Merge pull request #439 from EBISPOT/goci#166_split_and_index_bg_traits

Goci#166 split and index bg traits
EBISPOT · Jul 26, 2021 · fbcbfd9 · fbcbfd9
2 parents e6b267d + 1d0190b
commit fbcbfd9
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Showing 18 changed files with 202 additions and 8 deletions.
diff --git a/...ci-db-binding/src/main/resources/db/migration/V2.7_0_002__Add_background_associations.sql b/...ci-db-binding/src/main/resources/db/migration/V2.7_0_002__Add_background_associations.sql
@@ -0,0 +1,21 @@
+/*
+
+################################################################################
+
+Migration script to create table ASSOCIATION_BKG_EFO_TRAIT and its constraints
+
+author: Ala Abid
+date:    07 jun 2021
+version: 2.7.0.002
+################################################################################
+*/
+
+--------------------------------------------------------
+--  CREATE TABLE, INDEX, FOREIGN KEY
+--------------------------------------------------------
+
+CREATE TABLE ASSOCIATION_BKG_EFO_TRAIT (ASSOCIATION_ID NUMBER(19,0), EFO_TRAIT_ID NUMBER(19,0));
+ALTER TABLE ASSOCIATION_BKG_EFO_TRAIT MODIFY (EFO_TRAIT_ID NOT NULL);
+ALTER TABLE ASSOCIATION_BKG_EFO_TRAIT MODIFY (ASSOCIATION_ID NOT NULL);
+ALTER TABLE ASSOCIATION_BKG_EFO_TRAIT ADD CONSTRAINT ASSC_BKG_EFO_ASSC_ID_FK FOREIGN KEY (ASSOCIATION_ID) REFERENCES ASSOCIATION (ID);
+ALTER TABLE ASSOCIATION_BKG_EFO_TRAIT ADD CONSTRAINT ASSC_BKG_EFO_TRAIT_ID_FK FOREIGN KEY (EFO_TRAIT_ID) REFERENCES EFO_TRAIT (ID);
diff --git a/goci-core/goci-model/src/main/java/uk/ac/ebi/spot/goci/model/Association.java b/goci-core/goci-model/src/main/java/uk/ac/ebi/spot/goci/model/Association.java
@@ -80,6 +80,12 @@ public class Association implements Trackable {
                inverseJoinColumns = @JoinColumn(name = "EFO_TRAIT_ID"))
     private Collection<EfoTrait> efoTraits = new ArrayList<>();
 
+    @ManyToMany
+    @JoinTable(name = "ASSOCIATION_BKG_EFO_TRAIT",
+            joinColumns = @JoinColumn(name = "ASSOCIATION_ID"),
+            inverseJoinColumns = @JoinColumn(name = "EFO_TRAIT_ID"))
+    private Collection<EfoTrait> bkgEfoTraits = new ArrayList<>();
+
     @JsonIgnore
     @OneToOne(mappedBy = "association", orphanRemoval = true)
     private AssociationReport associationReport;
@@ -165,6 +171,7 @@ public Association(String riskFrequency,
                        Study study,
                        Collection<Locus> loci,
                        Collection<EfoTrait> efoTraits,
+                       Collection<EfoTrait> bkgEfoTraits,
                        AssociationReport associationReport,
                        Collection<AssociationValidationReport> associationValidationReport,
                        Date lastMappingDate,
@@ -193,6 +200,7 @@ public Association(String riskFrequency,
         this.study = study;
         this.loci = loci;
         this.efoTraits = efoTraits;
+        this.bkgEfoTraits = bkgEfoTraits;
         this.associationReport = associationReport;
         this.associationValidationReports = associationValidationReport;
         this.lastMappingDate = lastMappingDate;
@@ -343,6 +351,18 @@ public void addEfoTrait(EfoTrait efoTrait) {
         efoTraits.add(efoTrait);
     }
 
