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Merge branch 'release-1.1.3'
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@JacobsonMT
JacobsonMT committed May 25, 2018
2 parents 1126a61 + 22329d4 commit 0c1c7de
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Showing 6 changed files with 123 additions and 24 deletions.
2 changes: 1 addition & 1 deletion pom.xml
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Expand Up @@ -5,7 +5,7 @@

<groupId>ubc.pavlab</groupId>
<artifactId>rdp</artifactId>
<version>1.1.2</version>
<version>1.1.3</version>

<parent>
<groupId>org.springframework.boot</groupId>
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2 changes: 1 addition & 1 deletion src/main/java/ubc/pavlab/rdp/controllers/UserController.java
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Expand Up @@ -80,7 +80,7 @@ public Collection<UserGene> getGenes() {
}

@RequestMapping(value = "/user/term", method = RequestMethod.GET)
public Set<UserTerm> getTerms() {
public List<UserTerm> getTerms() {
return userService.findCurrentUser().getUserTerms();
}

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7 changes: 2 additions & 5 deletions src/main/java/ubc/pavlab/rdp/model/User.java
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Expand Up @@ -12,10 +12,7 @@
import ubc.pavlab.rdp.model.enums.TierType;

import javax.persistence.*;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.*;
import java.util.stream.Collectors;


Expand Down Expand Up @@ -75,7 +72,7 @@ public class User {
@org.hibernate.annotations.Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
@OneToMany(cascade = CascadeType.ALL, orphanRemoval = true)
@JoinColumn(name = "user_id")
private Set<UserTerm> userTerms = new HashSet<>();
private List<UserTerm> userTerms = new ArrayList<>();

@org.hibernate.annotations.Cache(usage = CacheConcurrencyStrategy.READ_WRITE)
@OneToMany(cascade = CascadeType.ALL, orphanRemoval = true, mappedBy = "user")
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2 changes: 1 addition & 1 deletion src/main/java/ubc/pavlab/rdp/model/UserGene.java
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Expand Up @@ -24,7 +24,7 @@
@Getter
@Setter
@NoArgsConstructor
@ToString
@ToString(callSuper = true)
public class UserGene extends Gene {

@Id
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2 changes: 1 addition & 1 deletion src/main/java/ubc/pavlab/rdp/services/UserServiceImpl.java
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Expand Up @@ -392,7 +392,7 @@ public User confirmVerificationToken( String token ) {
}

private Collection<Gene> calculatedGenesInTaxon( User user, Taxon taxon ) {
return goService.getGenes( user.getUserTerms(), taxon );
return goService.getGenes( user.getTermsByTaxon( taxon ), taxon );
}

private boolean removeGenesFromUserByTaxon( User user, Taxon taxon ) {
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132 changes: 117 additions & 15 deletions src/test/java/ubc/pavlab/rdp/services/UserServiceImplTest.java
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Expand Up @@ -715,12 +715,12 @@ public void updateTermsAndGenesInTaxon_whenUserHasNoGeneOrTerms() {

userService.updateTermsAndGenesInTaxon( user, taxon, geneTierMap, terms );

assertThatUserTermsAreEqualTo( user, terms );
assertThatUserTermsAreEqualTo( user, taxon, terms );

Map<Gene, TierType> expectedGenes = new HashMap<>( geneTierMap );
calculatedGenes.forEach( g -> expectedGenes.putIfAbsent( g, TierType.TIER3 ) );

assertThatUserGenesAreEqualTo( user, expectedGenes );
assertThatUserGenesAreEqualTo( user, taxon, expectedGenes );

}

Expand Down Expand Up @@ -757,12 +757,70 @@ public void updateTermsAndGenesInTaxon_whenUserHasGenesAndTerms() {

userService.updateTermsAndGenesInTaxon( user, taxon, geneTierMap, terms );

assertThatUserTermsAreEqualTo( user, terms );
assertThatUserTermsAreEqualTo( user, taxon, terms );

Map<Gene, TierType> expectedGenes = new HashMap<>( geneTierMap );
calculatedGenes.forEach( g -> expectedGenes.putIfAbsent( g, TierType.TIER3 ) );

assertThatUserGenesAreEqualTo( user, expectedGenes );
assertThatUserGenesAreEqualTo( user, taxon, expectedGenes );

}

@Test
public void updateTermsAndGenesInTaxon_whenUserHasGenesAndTermsInMultipleTaxons() {
User user = createUser( 1 );

Taxon taxon = createTaxon( 1 );
Gene geneWillBeRemoved = createGene( 999, taxon );
GeneOntologyTerm termWillBeRemoved = createTermWithGene( toGOId( geneWillBeRemoved.getGeneId() ), geneWillBeRemoved );
user.getUserTerms().add( createUserTerm( 1, termWillBeRemoved, taxon ) );
user.getUserGenes().put( geneWillBeRemoved.getGeneId(), createUserGene( 1, geneWillBeRemoved, user, TierType.TIER1 ) );

