erd

build.gradle.kts

@@ -33,6 +33,7 @@ dependencies {
 	annotationProcessor("org.projectlombok:lombok")
 	testImplementation("org.springframework.boot:spring-boot-starter-test")
 	testImplementation("de.flapdoodle.embed:de.flapdoodle.embed.mongo.spring30x:4.6.1")
+
 }
 
 //dependencyManagement {
@@ -61,12 +62,6 @@ testing {
 				implementation("org.springframework.boot:spring-boot-starter-web")
 			}
 
-//			sources {
-//				java {
-//					setSrcDirs(listOf("src/integrationTest/java"))
-//				}
-//			}
-
 			targets {
 				all {
 					testTask.configure {

erd.md

@@ -0,0 +1,33 @@
+```mermaid
+erDiagram
+    Cohort {
+        string name
+        number enrollment
+
+    }
+
+    Dataset {
+        string name
+        URL url
+    }
+
+    StandardField {
+        string name
+        type type
+        ontology ontology
+    }
+
+    CohortField {
+        string category
+        string name
+        type type
+        range range
+        MappingStrategy mappingStrategy
+    }
+
+
+
+    CohortField 1--1 StandardField: ""
+    Cohort 1--1+ CohortField: ""
+    Cohort 1--1+ Dataset: ""
+```

src/integrationTest/java/uk/ac/ebi/biosamples/cohortatlas/repository/CohortSearchRepositoryIntegrationTest.java

@@ -19,7 +19,7 @@ class CohortSearchRepositoryIntegrationTest {
   @Autowired
   private CohortService cohortService;
   @Autowired
-  private CohortSearchRepository cohortSearchRepository;
+  private CohortRepository cohortSearchRepository;
 
 
   @Test
@@ -36,7 +36,7 @@ void findPage() {
     cohort.setAcronym("CHILD");
     cohortService.saveCohort(cohort);
 
-    Page<Cohort> page = cohortSearchRepository.findPageWithFilters(PageRequest.of(0, 5), "CohortSearchRepositoryIntegrationTest", "cohortName", Collections.emptyList());
+    Page<Cohort> page = cohortSearchRepository.findByFilters(PageRequest.of(0, 5), "CohortSearchRepositoryIntegrationTest", "cohortName", Collections.emptyList());
     Assertions.assertTrue(page.getSize() > 1);
     Assertions.assertEquals("SearchRepositoryIntegrationTest_freeTextSearch_1", page.getContent().get(0).getCohortName());
   }

src/main/java/uk/ac/ebi/biosamples/cohortatlas/repository/CohortRepository.java

@@ -8,6 +8,6 @@
 import uk.ac.ebi.biosamples.cohortatlas.model.Cohort;
 
 @Repository
-public interface CohortRepository extends MongoRepository<Cohort, String> {
+public interface CohortRepository extends MongoRepository<Cohort, String>, SearchRepository {
   Page<Cohort> findAllBy(TextCriteria criteria, Pageable pageable);
 }

src/main/java/uk/ac/ebi/biosamples/cohortatlas/repository/CohortSearchRepository.java

@@ -1,24 +1,23 @@
 package uk.ac.ebi.biosamples.cohortatlas.repository;
 
+import lombok.RequiredArgsConstructor;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.mongodb.core.MongoTemplate;
 import org.springframework.data.mongodb.core.query.Query;
 import org.springframework.data.support.PageableExecutionUtils;
-import org.springframework.stereotype.Repository;
 import uk.ac.ebi.biosamples.cohortatlas.model.Cohort;
 
 import java.util.List;
 
-@Repository
-public class CohortSearchRepository extends SearchRepository {
+@RequiredArgsConstructor
+public class CohortSearchRepository implements SearchRepository <Cohort>{
 
-  public CohortSearchRepository(MongoTemplate mongoTemplate) {
-    super(mongoTemplate);
-  }
+  private final SearchQueryHelper searchQueryHelper = new SearchQueryHelper();
+  protected MongoTemplate mongoTemplate;
 
