ancestralGroups = new LinkedHashSet<>();
         this.countriesOfOrigin = new LinkedHashSet<>();
         this.countriesOfRecruitment = new LinkedHashSet<>();
@@ -351,6 +363,18 @@ public void addMappedUri(String mappedUri) {
         this.mappedUris.add(mappedUri);
     }
 
+    public void addBackgroundTraitName(String traitName) {
+        this.backgroundTraitNames.add(traitName);
+    }
+
+    public void addBackgroundEfoLabel(String mappedLabel) {
+        this.backgroundEfoLabels.add(mappedLabel);
+    }
+
+    public void addBackgroundEfoUri(String mappedUri) {
+        this.backgroundEfoUris.add(mappedUri);
+    }
+
     public void addStudyId(String studyId) {
         this.studyIds.add(studyId);
     }

goci-tools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/model/StudyDocument.java

@@ -76,6 +76,13 @@ public class StudyDocument extends OntologyEnabledDocument<Study> {
     @Field("mappedLabel") private Collection<String> mappedLabels;
     @Field("mappedUri") private Collection<String> mappedUris;
 
+    // embedded DiseaseTrait info
+    @Field("backgroundTraitName") private Collection<String> backgroundTraitNames;
+
+    // embedded EfoTrait info
+    @Field("backgroundEfoLabel") private Collection<String> backgroundEfoLabels;
+    @Field("backgroundEfoUri") private Collection<String> backgroundEfoUris;
+
     public StudyDocument(Study study) {
         super(study);
         this.pubmedId = study.getPublicationId().getPubmedId();
@@ -146,6 +153,11 @@ public StudyDocument(Study study) {
 
         this.mappedLabels = new LinkedHashSet<>();
         this.mappedUris = new LinkedHashSet<>();
+
+        this.backgroundTraitNames = new LinkedHashSet<>();
+
+        this.backgroundEfoLabels = new LinkedHashSet<>();
+        this.backgroundEfoUris = new LinkedHashSet<>();
     }
 
     public String getPubmedId() {
@@ -273,6 +285,18 @@ public void addMappedUri(String mappedUri) {
         this.mappedUris.add(mappedUri);
     }
 
+    public void addBackgroundTraitName(String traitName) {
+        this.backgroundTraitNames.add(traitName);
+    }
+
+    public void addBackgroundEfoLabel(String mappedLabel) {
+        this.backgroundEfoLabels.add(mappedLabel);
+    }
+
+    public void addBackgroundEfoUri(String mappedUri) {
+        this.backgroundEfoUris.add(mappedUri);
+    }
+
     public Collection<String> getAncestralGroups() {
         return ancestralGroups;
     }

goci-tools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/service/AssociationEnrichmentService.java

@@ -2,10 +2,7 @@
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
-import uk.ac.ebi.spot.goci.model.AssociationDocument;
-import uk.ac.ebi.spot.goci.model.DiseaseTraitDocument;
-import uk.ac.ebi.spot.goci.model.EfoDocument;
-import uk.ac.ebi.spot.goci.model.StudyDocument;
+import uk.ac.ebi.spot.goci.model.*;
 
 /**
  * Javadocs go here!
@@ -14,7 +11,7 @@
  * @date 13/02/15
  */
 @Service
-public class AssociationEnrichmentService implements DocumentEnrichmentService<AssociationDocument> {
+public class AssociationEnrichmentService implements DocumentEnrichmentService<AssociationDocument, Association> {
     private final DiseaseTraitDocumentCache diseaseTraitCache;
     private final StudyDocumentCache studyCache;
     private StudyService studyService;
@@ -36,7 +33,7 @@ public AssociationEnrichmentService(StudyService studyService, TraitService trai
         return 2;
     }
 
-    @Override public void doEnrichment(AssociationDocument document) {
+    @Override public void doEnrichment(AssociationDocument document, Association association) {
         long id = Long.valueOf(document.getId().split(":")[1]);
 
         studyService.findByAssociationId(id).forEach(

goci-tools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/service/DocumentEnrichmentService.java

@@ -9,7 +9,7 @@
  * @author Tony Burdett
  * @date 19/01/15
  */
-public interface DocumentEnrichmentService<D extends Document> {
+public interface DocumentEnrichmentService<D extends Document, T> {
     /**
      * The priority of a document enrichment service indicates the order in which enrichments will be run, lowest value
      * first.  This enables enrichment chaining.
@@ -18,5 +18,5 @@ public interface DocumentEnrichmentService<D extends Document> {
      */
     int getPriority();
 
-    void doEnrichment(D document);
+    void doEnrichment(D document, T dbObject);
 }

goci-tools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/service/ObjectConverter.java

@@ -63,7 +63,7 @@ public <O, D extends Document<O>> D convert(O object, Class<D> documentType) {
                             return des1.getPriority() - des2.getPriority();
                         }
                     })
-                    .forEach(documentEnrichmentService -> documentEnrichmentService.doEnrichment(document));
+                    .forEach(documentEnrichmentService -> documentEnrichmentService.doEnrichment(document, object));
 
             // and return
             return document;

goci-tools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/service/OntologyExpansionService.java

