Concept modifiers

open-api/swagger.yaml

@@ -1876,6 +1876,32 @@ paths:
           description: >
             No concept exists with the concept code, or the user does not have
             access to the concept.
+  '/v2/concepts/{conceptCode}/modifiers':
+    get:
+      description: >
+        Gets the modifiers associated with a particular concept code if it exists
+        and the user has access to it.
+      tags:
+        - v2
+      parameters:
+        - name: conceptCode
+          required: true
+          in: path
+          description: Concept code of the concept.
+          schema:
+            type: string
+      responses:
+        '200':
+          description: |
+            Returns a list of modifier names associated with the given concept.
+          content:
+            '*/*':
+              schema:
+                $ref: '#/components/schemas/ConceptModifiers'
+        '404':
+          description: >
+            No concept exists with the concept code, or the user does not have
+            access to the concept.
 
   /v2/tree_nodes:
     get:
@@ -3383,6 +3409,14 @@ components:
         name:
           type: string
 
+    ConceptModifiers:
+      type: object
+      properties:
+        modifiers:
+          type: array
+          items:
+            type: string
+
     VariableMetadata:
       type: object
       properties:

transmart-core-api/src/main/groovy/org/transmartproject/core/concept/ConceptsResource.groovy

@@ -49,4 +49,5 @@ interface ConceptsResource {
      */
     String getConceptCodeByConceptPath(String conceptPath) throws NoSuchResourceException
 
+    List<String> getModifiersByConceptCode(String conceptCode, User user) throws NoSuchResourceException
 }

transmart-core-api/src/main/groovy/org/transmartproject/core/multidimquery/MultiDimensionalDataResource.groovy

@@ -69,4 +69,5 @@ interface MultiDimensionalDataResource {
 
     Iterable<Dimension> getSupportedDimensions(Constraint constraint)
 
+    List<String> getModifiersForConcept(String conceptCode)
 }

transmart-core-db/grails-app/services/org/transmartproject/db/clinical/MultidimensionalDataResourceService.groovy

@@ -18,6 +18,7 @@ import org.hibernate.criterion.Restrictions
 import org.hibernate.criterion.Subqueries
 import org.hibernate.internal.CriteriaImpl
 import org.hibernate.internal.StatelessSessionImpl
+import org.hibernate.transform.Transformers
 import org.springframework.beans.factory.annotation.Autowired
 import org.transmartproject.core.IterableResult
 import org.transmartproject.core.multidimquery.datatable.PaginationParameters
@@ -179,6 +180,21 @@ class MultidimensionalDataResourceService extends AbstractDataResourceService im
         getAvailableDimensions(getConstraintStudies(constraint))
     }
 
+    @CompileDynamic
+    List<String> getModifiersForConcept(String conceptCode) {
+        def session = (StatelessSessionImpl) sessionFactory.openStatelessSession()
+        session.connection().autoCommit = false
+        def results = (List)session.createSQLQuery("SELECT DISTINCT of.concept_cd, of.modifier_cd, mod.name_char " + \
+                "FROM i2b2demodata.observation_fact as of " + \
+                "INNER JOIN i2b2demodata.modifier_dimension as mod ON of.modifier_cd = mod.modifier_cd " + \
+                "WHERE of.concept_cd = :conceptCode")
+            .setString("conceptCode", conceptCode)
+            .setResultTransformer(Transformers.ALIAS_TO_ENTITY_MAP)
+            .list()
+        session.close()
+        results.collect{ Map result -> (String)result.get('name_char') }
+    }
+
     // FIXME: Enable static compilation
     @CompileDynamic
     private Query buildCriteria(Set<DimensionImpl> dimensions, ImmutableMap<DimensionImpl, SortOrder> orderDims) {

transmart-core-db/grails-app/services/org/transmartproject/db/concept/ConceptsService.groovy