+    public Collection<EfoTrait> getBkgEfoTraits() {
+        return bkgEfoTraits;
+    }
+
+    public void setBkgEfoTraits(Collection<EfoTrait> bkgEfoTraits) {
+        this.bkgEfoTraits = bkgEfoTraits;
+    }
+
+    public void addBkgEfoTrait(EfoTrait bkgEfoTrait) {
+        bkgEfoTraits.add(bkgEfoTrait);
+    }
+
     public Boolean getSnpApproved() {
         return snpApproved;
     }

diff --git a/goci-core/goci-model/src/main/java/uk/ac/ebi/spot/goci/model/EfoTrait.java b/goci-core/goci-model/src/main/java/uk/ac/ebi/spot/goci/model/EfoTrait.java
@@ -33,9 +33,15 @@ public class EfoTrait {
     @ManyToMany(mappedBy = "efoTraits")
     private Collection<Study> studies;
 
+    @ManyToMany(mappedBy = "mappedBackgroundTraits")
+    private Collection<Study> studiesBkg;
+
     @ManyToMany(mappedBy = "efoTraits")
     private Collection<Association> associations;
 
+    @ManyToMany(mappedBy = "bkgEfoTraits")
+    private Collection<Association> associationsBkg;
+
     // JPA no-args constructor
     public EfoTrait() {
     }
@@ -84,6 +90,14 @@ public void setStudies(Collection<Study> studies) {
         this.studies = studies;
     }
 
+    public Collection<Study> getStudiesBkg() {
+        return studiesBkg;
+    }
+
+    public void setStudiesBkg(Collection<Study> studiesBkg) {
+        this.studiesBkg = studiesBkg;
+    }
+
     public Collection<Association> getAssociations() {
         return associations;
     }
@@ -92,6 +106,14 @@ public void setAssociations(Collection<Association> associations) {
         this.associations = associations;
     }
 
+    public Collection<Association> getAssociationsBkg() {
+        return associationsBkg;
+    }
+
+    public void setAssociationsBkg(Collection<Association> associationsBkg) {
+        this.associationsBkg = associationsBkg;
+    }
+
     public String getShortForm() {
         return shortForm;
     }

diff --git a/goci-core/goci-model/src/main/java/uk/ac/ebi/spot/goci/model/Study.java b/goci-core/goci-model/src/main/java/uk/ac/ebi/spot/goci/model/Study.java
@@ -93,7 +93,7 @@ public class Study implements Trackable {
             inverseJoinColumns = @JoinColumn(name = "DISEASE_TRAIT_ID"))
     private DiseaseTrait backgroundTrait;
 
-    @ManyToMany()
+    @ManyToMany
     @JoinTable(name = "STUDY_BACKGROUND_EFO_TRAIT",
             joinColumns = @JoinColumn(name = "STUDY_ID"),
             inverseJoinColumns = @JoinColumn(name = "EFO_TRAIT_ID"))

diff --git a/...core/goci-repository/src/main/java/uk/ac/ebi/spot/goci/repository/EfoTraitRepository.java b/...core/goci-repository/src/main/java/uk/ac/ebi/spot/goci/repository/EfoTraitRepository.java
@@ -35,6 +35,10 @@ public interface EfoTraitRepository extends JpaRepository<EfoTrait, Long> {
     List<EfoTrait> findByStudiesIdAndStudiesHousekeepingCatalogPublishDateIsNotNullAndStudiesHousekeepingCatalogUnpublishDateIsNull(
             Long studyId);
 
+    @RestResource(exported = false)
+    List<EfoTrait> findByStudiesBkgIdAndStudiesBkgHousekeepingCatalogPublishDateIsNotNullAndStudiesBkgHousekeepingCatalogUnpublishDateIsNull(
+            Long studyId);
+
     @RestResource(exported = false)
     List<EfoTrait> findByStudiesIdAndStudiesHousekeepingCatalogPublishDateIsNotNullAndStudiesHousekeepingCatalogUnpublishDateIsNull(
             Sort sort,
@@ -51,6 +55,10 @@ Page<EfoTrait> findByStudiesIdAndStudiesHousekeepingCatalogPublishDateIsNotNullA
     @Query("select e.trait from EfoTrait e join e.associations a where a.id = :associationId")
     List<String> findTraitNamesByAssociationsId(Long associationId);
 
