OpenConceptLab/ocl_issues#280 create concept map

OpenConceptLab · Mar 12, 2021 · 38a06fe · 38a06fe
1 parent ea6db50
commit 38a06fe
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Showing 9 changed files with 369 additions and 21 deletions.
diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/converter/ConceptMapConverter.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/converter/ConceptMapConverter.java
diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/converter/ValueSetConverter.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/converter/ValueSetConverter.java
@@ -46,7 +46,7 @@ public class ValueSetConverter extends BaseConverter {
                     "on c1.mnemonic = c3.mnemonic and c1.created_at = c3.created_at";
 
     private static final Map<String,Object> collReferenceParamMap = new HashMap<>();
-    private static final String insertCollectionsReferences = "insert into collections_references (collection_id,collectionreference_id) values (?,?)";
+    private static final String insertCollectionsReferences = "insert into collections_references (collection_id,collectionreference_id) values (?,?) on conflict do nothing";
     private static final String insertCollectionsConcepts = "insert into collections_concepts (collection_id,concept_id) values (?,?) on conflict do nothing";
 
     public ValueSetConverter(SourceRepository sourceRepository, ConceptRepository conceptRepository, OclFhirUtil oclFhirUtil,

diff --git a/...ts/src/main/java/org/openconceptlab/fhir/interceptor/OclFhirAuthorizationInterceptor.java b/...ts/src/main/java/org/openconceptlab/fhir/interceptor/OclFhirAuthorizationInterceptor.java
@@ -5,6 +5,7 @@
 import ca.uhn.fhir.rest.server.interceptor.auth.IAuthRule;
 import ca.uhn.fhir.rest.server.interceptor.auth.RuleBuilder;
 import org.hl7.fhir.r4.model.CodeSystem;
+import org.hl7.fhir.r4.model.ConceptMap;
 import org.hl7.fhir.r4.model.ValueSet;
 import org.springframework.stereotype.Component;
 
@@ -31,7 +32,9 @@ private RuleBuilder getDefaultRuleBuilder() {
               .allow().write().resourcesOfType(CodeSystem.class).withAnyId().andThen()
               .allow().delete().resourcesOfType(CodeSystem.class).withAnyId().andThen()
               .allow().write().resourcesOfType(ValueSet.class).withAnyId().andThen()
-              //.allow().write().resourcesOfType(ConceptMap.class).withAnyId().andThen()
+              .allow().delete().resourcesOfType(ValueSet.class).withAnyId().andThen()
+              .allow().write().resourcesOfType(ConceptMap.class).withAnyId().andThen()
+              .allow().delete().resourcesOfType(ConceptMap.class).withAnyId().andThen()
               .allow().operation().withAnyName().atAnyLevel().andAllowAllResponses();
       return ruleBuilder;
    }

diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/model/Mapping.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/model/Mapping.java
@@ -27,6 +27,9 @@ public class Mapping extends BaseOclEntity implements Serializable {
 	@GeneratedValue(strategy=GenerationType.IDENTITY)
 	private Long id;
 
+	@Column
+	private String mnemonic;
+
 	@Column
 	private String comment;
 
@@ -146,6 +149,14 @@ public void setId(Long id) {
 		this.id = id;
 	}
 
+	public String getMnemonic() {
+		return this.mnemonic;
+	}
+
+	public void setMnemonic(String mnemonic) {
+		this.mnemonic = mnemonic;
+	}
+
 	public String getComment() {
 		return this.comment;
 	}

diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/provider/BaseProvider.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/provider/BaseProvider.java
@@ -52,25 +52,7 @@ protected List<Source> getSources(List<String> access) {
     }
 
     protected List<Source> getSourceByUrl(StringType url, StringType version, List<String> access) {
-        List<Source> sources = new ArrayList<>();
-        if (isVersionAll(version)) {
-            // get all versions
-            sources.addAll(sourceRepository.findByCanonicalUrlAndPublicAccessIn(url.getValue(), access).stream()
-                    .sorted(Comparator.comparing(Source::getVersion).reversed()).collect(Collectors.toList()));
-        } else {
-            final Source source;
-            if (!isValid(version)) {
-                // get most recent released version
-                source = oclFhirUtil.getMostRecentReleasedSourceByUrl(url, access);
-            } else {
-                // get a given version
-                source = sourceRepository.findFirstByCanonicalUrlAndVersionAndPublicAccessIn(url.getValue(), version.getValue(), access);
-            }
-            if (source != null) sources.add(source);
-        }
-        if (sources.isEmpty())
-            throw new ResourceNotFoundException(notFound(CodeSystem.class, url, version));
-        return sources;
+        return oclFhirUtil.getSourceByUrl(url, version, access);
     }
 
     protected List<Source> getSourceByOwner(StringType owner, List<String> access) {

diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/provider/ConceptMapResourceProvider.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/provider/ConceptMapResourceProvider.java
@@ -1,6 +1,7 @@
 package org.openconceptlab.fhir.provider;
 
 import ca.uhn.fhir.rest.annotation.*;
+import ca.uhn.fhir.rest.api.MethodOutcome;
 import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.server.IResourceProvider;
 import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@@ -18,6 +19,7 @@
 import org.springframework.stereotype.Component;
 
 import javax.transaction.Transactional;
+import java.util.Collections;
 import java.util.List;
 
 import static org.openconceptlab.fhir.util.OclFhirConstants.*;
@@ -43,6 +45,23 @@ public Class<? extends IBaseResource> getResourceType() {
         return ConceptMap.class;
     }
 