Gene geneWillChangeTier = createGene( 5, taxon );
GeneOntologyTerm termWillRemain = createTermWithGene( toGOId( geneWillChangeTier.getGeneId() ), geneWillChangeTier );
user.getUserTerms().add( createUserTerm( 2, termWillRemain, taxon ) );
user.getUserGenes().put( geneWillChangeTier.getGeneId(), createUserGene( 2, geneWillChangeTier, user, TierType.TIER3 ) );

// Taxon 2
Taxon taxon2 = createTaxon( 2 );
Gene geneOtherTaxon = createGene( 9999, taxon2 );
GeneOntologyTerm termOtherTaxon = createTermWithGene( toGOId( geneOtherTaxon.getGeneId() ), geneOtherTaxon );
user.getUserTerms().add( createUserTerm( 3, termOtherTaxon, taxon2 ) );
user.getUserGenes().put( geneOtherTaxon.getGeneId(), createUserGene( 3, geneOtherTaxon, user, TierType.TIER1 ) );

Gene geneOtherTaxon2 = createGene( 5555, taxon2 );
GeneOntologyTerm termOtherTaxon2 = createTermWithGene( toGOId( geneOtherTaxon2.getGeneId() ), geneOtherTaxon2 );
user.getUserTerms().add( createUserTerm( 4, termOtherTaxon2, taxon2 ) );
user.getUserGenes().put( geneOtherTaxon2.getGeneId(), createUserGene( 4, geneOtherTaxon2, user, TierType.TIER3 ) );

becomeUser( user );

Collection<GeneOntologyTerm> terms = IntStream.range( 1, 10 ).boxed().map(
nbr -> createTermWithGene( toGOId( nbr ), createGene( nbr, taxon ) )
).collect( Collectors.toSet() );

Mockito.when( goService.getGenes( Mockito.anyCollectionOf( GeneOntologyTerm.class ), Mockito.any() ) )
.then( i -> {
Collection<GeneOntologyTerm> givenTerms = i.getArgumentAt( 0, Collection.class );
return givenTerms.stream().flatMap( t -> t.getDirectGenes().stream() ).collect( Collectors.toSet() );
} );

Map<Gene, TierType> geneTierMap = Maps.newHashMap( geneWillChangeTier, TierType.TIER1 );

userService.updateTermsAndGenesInTaxon( user, taxon, geneTierMap, terms );

assertThatUserTermsAreEqualTo( user, taxon, terms );
assertThatUserTermsAreEqualTo( user, taxon2, Sets.newSet( termOtherTaxon, termOtherTaxon2 ) );

Map<Gene, TierType> expectedGenes = new HashMap<>( geneTierMap );
terms.stream().flatMap( t -> t.getDirectGenes().stream() ).forEach( g -> expectedGenes.putIfAbsent( g, TierType.TIER3 ) );

Map<Gene, TierType> expectedGenesTaxon2 = new HashMap<>();
expectedGenesTaxon2.put( geneOtherTaxon, TierType.TIER1 );
expectedGenesTaxon2.put( geneOtherTaxon2, TierType.TIER3 );

assertThatUserGenesAreEqualTo( user, taxon, expectedGenes );
assertThatUserGenesAreEqualTo( user, taxon2, expectedGenesTaxon2 );

}

Expand All @@ -788,12 +846,12 @@ public void updateTermsAndGenesInTaxon_whenManualAndCalculatedGenesOverlap_thenK

userService.updateTermsAndGenesInTaxon( user, taxon, geneTierMap, terms );

assertThatUserTermsAreEqualTo( user, terms );
assertThatUserTermsAreEqualTo( user, taxon, terms );

Map<Gene, TierType> expectedGenes = new HashMap<>( geneTierMap );
calculatedGenes.forEach( g -> expectedGenes.putIfAbsent( g, TierType.TIER3 ) );

assertThatUserGenesAreEqualTo( user, expectedGenes );
assertThatUserGenesAreEqualTo( user, taxon, expectedGenes );
}

@Test
Expand Down Expand Up @@ -827,12 +885,12 @@ public void updateTermsAndGenesInTaxon_whenOldAndNewOverlap_thenRetainIds() {
userService.updateTermsAndGenesInTaxon( user, taxon, geneTierMap, terms );

// Might as well test this
assertThatUserTermsAreEqualTo( user, terms );
assertThatUserTermsAreEqualTo( user, taxon, terms );

Map<Gene, TierType> expectedGenes = new HashMap<>( geneTierMap );
calculatedGenes.forEach( g -> expectedGenes.putIfAbsent( g, TierType.TIER3 ) );

assertThatUserGenesAreEqualTo( user, expectedGenes );
assertThatUserGenesAreEqualTo( user, taxon, expectedGenes );