+    @RestResource(exported = false)
+    @Query("select e.trait from EfoTrait e join e.associationsBkg a where a.id = :associationId")
+    List<String> findBkgTraitNamesByAssociationsId(Long associationId);
+
     @RestResource(exported = false)
     List<EfoTrait> findByAssociationsId(Sort sort, Long associationId);
 

diff --git a/goci-core/goci-service/src/main/java/uk/ac/ebi/spot/goci/service/TraitService.java b/goci-core/goci-service/src/main/java/uk/ac/ebi/spot/goci/service/TraitService.java
@@ -44,6 +44,11 @@ public Collection<EfoTrait> findMappedTraitByStudyId(Long studyId) {
                 studyId);
     }
 
+    public Collection<EfoTrait> findMappedBkgTraitByStudyId(Long studyId) {
+        return efoTraitRepository.findByStudiesBkgIdAndStudiesBkgHousekeepingCatalogPublishDateIsNotNullAndStudiesBkgHousekeepingCatalogUnpublishDateIsNull(
+                studyId);
+    }
+
     public Collection<EfoTrait> findMappedTraitByAssociationId(Long associationId) {
         return efoTraitRepository.findByAssociationsId(associationId);
     }
@@ -52,6 +57,10 @@ public Collection<String> findMappedTraitNamesByAssociationId(Long associationId
         return efoTraitRepository.findTraitNamesByAssociationsId(associationId);
     }
 
+    public Collection<String> findMappedBkgTraitNamesByAssociationId(Long associationId) {
+        return efoTraitRepository.findBkgTraitNamesByAssociationsId(associationId);
+    }
+
     @Transactional(readOnly = true)
     public List<EfoTrait> findAllEfoTraits() {
         List<EfoTrait> allEfoTraits = efoTraitRepository.findAll();

diff --git a/...curation/src/main/java/uk/ac/ebi/spot/goci/curation/controller/AssociationController.java b/...curation/src/main/java/uk/ac/ebi/spot/goci/curation/controller/AssociationController.java
@@ -1300,6 +1300,7 @@ public String applyStudyEFOtraitToSnps(Model model, @PathVariable Long studyId,
         associations.addAll(associationRepository.findByStudyId(studyId));
         Study study = studyRepository.findOne((studyId));
         Collection<EfoTrait> efoTraits = study.getEfoTraits();
+        Collection<EfoTrait> backgroundEfoTraits = study.getMappedBackgroundTraits();
 
 
         if (associations.size() == 0 || efoTraits.size() == 0) {
@@ -1321,6 +1322,8 @@ public String applyStudyEFOtraitToSnps(Model model, @PathVariable Long studyId,
                 associationTraits.add(efoTrait);
             }
 
+            Collection<EfoTrait> associationBackgroundTraits = new ArrayList<>(backgroundEfoTraits);
+
             for (Association association : associations) {
                 if (association.getEfoTraits().size() != 0 && !overwrite) {
                     for (EfoTrait trait : associationTraits) {
@@ -1332,6 +1335,7 @@ public String applyStudyEFOtraitToSnps(Model model, @PathVariable Long studyId,
                 else {
                     association.setEfoTraits(associationTraits);
                 }
+                association.setBkgEfoTraits(associationBackgroundTraits);
                 association.setLastUpdateDate(new Date());
                 associationRepository.save(association);
             }
@@ -1677,4 +1681,4 @@ public String getValidationResult(@PathVariable Long studyId, HttpSession sessio
     }
 
 
-}
+}
diff --git a/...ci-curation/src/main/java/uk/ac/ebi/spot/goci/curation/model/SnpAssociationTableView.java b/...ci-curation/src/main/java/uk/ac/ebi/spot/goci/curation/model/SnpAssociationTableView.java
@@ -41,6 +41,8 @@ public class SnpAssociationTableView {
 
     private String efoTraits;
 