-  public Page<Cohort> findPageWithFilters(Pageable page, String text, String sort, List<String> filters) {
-    Query query = getSearchQuery(page, text, sort, filters);
+  public Page<Cohort> findByFilters(Pageable page, String text, String sort, List<String> filters) {
+    Query query = searchQueryHelper.getSearchQuery(page, text, sort, filters);
     List<Cohort> cohorts = mongoTemplate.find(query, Cohort.class);
 
     return PageableExecutionUtils.getPage(cohorts, page,

src/main/java/uk/ac/ebi/biosamples/cohortatlas/repository/FieldRepository.java

@@ -8,7 +8,7 @@
 import java.util.List;
 import java.util.Map;
 
-public interface FieldRepository extends MongoRepository<DictionaryField, String> {
+public interface FieldRepository extends MongoRepository<DictionaryField, String>, SearchRepository<DictionaryField> {
   List<DictionaryField> findByCohort(String cohort);
 
   @Aggregation(pipeline = {

src/main/java/uk/ac/ebi/biosamples/cohortatlas/repository/FieldSearchRepository.java

@@ -1,5 +1,6 @@
 package uk.ac.ebi.biosamples.cohortatlas.repository;
 
+import lombok.RequiredArgsConstructor;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.mongodb.core.MongoTemplate;
@@ -10,14 +11,13 @@
 
 import java.util.List;
 
-@Repository
-public class FieldSearchRepository extends SearchRepository {
-  public FieldSearchRepository(MongoTemplate mongoTemplate) {
-    super(mongoTemplate);
-  }
+@RequiredArgsConstructor
+public class FieldSearchRepository implements SearchRepository<DictionaryField> {
+  protected MongoTemplate mongoTemplate;
+  private final SearchQueryHelper searchQueryHelper = new SearchQueryHelper();
 
-  public Page<DictionaryField> findFieldPageWithFilters(Pageable page, String text, String sort, List<String> filters) {
-    Query query = getSearchQuery(page, text, sort, filters);
+  public Page<DictionaryField> findByFilters(Pageable page, String text, String sort, List<String> filters) {
+    Query query = searchQueryHelper.getSearchQuery(page, text, sort, filters);
     List<DictionaryField> cohorts = mongoTemplate.find(query, DictionaryField.class);
 
     return PageableExecutionUtils.getPage(cohorts, page,

src/main/java/uk/ac/ebi/biosamples/cohortatlas/repository/RelationshipRepository.java

@@ -4,6 +4,6 @@
 import uk.ac.ebi.biosamples.cohortatlas.model.DictionaryField;
 import uk.ac.ebi.biosamples.cohortatlas.model.Relationship;
 
-public interface RelationshipRepository extends MongoRepository<Relationship, String> {
+public interface RelationshipRepository extends MongoRepository<Relationship, String>, SearchRepository<Relationship> {
 
 }

src/main/java/uk/ac/ebi/biosamples/cohortatlas/repository/RelationshipSearchRepository.java

@@ -1,5 +1,6 @@
 package uk.ac.ebi.biosamples.cohortatlas.repository;
 
+import lombok.RequiredArgsConstructor;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.mongodb.core.MongoTemplate;
@@ -10,14 +11,13 @@
 
 import java.util.List;
 
-@Repository
-public class RelationshipSearchRepository extends CohortSearchRepository {
-  public RelationshipSearchRepository(MongoTemplate mongoTemplate) {
-    super(mongoTemplate);
-  }
+@RequiredArgsConstructor
+public class RelationshipSearchRepository implements SearchRepository<Relationship> {
+  private final SearchQueryHelper searchQueryHelper = new SearchQueryHelper();
+  protected MongoTemplate mongoTemplate;
 
-  public Page<Relationship> findFieldPageWithFilters(Pageable page, String text, String sort, List<String> filters) {
-    Query query = getSearchQuery(page, text, sort, filters);
+  public Page<Relationship> findByFilters(Pageable page, String text, String sort, List<String> filters) {
+    Query query = searchQueryHelper.getSearchQuery(page, text, sort, filters);
     List<Relationship> relationships = mongoTemplate.find(query, Relationship.class);
 
