Fix skipping rows in generic assay data

MyBatis does not like if result does not have <id ...>
If it is not specified, it picks first field as a key.
Rows that would have the same key will be skipped!

Author: forus

src/main/java/org/cbioportal/application/file/export/exporters/GenericAssayLimitValueDatatypeExporter.java

@@ -20,7 +20,6 @@
 
 public class GenericAssayLimitValueDatatypeExporter extends GeneticProfileDatatypeExporter {
 
-    private static final org.slf4j.Logger LOG = org.slf4j.LoggerFactory.getLogger(GenericAssayLimitValueDatatypeExporter.class);
     private final GeneticProfileDataService geneticProfileDataService;
 
     public GenericAssayLimitValueDatatypeExporter(GeneticProfileService geneticProfileService, GeneticProfileDataService geneticProfileDataService) {
@@ -92,9 +91,7 @@ public TableRow next() {
                         GenericEntityProperty property = null;
                         while (propertyPeekingIterator.hasNext() && propertyPeekingIterator.peek().getGeneticEntityId() <= data.getGeneticEntity().getGeneticEntityId()) {
                             if (propertyPeekingIterator.peek().getGeneticEntityId() < data.getGeneticEntity().getGeneticEntityId()) {
-                                LOG.warn("Skipping {} property with genetic entity ID {} as such ID is not present in the result set.", propertyPeekingIterator.peek().getName(), propertyPeekingIterator.peek().getGeneticEntityId());
-                                propertyPeekingIterator.next();
-                                continue;
+                                throw new IllegalStateException(String.format("%s property with genetic entity ID %d is not present in the result set.", propertyPeekingIterator.peek().getName(), propertyPeekingIterator.peek().getGeneticEntityId()));
                             }
                             property = propertyPeekingIterator.next();
                             if (property.getName() == null) {

src/main/resources/mappers/export/CaseListMetadataMapper.xml

@@ -3,6 +3,7 @@
 
 <mapper namespace="org.cbioportal.application.file.export.mappers.CaseListMetadataMapper">
     <resultMap id="CaseListMetadataResultMap" type="org.cbioportal.application.file.model.CaseListMetadata">
+        <id column="LIST_ID"/>
         <result property="cancerStudyIdentifier" column="cancerStudyIdentifier"/>
         <result property="stableId" column="stableId"/>
         <result property="name" column="name"/>
@@ -15,11 +16,12 @@
             id="getCaseListsMetadata"
             resultMap="CaseListMetadataResultMap">
         SELECT
-        cs.CANCER_STUDY_IDENTIFIER as cancerStudyIdentifier,
-        sl.STABLE_ID as stableId,
-        sl.NAME as name,
-        sl.DESCRIPTION as description,
-        s.STABLE_ID as sampleId
+            sl.LIST_ID,
+            cs.CANCER_STUDY_IDENTIFIER as cancerStudyIdentifier,
+            sl.STABLE_ID as stableId,
+            sl.NAME as name,
+            sl.DESCRIPTION as description,
+            s.STABLE_ID as sampleId
         FROM sample_list sl
         JOIN cancer_study cs ON cs.CANCER_STUDY_ID = sl.CANCER_STUDY_ID
         JOIN sample_list_list sll ON sll.LIST_ID = sl.LIST_ID

src/main/resources/mappers/export/GeneticProfileDataMapper.xml

@@ -19,6 +19,7 @@
         ORDER BY jt.idx ASC
     </select>
     <resultMap id="GeneticProfileDataResultMap" type="org.cbioportal.application.file.model.GeneticProfileData">
+        <id column="GENETIC_ENTITY_ID"/>
         <result property="commaSeparatedValues" column="VALUES"/>
         <association property="geneticEntity" javaType="org.cbioportal.application.file.model.GeneticEntity">
             <id property="geneticEntityId" column="GENETIC_ENTITY_ID"/>
@@ -46,6 +47,7 @@
         ORDER BY ga.GENETIC_ENTITY_ID
     </select>
     <resultMap id="GeneticEntityPropertyResultMap" type="org.cbioportal.application.file.model.GenericEntityProperty">
+        <id column="ID"/>
         <result property="geneticEntityId" column="GENETIC_ENTITY_ID"/>
         <result property="name" column="NAME"/>
         <result property="value" column="VALUE"/>