+    private String backgroundEfoTraits;
+
     private Float orPerCopyNum;
 
     private Float orPerCopyRecip;
@@ -93,6 +95,7 @@ public SnpAssociationTableView(Long associationId,
                                    String betaUnit,
                                    String description,
                                    String efoTraits,
+                                   String backgroundEfoTraits,
                                    String lastMappingDate,
                                    String lastMappingPerformedBy,
                                    String multiSnpHaplotype,
@@ -120,6 +123,7 @@ public SnpAssociationTableView(Long associationId,
         this.betaUnit = betaUnit;
         this.description = description;
         this.efoTraits = efoTraits;
+        this.backgroundEfoTraits = backgroundEfoTraits;
         this.lastMappingDate = lastMappingDate;
         this.lastMappingPerformedBy = lastMappingPerformedBy;
         this.multiSnpHaplotype = multiSnpHaplotype;
@@ -213,6 +217,14 @@ public void setEfoTraits(String efoTraits) {
         this.efoTraits = efoTraits;
     }
 
+    public String getBackgroundEfoTraits() {
+        return backgroundEfoTraits;
+    }
+
+    public void setBackgroundEfoTraits(String backgroundEfoTraits) {
+        this.backgroundEfoTraits = backgroundEfoTraits;
+    }
+
     public String getLastMappingDate() {
         return lastMappingDate;
     }
@@ -376,4 +388,4 @@ public AssociationExtension getAssociationExtension() {
     public void setAssociationExtension(AssociationExtension associationExtension) {
         this.associationExtension = associationExtension;
     }
-}
+}
diff --git a/...on/src/main/java/uk/ac/ebi/spot/goci/curation/service/SnpAssociationTableViewService.java b/...on/src/main/java/uk/ac/ebi/spot/goci/curation/service/SnpAssociationTableViewService.java
@@ -223,6 +223,13 @@ public SnpAssociationTableView createSnpAssociationTableView(Association associa
         associationEfoTraits = String.join(", ", efoTraits);
         snpAssociationTableView.setEfoTraits(associationEfoTraits);
 
+        Collection<String> backgroundEfoTraits = new ArrayList<>();
+        for (EfoTrait efoTrait: association.getBkgEfoTraits()) {
+            backgroundEfoTraits.add(efoTrait.getTrait());
+        }
+        String associationBackgroundEfoTraits = String.join(",", backgroundEfoTraits);
+        snpAssociationTableView.setBackgroundEfoTraits(associationBackgroundEfoTraits);
+
         // Set OR values
         snpAssociationTableView.setOrPerCopyNum(association.getOrPerCopyNum());
         snpAssociationTableView.setOrPerCopyRecip(association.getOrPerCopyRecip());

diff --git a/goci-interfaces/goci-curation/src/main/resources/templates/study_association.html b/goci-interfaces/goci-curation/src/main/resources/templates/study_association.html
@@ -182,6 +182,7 @@
                     <th style="font-size: small">p-Value (mantissa x 10 exponent)</th>
                     <th style="font-size: small">p-Value Description</th>
                     <th style="font-size: small">EFO trait</th>
+                    <th style="font-size: small">Background EFO trait</th>
                     <th style="font-size: small">OR</th>
                     <th style="font-size: small">OR reciprocal</th>
                     <th style="font-size: small">Beta</th>
@@ -485,6 +486,13 @@
                                        th:text="'Warning: EFO trait not assigned'"></span>
                                 </td>
 
+                                <td>
+                                    <p th:text="${snpAssociationTableView.backgroundEfoTraits} ?: ''"></p>
+                                    <span style="font-style: italic; color:red; font-size: small"
+                                          th:if="*{#strings.isEmpty(snpAssociationTableView.backgroundEfoTraits)}"
+                                          th:text="'Warning: EFO trait not assigned'"></span>
+                                </td>
+
                                 <td th:text="${snpAssociationTableView.orPerCopyNum} ?: ''"></td>
                                 <td>
                                     <p th:text="${snpAssociationTableView.orPerCopyRecip} ?: ''"></p>
@@ -616,4 +624,4 @@
 </script>
 