     return PageableExecutionUtils.getPage(relationships, page,

src/main/java/uk/ac/ebi/biosamples/cohortatlas/repository/SearchQueryHelper.java

@@ -0,0 +1,53 @@
+package uk.ac.ebi.biosamples.cohortatlas.repository;
+
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Sort;
+import org.springframework.data.mongodb.core.query.Criteria;
+import org.springframework.data.mongodb.core.query.Query;
+import org.springframework.data.mongodb.core.query.TextCriteria;
+import org.springframework.util.CollectionUtils;
+import org.springframework.util.StringUtils;
+
+import java.util.List;
+
+public class SearchQueryHelper {
+    public SearchQueryHelper() {
+    }
+
+    public Query getSearchQuery(Pageable page, String text, String sort, List<String> filters) {
+        Query query = new Query().with(page);
+        populateQueryWithSort(query, sort);
+        populateQueryWithFreeTextSearch(query, text);
+        populateQueryWithFilters(query, filters);
+        return query;
+    }
+
+    void populateQueryWithSort(Query query, String sort) {
+        if (StringUtils.hasText(sort)) {
+            query.with(Sort.by(sort).ascending());
+        }
+    }
+
+    void populateQueryWithFreeTextSearch(Query query, String text) {
+        if (StringUtils.hasText(text)) {
+            query.addCriteria(TextCriteria.forDefaultLanguage().matchingAny(text));
+        }
+    }
+
+    void populateQueryWithFilters(Query query, List<String> filters) {
+        if (CollectionUtils.isEmpty(filters)) {
+            return;
+        }
+
+        for (String filter : filters) {
+            String[] filterParts = filter.split(":");
+            if (filterParts.length > 1) {
+                String field = filterParts[0];
+                String value = filterParts[1];
+                query.addCriteria(Criteria.where(field).is(value));
+            } else {
+                throw new IllegalArgumentException("filter should contain a colon");
+            }
+        }
+    }
+}

src/main/java/uk/ac/ebi/biosamples/cohortatlas/repository/SearchRepository.java

@@ -2,60 +2,13 @@
 
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
-import org.springframework.data.domain.Sort;
-import org.springframework.data.mongodb.core.MongoTemplate;
-import org.springframework.data.mongodb.core.query.Criteria;
-import org.springframework.data.mongodb.core.query.Query;
-import org.springframework.data.mongodb.core.query.TextCriteria;
-import org.springframework.data.support.PageableExecutionUtils;
-import org.springframework.stereotype.Repository;
-import org.springframework.util.CollectionUtils;
-import org.springframework.util.StringUtils;
 import uk.ac.ebi.biosamples.cohortatlas.model.Cohort;
 
 import java.util.List;
 
-@Repository
-public abstract class SearchRepository {
-  protected final MongoTemplate mongoTemplate;
+public interface SearchRepository<T> {
 
-  public SearchRepository(MongoTemplate mongoTemplate) {
-    this.mongoTemplate = mongoTemplate;
-  }
+  Page<T> findByFilters(Pageable page, String text, String sort, List<String> filters);
 
-  protected Query getSearchQuery(Pageable page, String text, String sort, List<String> filters) {
-    Query query = new Query().with(page);
-    populateQueryWithSort(query, sort);
-    populateQueryWithFreeTextSearch(query, text);
-    populateQueryWithFilters(query, filters);
-    return query;
-  }
-
-  private void populateQueryWithSort(Query query, String sort) {
-    if (StringUtils.hasText(sort)) {
-      query.with(Sort.by(sort).ascending());
-    }
-  }
-
-  private void populateQueryWithFreeTextSearch(Query query, String text) {
-    if (StringUtils.hasText(text)) {
-      query.addCriteria(TextCriteria.forDefaultLanguage().matchingAny(text));
-    }
-  }
-
-  private void populateQueryWithFilters(Query query, List<String> filters) {
-    if (CollectionUtils.isEmpty(filters)) {
-      return;
-    }
-
-    for (String filter : filters) {
-      String[] filterParts = filter.split(":");
-      if (filterParts.length > 1) {
-        String field = filterParts[0];
-        String value = filterParts[1];
-        query.addCriteria(Criteria.where(field).is(value));
-      }
-    }
-  }
 
 }

src/main/java/uk/ac/ebi/biosamples/cohortatlas/service/CohortService.java

@@ -14,19 +14,17 @@
 @Service
 public class CohortService {
   private final CohortRepository cohortRepository;
-  private final CohortSearchRepository cohortSearchRepository;
 