@@ -12,10 +12,16 @@ import org.transmartproject.core.exceptions.NoSuchResourceException
 import org.transmartproject.core.concept.Concept
 import org.transmartproject.core.concept.ConceptsResource
 import org.transmartproject.core.multidimquery.MultiDimensionalDataResource
+import org.transmartproject.core.multidimquery.query.AndConstraint
+import org.transmartproject.core.multidimquery.query.Constraint
+import org.transmartproject.core.multidimquery.query.Field
+import org.transmartproject.core.multidimquery.query.FieldConstraint
+import org.transmartproject.core.multidimquery.query.Operator
 import org.transmartproject.core.users.User
 import org.transmartproject.db.i2b2data.ConceptDimension
 import org.transmartproject.core.multidimquery.query.ConceptConstraint
 import org.transmartproject.core.multidimquery.query.TrueConstraint
+import org.transmartproject.db.i2b2data.ObservationFact
 
 import java.util.concurrent.ConcurrentHashMap
 
@@ -122,4 +128,9 @@ class ConceptsService implements ConceptsResource, ApplicationRunner {
         code
     }
 
+    @Override
+    List<String> getModifiersByConceptCode(String conceptCode, User user) throws NoSuchResourceException {
+        getConceptByConceptCodeForUser(conceptCode, user)
+        multiDimService.getModifiersForConcept(conceptCode)
+    }
 }

transmart-rest-api/grails-app/controllers/org/transmartproject/rest/ConceptController.groovy

@@ -5,6 +5,7 @@ import org.springframework.web.bind.annotation.PathVariable
 import org.springframework.web.bind.annotation.RequestParam
 import org.transmartproject.core.concept.Concept
 import org.transmartproject.core.concept.ConceptsResource
+import org.transmartproject.rest.marshallers.ConceptModifiersWrapper
 import org.transmartproject.rest.marshallers.ConceptWrapper
 import org.transmartproject.rest.marshallers.ContainerResponseWrapper
 
@@ -43,6 +44,13 @@ class ConceptController extends AbstractQueryController {
         )
     }
 
+    def getModifiers(@RequestParam('api_version') String apiVersion, @PathVariable('conceptCode') String conceptCode) {
+        checkForUnsupportedParams(params, ['conceptCode'])
+        respond new ConceptModifiersWrapper(
+                modifiers: conceptsResource.getModifiersByConceptCode(conceptCode, authContext.user)
+        )
+    }
+
     private static wrapConcepts(String apiVersion, Collection<Concept> source) {
         new ContainerResponseWrapper(
                 key: 'concepts',

transmart-rest-api/grails-app/controllers/org/transmartproject/rest/RestApiUrlMappings.groovy

@@ -122,6 +122,9 @@ class RestApiUrlMappings {
             "/concepts/${conceptCode}"(method: 'GET', controller: 'concept', action: 'show') {
                 apiVersion = 'v2'
             }
+            "/concepts/${conceptCode}/modifiers"(method: 'GET', controller: 'concept', action: 'getModifiers') {
+                apiVersion = 'v2'
+            }
             "/tree_nodes"(method: 'GET', controller: 'tree', action: 'index') {
                 apiVersion = 'v2'
             }

transmart-rest-api/src/main/groovy/org/transmartproject/rest/marshallers/ConceptModifiersSerializationHelper.groovy

@@ -0,0 +1,17 @@
+package org.transmartproject.rest.marshallers
+
+import grails.rest.Link
+
+import static grails.rest.render.util.AbstractLinkingRenderer.RELATIONSHIP_SELF
+
+class ConceptModifiersSerializationHelper extends AbstractHalOrJsonSerializationHelper<ConceptModifiersWrapper> {
+
+    final Class targetType = ConceptModifiersWrapper
+
+    final String collectionName = 'modifiers'
+
+    @Override
+    Map<String, Object> convertToMap(ConceptModifiersWrapper object) {
+        [modifiers: object.modifiers]
+    }
+}

transmart-rest-api/src/main/groovy/org/transmartproject/rest/marshallers/ConceptModifiersWrapper.groovy

@@ -0,0 +1,5 @@
+package org.transmartproject.rest.marshallers
+
+class ConceptModifiersWrapper {
+    List<String> modifiers
+}