 </body>
-</html>
+</html>
diff --git a/goci-interfaces/goci-solr/src/main/resources/solr/solr/gwas/conf/schema.xml b/goci-interfaces/goci-solr/src/main/resources/solr/solr/gwas/conf/schema.xml
@@ -190,6 +190,10 @@
     <field name="mappedLabel" type="text_general" indexed="true" stored="true" multiValued="true" />
     <field name="mappedUri" type="text_general" indexed="true" stored="true" multiValued="true" />
 
+    <!-- background efotrait -->
+    <field name="mappedBkgLabel" type="text_general" indexed="true" stored="true" multiValued="true" />
+    <field name="mappedBkgUri" type="text_general" indexed="true" stored="true" multiValued="true" />
+
     <!-- ontology expanded info -->
     <field name="trait" type="text_general" indexed="true" stored="true" multiValued="true" />
     <field name="traitUri" type="text_general" indexed="true" stored="true" multiValued="true" />
@@ -401,6 +405,8 @@
     <copyField source="traitName" dest="text" />
     <copyField source="mappedLabel" dest="text" />
     <copyField source="mappedUri" dest="text" />
+    <copyField source="mappedBkgLabel" dest="text" />
+    <copyField source="mappedBkgUri" dest="text" />
     <copyField source="trait" dest="text" />
     <copyField source="traitUri" dest="text" />
     <copyField source="shortForm" dest="text" />

diff --git a/...-tools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/model/AssociationDocument.java b/...-tools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/model/AssociationDocument.java
@@ -174,6 +174,12 @@ public class AssociationDocument extends OntologyEnabledDocument<Association> {
     @Field("mappedUri")
     private Collection<String> mappedUris;
 
+    // embedded background EfoTrait info
+    @Field("mappedBkgLabel")
+    private Collection<String> mappedBkgLabels;
+    @Field("mappedBkgUri")
+    private Collection<String> mappedBkgUris;
+
     public AssociationDocument(Association association) {
         super(association);
         this.riskFrequency = association.getRiskFrequency();
@@ -221,6 +227,9 @@ public AssociationDocument(Association association) {
         this.mappedLabels = new LinkedHashSet<>();
         this.mappedUris = new LinkedHashSet<>();
 
+        this.mappedBkgLabels = new LinkedHashSet<>();
+        this.mappedBkgUris = new LinkedHashSet<>();
+
         this.ancestralGroups = new LinkedHashSet<>();
         this.countriesOfOrigin = new LinkedHashSet<>();
         this.countriesOfRecruitment = new LinkedHashSet<>();
@@ -434,6 +443,14 @@ public void addMappedUri(String mappedUri) {
         this.mappedUris.add(mappedUri);
     }
 
+    public void addMappedBkgUri(String mappedBkgUri) {
+        this.mappedBkgUris.add(mappedBkgUri);
+    }
+
+    public void addMappedBkgLabel(String mappedBkgLabel) {
+        this.mappedBkgLabels.add(mappedBkgLabel);
+    }
+
     public void addStudyId(String studyId) {
         this.studyIds.add(studyId);
     }

diff --git a/...ools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/model/BackgroundEfoDocument.java b/...ools/goci-solr-indexer/src/main/java/uk/ac/ebi/spot/goci/model/BackgroundEfoDocument.java
@@ -0,0 +1,29 @@
+package uk.ac.ebi.spot.goci.model;
+
+import org.apache.solr.client.solrj.beans.Field;
+
+/**
+ * Javadocs go here!
+ *
+ * @author Ala Abid
+ * @date 26/05/21
+ */
+public class BackgroundEfoDocument extends OntologyEnabledDocument<EfoTrait> {
+    @Field private String mappedBkgLabel;
+    @Field private String mappedBkgUri;
+
+    public BackgroundEfoDocument(EfoTrait efoTrait) {
+        super(efoTrait);
+        this.mappedBkgLabel = efoTrait.getTrait();
+        this.mappedBkgUri = efoTrait.getUri();
+        // addTraitUri(mappedBkgUri);
+    }
+
+    public String getMappedBkgLabel() {
+        return mappedBkgLabel;
+    }
+
+    public String getMappedBkgUri() {
+        return mappedBkgUri;
+    }
+}