+    @Create
+    @Transactional
+    public MethodOutcome createConceptMap(@ResourceParam ConceptMap conceptMap, RequestDetails requestDetails) {
+        if (conceptMap == null) {
+            throw new InvalidRequestException("The ConceptMap can not be empty");
+        }
+        String accessionId = getAccessionIdentifier(Collections.singletonList(conceptMap.getIdentifier()));
+        if (!isValid(accessionId)) {
+            throw new InvalidRequestException("The ConceptMap.identifier is empty or identifier of type ACSN is empty.");
+        }
+        if (!isValid(conceptMap.getUrl())) {
+            throw new InvalidRequestException("The ConceptMap.url can not be empty. Please provide canonical url.");
+        }
+        conceptMapConverter.createConceptMap(conceptMap, accessionId, requestDetails.getHeader(AUTHORIZATION));
+        return new MethodOutcome();
+    }
+
     /**
      * Returns all public {@link ConceptMap}.
      *

diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/repository/ConceptIdMnemonic.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/repository/ConceptIdMnemonic.java
@@ -0,0 +1,6 @@
+package org.openconceptlab.fhir.repository;
+
+public interface ConceptIdMnemonic {
+    Long getId();
+    String getMnemonic();
+}
diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/repository/ConceptRepository.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/repository/ConceptRepository.java
@@ -28,6 +28,15 @@ public interface ConceptRepository extends BaseOclRepository<Concept>{
             ") order by c2.mnemonic asc")
     Page<Concept> findConcepts(@Param("sourceId") Long sourceId, Pageable pageable);
 
+    @Query(nativeQuery = true, value = "select c2.id, c2.mnemonic from concepts c2 where c2.id in (" +
+            "select concept_id from (\n" +
+            "select max(cs.concept_id) as concept_id , c1.mnemonic from concepts_sources cs \n" +
+            "inner join concepts c1 on c1.id = cs.concept_id \n" +
+            "where cs.source_id = :sourceId\n" +
+            "group by c1.mnemonic) as val \n" +
+            ") order by c2.mnemonic asc")
+    List<ConceptIdMnemonic> findConceptIds(@Param("sourceId") Long sourceId);
+
     @Query(nativeQuery = true, value = "select count(*) from (select max(cs.concept_id) as concept_id , c1.mnemonic from concepts_sources cs \n" +
             "inner join concepts c1 on c1.id = cs.concept_id \n" +
             "where cs.source_id = :sourceId\n" +

diff --git a/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/util/OclFhirConstants.java b/ocl-fhir-ts/src/main/java/org/openconceptlab/fhir/util/OclFhirConstants.java
@@ -122,6 +122,7 @@ public final class OclFhirConstants {
 	public static final String CONCEPTS = "concepts";
 	public static final String COLLECTIONS = "collections";
 	public static final String SOURCES = "sources";
+	public static final String MAPPINGS = "mappings";
 	public static final String EXPRESSION = "expression";
 	public static final String LAST_RESOLVED_AT = "last_resolved_at";
 	public static final boolean True = true;
@@ -131,4 +132,17 @@ public final class OclFhirConstants {
 	public static final String TRANSLATE = "$translate";
 
 	public static final String OWNER_URL = "ownerUrl";
+	public static final String FROM_SOURCE_URL = "from_source_url";
+	public static final String FROM_SOURCE_VERSION = "from_source_version";
+	public static final String FROM_SOURCE_ID = "from_source_id";
+	public static final String FROM_CONCEPT_CODE = "from_concept_code";
+	public static final String FROM_CONCEPT_NAME = "from_concept_name";
+	public static final String FROM_CONCEPT_ID = "from_concept_id";
+	public static final String TO_SOURCE_URL = "to_source_url";
+	public static final String TO_SOURCE_VERSION = "to_source_version";
+	public static final String TO_SOURCE_ID = "to_source_id";
+	public static final String TO_CONCEPT_CODE = "to_concept_code";
+	public static final String TO_CONCEPT_NAME = "to_concept_name";
+	public static final String TO_CONCEPT_ID = "to_concept_id";
+	public static final String MAP_TYPE = "map_type";
 }