-  public CohortService(CohortRepository cohortRepository, CohortSearchRepository cohortSearchRepository) {
+  public CohortService(CohortRepository cohortRepository) {
     this.cohortRepository = cohortRepository;
-    this.cohortSearchRepository = cohortSearchRepository;
   }
 
   public Cohort saveCohort(Cohort cohort) {
     return cohortRepository.save(cohort);
   }
 
   public Page<Cohort> searchCohorts(Pageable pageRequest, String text, List<String> filters, String sort) {
-    return cohortSearchRepository.findPageWithFilters(pageRequest, text, sort, filters);
+    return cohortRepository.findByFilters(pageRequest, text, sort, filters);
   }
 
   @NonNull

src/main/java/uk/ac/ebi/biosamples/cohortatlas/service/FieldService.java

@@ -1,5 +1,6 @@
 package uk.ac.ebi.biosamples.cohortatlas.service;
 
+import lombok.RequiredArgsConstructor;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.stereotype.Service;
@@ -11,21 +12,17 @@
 import java.util.Map;
 
 @Service
+@RequiredArgsConstructor
 public class FieldService {
   private final FieldRepository fieldRepository;
   private final FieldSearchRepository fieldSearchRepository;
 
-  public FieldService(FieldRepository fieldRepository, FieldSearchRepository fieldSearchRepository) {
-    this.fieldRepository = fieldRepository;
-    this.fieldSearchRepository = fieldSearchRepository;
-  }
-
   public List<DictionaryField> searchFields(String cohort) {
     return fieldRepository.findByCohort(cohort);
   }
 
   public Page<DictionaryField> searchFields(Pageable pageRequest, String text, List<String> filters, String sort) {
-    return fieldSearchRepository.findFieldPageWithFilters(pageRequest, text, sort, filters);
+    return fieldSearchRepository.findByFilters(pageRequest, text, sort, filters);
   }
 
   public List<Map<String, Integer>> fieldCountGroupByCohort() {

src/main/java/uk/ac/ebi/biosamples/cohortatlas/service/RelationshipService.java

@@ -12,15 +12,13 @@
 @Service
 public class RelationshipService {
   private final RelationshipRepository relationshipRepository;
-  private final RelationshipSearchRepository relationshipSearchRepository;
 
   public RelationshipService(RelationshipRepository relationshipRepository, RelationshipSearchRepository relationshipSearchRepository) {
     this.relationshipRepository = relationshipRepository;
-    this.relationshipSearchRepository = relationshipSearchRepository;
   }
 
   public Page<Relationship> searchRelationships(Pageable pageRequest, String text, List<String> filters, String sort) {
-    return relationshipSearchRepository.findFieldPageWithFilters(pageRequest, text, sort, filters);
+    return relationshipRepository.findByFilters(pageRequest, text, sort, filters);
   }
 
 }

src/test/java/uk/ac/ebi/biosamples/cohortatlas/service/CohortServiceTest.java

@@ -37,7 +37,7 @@ public void search_should_return_a_list_of_cohorts() {
     String sort = "";
 
     Page<Cohort> cohortPage = new PageImpl<>(getTestCohorts(), pageRequest, getTestCohorts().size());
-    Mockito.when(cohortSearchRepository.findPageWithFilters(pageRequest, text, sort, filters)).thenReturn(cohortPage);
+    Mockito.when(cohortSearchRepository.findByFilters(pageRequest, text, sort, filters)).thenReturn(cohortPage);
 
     Page<Cohort> cohorts = cohortService.searchCohorts(pageRequest, text, filters, sort);
     Assertions.assertNotNull(cohorts);

src/test/java/uk/ac/ebi/biosamples/cohortatlas/service/FieldServiceTest.java

@@ -38,7 +38,7 @@ public void search_should_return_a_list_of_fields() {
     String sort = "";
 
     Page<DictionaryField> fieldPage = new PageImpl<>(getTestFields(), pageRequest, getTestFields().size());
-    Mockito.when(fieldSearchRepository.findFieldPageWithFilters(pageRequest, text, sort, filters)).thenReturn(fieldPage);
+    Mockito.when(fieldSearchRepository.findByFilters(pageRequest, text, sort, filters)).thenReturn(fieldPage);
 
     Page<DictionaryField> fields = fieldService.searchFields(pageRequest, text, filters, sort);
     Assertions.assertNotNull(fields);