@@ -5,6 +5,7 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
+import uk.ac.ebi.spot.goci.model.DiseaseTrait;
 import uk.ac.ebi.spot.goci.model.OntologyEnabledDocument;
 import uk.ac.ebi.spot.goci.ontology.owl.OntologyLoader;
 
@@ -18,7 +19,7 @@
  * @date 19/01/15
  */
 @Service
-public class OntologyExpansionService implements DocumentEnrichmentService<OntologyEnabledDocument<?>> {
+public class OntologyExpansionService implements DocumentEnrichmentService<OntologyEnabledDocument<?>, Object> {
     private OntologyLoader ontologyLoader;
 
     private final Logger log = LoggerFactory.getLogger(getClass());
@@ -36,7 +37,7 @@ public OntologyExpansionService(OntologyLoader ontologyLoader) {
         return 4;
     }
 
-    @Override public void doEnrichment(OntologyEnabledDocument<?> document) {
+    @Override public void doEnrichment(OntologyEnabledDocument<?> document, Object o) {
         // improve trait document with parent and child terms etc here
         for (String traitUriString : document.getTraitUris()) {
             traitUriString = traitUriString.trim();

goci-tools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/service/StudyEnrichmentService.java

@@ -2,11 +2,7 @@
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
-import uk.ac.ebi.spot.goci.model.Association;
-import uk.ac.ebi.spot.goci.model.AssociationDocument;
-import uk.ac.ebi.spot.goci.model.DiseaseTraitDocument;
-import uk.ac.ebi.spot.goci.model.EfoDocument;
-import uk.ac.ebi.spot.goci.model.StudyDocument;
+import uk.ac.ebi.spot.goci.model.*;
 
 import java.util.Collection;
 
@@ -17,7 +13,7 @@
  * @date 13/02/15
  */
 @Service
-public class StudyEnrichmentService implements DocumentEnrichmentService<StudyDocument> {
+public class StudyEnrichmentService implements DocumentEnrichmentService<StudyDocument, Study> {
     private final EfoDocumentCache efoCache;
     private final DiseaseTraitDocumentCache diseaseTraitCache;
     private final StudyDocumentCache studyDocumentCache;
@@ -39,19 +35,24 @@ public StudyEnrichmentService(AssociationService associationService,
         return 1;
     }
 
-    @Override public void doEnrichment(StudyDocument document) {
+    @Override public void doEnrichment(StudyDocument document, Study study) {
         long id = Long.valueOf(document.getId().split(":")[1]);
-        if(!studyDocumentCache.hasDocument(id)){
-            studyDocumentCache.addDocument(id, document);
-        }
+//        if(!studyDocumentCache.hasDocument(id)){
+//            studyDocumentCache.addDocument(id, document);
+//        }
 
-        Collection<Association> associations = associationService.findPublishedAssociationsByStudyId(id);
+        Collection<Association> associations = study.getAssociations();
         document.setAssociationCount(associations.size());
         associations.forEach(association -> document.embed(new AssociationDocument(association)));
 
-        traitService.findReportedTraitByStudyId(id).forEach(
-                trait -> document.embed(diseaseTraitCache.getDocument(trait.getTrait())));
-        traitService.findMappedTraitByStudyId(id).forEach(
+        document.embed(diseaseTraitCache.getDocument(study.getDiseaseTrait().getTrait()));
+        study.getEfoTraits().forEach(
                 trait -> document.embed(efoCache.getDocument(trait.getTrait())));
+        document.addBackgroundTraitName(study.getBackgroundTrait().getTrait());
+        study.getMappedBackgroundTraits().forEach(efoTrait -> {
+                document.addBackgroundEfoLabel(efoTrait.getTrait());
+                document.addBackgroundEfoUri(efoTrait.getUri());
+            }
+        );
     }
 }

goci-tools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/service/TraitEnrichmentService.java

@@ -2,11 +2,7 @@
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
-import uk.ac.ebi.spot.goci.model.AssociationDocument;
-import uk.ac.ebi.spot.goci.model.DiseaseTraitDocument;
-import uk.ac.ebi.spot.goci.model.EfoDocument;
-import uk.ac.ebi.spot.goci.model.EfoTrait;
-import uk.ac.ebi.spot.goci.model.StudyDocument;
+import uk.ac.ebi.spot.goci.model.*;
 
 import java.util.HashSet;
 import java.util.Set;
@@ -18,7 +14,7 @@
  * @date 13/02/15
  */
 @Service
-public class TraitEnrichmentService implements DocumentEnrichmentService<DiseaseTraitDocument> {
+public class TraitEnrichmentService implements DocumentEnrichmentService<DiseaseTraitDocument, DiseaseTrait> {
     private final EfoDocumentCache efoCache;
     private StudyService studyService;
     private AssociationService associationService;
@@ -38,7 +34,7 @@ public TraitEnrichmentService(StudyService studyService,
         return 3;
     }
 
-    @Override public void doEnrichment(DiseaseTraitDocument document) {
+    @Override public void doEnrichment(DiseaseTraitDocument document, DiseaseTrait diseaseTrait) {
         long id = Long.valueOf(document.getId().split(":")[1]);
         // Comment this part if you want to exclude the DiseaseTrait Doc Enrichment
         studyService.findByDiseaseTraitId(id).forEach(