Concept Set Source Code Evaluation

Author: anthonysena

src/main/java/org/ohdsi/webapi/service/ConceptSetService.java

@@ -84,10 +84,10 @@ public ConceptSetExpression getConceptSetExpression(@PathParam("id") final int i
     expression.items = new ConceptSetExpression.ConceptSetItem[map.size()];
 
     // lookup the concepts we need information for
-    String[] identifiers = new String[map.size()];
+    long[] identifiers = new long[map.size()];
     int identifierIndex = 0;
     for (Long identifier : map.keySet()) {
-      identifiers[identifierIndex] = identifier.toString();
+      identifiers[identifierIndex] = identifier;
       identifierIndex++;
     }
 

src/main/java/org/ohdsi/webapi/service/VocabularyService.java

@@ -78,28 +78,17 @@ public Concept mapRow(final ResultSet resultSet, final int arg1) throws SQLExcep
   @POST
   @Produces(MediaType.APPLICATION_JSON)
   @Consumes(MediaType.APPLICATION_JSON)
-  public Collection<Concept> executeIdentifierLookup(@PathParam("sourceKey") String sourceKey, String[] identifiers) {
+  public Collection<Concept> executeIdentifierLookup(@PathParam("sourceKey") String sourceKey, long[] identifiers) {
     if (identifiers.length == 0) {
       return new ArrayList<>();
     }
 
-    int[] intIdentifiers =new int[identifiers.length];
-    int i=0;
-    for(String identifier:identifiers){
-        try {
-            intIdentifiers[i]=Integer.parseInt(identifier);
-            i++;
-        } catch (NumberFormatException e) {
-            throw new IllegalArgumentException("Not a number: " + identifier + " at index " + i, e);
-        }
-    }
-
     Source source = getSourceRepository().findBySourceKey(sourceKey);
     String tableQualifier = source.getTableQualifier(SourceDaimon.DaimonType.Vocabulary);
 
     String sql_statement = ResourceHelper.GetResourceAsString("/resources/vocabulary/sql/lookupIdentifiers.sql");
     sql_statement = SqlRender.renderSql(sql_statement, new String[]{"identifiers", "CDM_schema"}, new String[]{
-      JoinArray(intIdentifiers), tableQualifier});
+      JoinArray(identifiers), tableQualifier});
     sql_statement = SqlTranslate.translateSql(sql_statement, "sql server", source.getSourceDialect());
 
     return getSourceJdbcTemplate(source).query(sql_statement, this.rowMapper);
@@ -146,7 +135,7 @@ public Collection<Concept> executeSourcecodeLookup(@PathParam("sourceKey") Strin
   @POST
   @Produces(MediaType.APPLICATION_JSON)
   @Consumes(MediaType.APPLICATION_JSON)
-  public Collection<Concept> executeMappedLookup(@PathParam("sourceKey") String sourceKey, String[] identifiers) {
+  public Collection<Concept> executeMappedLookup(@PathParam("sourceKey") String sourceKey, long[] identifiers) {
     if (identifiers.length == 0) {
       return new ArrayList<>();
     }
@@ -511,16 +500,7 @@ public Collection<Concept> getRelatedConcepts(@PathParam("sourceKey") String sou
 
     ArrayList<String> filterList = new ArrayList<String>();
 
-    int[] conceptIds =new int[search.conceptId.length];
-    int i=0;
-    for (String conceptId : search.conceptId) {
-      try {
-        conceptIds[i] = Integer.parseInt(conceptId);
-        i++;
-      } catch (NumberFormatException e) {
-        throw new IllegalArgumentException("Not a number: " + conceptId + " at index " + i, e);
-      }
-    } 
+    long[] conceptIds = search.conceptId;
 
     if (search.vocabularyId != null && search.vocabularyId.length > 0) {
       filterList.add("VOCABULARY_ID IN (" + JoinArray(search.vocabularyId) + ")");
@@ -565,7 +545,7 @@ public Void mapRow(ResultSet resultSet, int arg1) throws SQLException {
     return concepts.values();
   }
 
-  private String JoinArray(final int[] array) {
+  private String JoinArray(final long[] array) {
     String result = "";
 
     for (int i = 0; i < array.length; i++) {

src/main/java/org/ohdsi/webapi/vocabulary/RelatedConceptSearch.java

@@ -23,5 +23,5 @@ public RelatedConceptSearch() {
     public String[] conceptClassId;    
 
     @JsonProperty("CONCEPT_ID")
-    public String[] conceptId;    
+    public long[] conceptId;    
 }

src/main/resources/resources/vocabulary/sql/getMappedSourcecodes.sql

@@ -1,8 +1,28 @@
+-- get all of the concepts that were part of the list of concepts provided
+
+Select concept_id, concept_name, ISNULL(standard_concept, 'N') standard_concept, ISNULL(invalid_reason, 'V') INVALID_REASON,
+CONCEPT_CODE, CONCEPT_CLASS_ID, DOMAIN_ID, VOCABULARY_ID
+from concept 
+where concept_id in (@identifiers)
+
+UNION
+
+--get all source codes that map to the list of concepts provided
+
 select CONCEPT_ID, CONCEPT_NAME, ISNULL(STANDARD_CONCEPT,'N') STANDARD_CONCEPT, ISNULL(c.INVALID_REASON,'V') INVALID_REASON, CONCEPT_CODE, CONCEPT_CLASS_ID, DOMAIN_ID, VOCABULARY_ID
 from @CDM_schema.concept_relationship cr
 join @CDM_schema.concept c on c.concept_id = cr.concept_id_1
 where cr.concept_id_2 in (@identifiers)
 and cr.INVALID_REASON is null
 and relationship_id in ('Maps to')
-and standard_concept IS NULL
+
+UNION
+
+--get anything that may be stashed in the source-to-concept-map table
+
+select 0 as CONCEPT_ID, SOURCE_CODE_DESCRIPTION as CONCEPT_NAME, 'N' as STANDARD_CONCEPT, ISNULL(INVALID_REASON,'V') INVALID_REASON,
+SOURCE_CODE as CONCEPT_CODE, NULL as CONCEPT_CLASS_ID, NULL as DOMAIN_ID, SOURCE_VOCABULARY_ID as VOCABULARY_ID
+from @CDM_schema.SOURCE_TO_CONCEPT_MAP
+where TARGET_CONCEPT_ID in (@identifiers)
+and INVALID_REASON is null
 order by domain_id, vocabulary_id