// This is really why we're here
assertThat( user.getUserTerms().iterator().next().getId() ).isEqualTo( 1 );
Expand Down Expand Up @@ -873,16 +931,60 @@ public void updateTermsAndGenesInTaxon_whenUserHasGenesAndTerms_thenUpdateFreque

}

private void assertThatUserTermsAreEqualTo( User user, Collection<GeneOntologyTerm> terms ) {
assertThat( user.getUserTerms() ).hasSize( terms.size() );
assertThat( user.getUserTerms().stream().map( GeneOntologyTerm::getGoId ).collect( Collectors.toSet() ) )
@Test
public void updateTermsAndGenesInTaxon_whenTermsOverlapInDifferentSpecies_thenKeepBothTerms() {
User user = createUser( 1 );
Taxon taxon = createTaxon( 1 );
Taxon taxon2 = createTaxon( 2 );

// These should retain ids so that Hibernate does not delete and re insert rows
Gene geneInTaxon1 = createGene( 5, taxon );
GeneOntologyTerm termInTaxon1 = createTermWithGene( toGOId( geneInTaxon1.getGeneId() ), geneInTaxon1 );
user.getUserTerms().add( createUserTerm( 1, termInTaxon1, taxon ) );
user.getUserGenes().put( geneInTaxon1.getGeneId(), createUserGene( 1, geneInTaxon1, user, TierType.TIER3 ) );

Gene geneInTaxon2 = createGene( 105, taxon2 );
GeneOntologyTerm termInTaxon2 = createTermWithGene( toGOId( geneInTaxon2.getGeneId() ), geneInTaxon2 );
user.getUserTerms().add( createUserTerm( 2, termInTaxon2, taxon2 ) );
user.getUserGenes().put( geneInTaxon2.getGeneId(), createUserGene( 2, geneInTaxon2, user, TierType.TIER3 ) );

becomeUser( user );

// Mock goService.getRelatedGenes
Collection<Gene> calculatedGenes = Collections.singleton( createGene( 205, taxon ) );
Mockito.when( goService.getGenes( Mockito.anyCollectionOf( GeneOntologyTerm.class ), Mockito.eq( taxon ) ) ).thenReturn( calculatedGenes );
Mockito.when( goService.getGenes( Mockito.anyCollectionOf( GeneOntologyTerm.class ), Mockito.eq( taxon2 ) ) ).thenReturn( Collections.emptySet() );

// Attempting to add term to taxon 1 that is already present in taxon 2
Collection<GeneOntologyTerm> terms = Collections.singleton( createTermWithGene( toGOId( 105 ), createGene( 1005, taxon ) ) );

Map<Gene, TierType> geneTierMap = terms.stream()
.flatMap( t -> t.getDirectGenes().stream() )
.collect( Collectors.toMap( Function.identity(), g -> TierType.TIER1 ) );

userService.updateTermsAndGenesInTaxon( user, taxon, geneTierMap, terms );

// Why we are here
assertThatUserTermsAreEqualTo( user, taxon, terms );
assertThatUserTermsAreEqualTo( user, taxon2, Collections.singleton( termInTaxon2 ));

Map<Gene, TierType> expectedGenes = new HashMap<>( geneTierMap );
calculatedGenes.forEach( g -> expectedGenes.putIfAbsent( g, TierType.TIER3 ) );

assertThatUserGenesAreEqualTo( user, taxon, expectedGenes );
assertThatUserGenesAreEqualTo( user, taxon2, Maps.newHashMap( geneInTaxon2, TierType.TIER3 ) );

}

private void assertThatUserTermsAreEqualTo( User user, Taxon taxon, Collection<GeneOntologyTerm> terms ) {
assertThat( user.getUserTerms().stream().filter( t -> t.getTaxon().equals( taxon ) ).count() ).isEqualTo( terms.size() );
assertThat( user.getUserTerms().stream().filter( t -> t.getTaxon().equals( taxon ) ).map( GeneOntologyTerm::getGoId ).collect( Collectors.toSet() ) )
.isEqualTo( terms.stream().map( GeneOntologyTerm::getGoId ).collect( Collectors.toSet() ) );
}

private void assertThatUserGenesAreEqualTo( User user, Map<Gene, TierType> expectedGenes ) {
assertThat( user.getUserGenes().keySet() )
.containsExactlyElementsOf( expectedGenes.keySet().stream().map( Gene::getGeneId )
.collect( Collectors.toSet() ) );
private void assertThatUserGenesAreEqualTo( User user, Taxon taxon, Map<Gene, TierType> expectedGenes ) {
assertThat( user.getGenesByTaxon( taxon ) )
.containsExactlyElementsOf( expectedGenes.keySet() );
expectedGenes.forEach( ( g, tier ) -> assertThat( user.getUserGenes().get( g.getGeneId() ).getTier() ).isEqualTo( tier ) );
}

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