Give error that generic asssay patient level data is not supported

src/main/java/org/mskcc/cbio/portal/scripts/ImportProfileData.java

@@ -116,6 +116,9 @@ public void run() {
                 // use a different importer for patient level data
                 String patientLevel = geneticProfile.getOtherMetaDataField("patient_level");
                 if (patientLevel != null && patientLevel.trim().toLowerCase().equals("true")) {
+                    if (overwriteExisting) {
+                        throw new UnsupportedOperationException("Incremental upload for generic assay patient_level data is not supported. Please use sample level instead.");
+                    }
                     ImportGenericAssayPatientLevelData genericAssayProfileImporter = new ImportGenericAssayPatientLevelData(dataFile, geneticProfile.getTargetLine(), geneticProfile.getGeneticProfileId(), genePanel, geneticProfile.getOtherMetaDataField("generic_entity_meta_properties"));
                     genericAssayProfileImporter.importData();
                 } else {

src/test/java/org/mskcc/cbio/portal/integrationTest/incremental/TestIncrementalGenericAssayImporter.java

@@ -41,6 +41,7 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertThrows;
 import static org.mskcc.cbio.portal.integrationTest.incremental.GeneticAlterationsTestHelper.assertNoChange;
 import static org.mskcc.cbio.portal.integrationTest.incremental.GeneticAlterationsTestHelper.assertPriorDataState;
 import static org.mskcc.cbio.portal.integrationTest.incremental.GeneticAlterationsTestHelper.geneStableIdToEntityId;
@@ -58,34 +59,28 @@
 @Transactional
 public class TestIncrementalGenericAssayImporter {
 
+    // stable_id: TCGA-A1-A0SB-01
+    final int newSampleId = 1;
+    // stable_id: TCGA-A1-A0SD-01
+    final int updateSampleId = 2;
+    // stable_id: TCGA-A1-A0SE-01
+    final int noChangeSampleId = 3;
+    final Set<Integer> beforeSampleIds = Set.of(updateSampleId, noChangeSampleId);
+
+    // Stable id that is part of the platform, but absent during the incremental upload
+    final String absentStableId = "L-685458";
+    final Set<String> noChangeStableIds = Set.of("Erlotinib", "Irinotecan", "Lapatinib");
+    final Set<String> beforeStableIds = new HashSet<>(noChangeStableIds);
+    { beforeStableIds.add(absentStableId); }
+
+    private GeneticProfile ic50Profile;
+    private HashMap<Integer, HashMap<Integer, String>> beforeResult;
+
     /**
      * Test incremental upload of GENERIC_ASSAY
      */
     @Test
-    public void testGenericAssay() throws DaoException, IOException {
-        /**
-         * Prior checks
-         */
-        // Stable id that is part of the platform, but absent during the incremental upload
-        final String absentStableId = "L-685458";
-        final Set<String> noChangeStableIds = Set.of("Erlotinib", "Irinotecan", "Lapatinib");
-        final Set<String> beforeStableIds = new HashSet<>(noChangeStableIds);
-        beforeStableIds.add(absentStableId);
-
-        // stable_id: TCGA-A1-A0SB-01
-        final int newSampleId = 1;
-        // stable_id: TCGA-A1-A0SD-01
-        final int updateSampleId = 2;
-        // stable_id: TCGA-A1-A0SE-01
-        final int noChangeSampleId = 3;
-        final Set<Integer> beforeSampleIds = Set.of(updateSampleId, noChangeSampleId);
-
-        GeneticProfile ic50Profile = DaoGeneticProfile.getGeneticProfileByStableId("study_tcga_pub_treatment_ic50");
-        assertNotNull(ic50Profile);
-
-        HashMap<Integer, HashMap<Integer, String>> beforeResult = DaoGeneticAlteration.getInstance().getGeneticAlterationMapForEntityIds(ic50Profile.getGeneticProfileId(), null);
-        Set<Integer> beforeEntityIds = geneStableIdsToEntityIds(beforeStableIds);
-        assertPriorDataState(beforeResult, beforeEntityIds, beforeSampleIds);
+    public void testGenericAssay() throws DaoException {
 
         File dataFolder = new File("src/test/resources/incremental/generic_assay/");
         File metaFile = new File(dataFolder, "meta_treatment_ic50.txt");
@@ -128,9 +123,40 @@ public void testGenericAssay() throws DaoException, IOException {
         assertNotNull("New generic entity has to be added", DaoGeneticEntity.getGeneticEntityByStableId("LBW242"));
     }
 
+    /**
+     * Test that incremental upload of GENERIC_ASSAY (patient level) is not supported
+     */
+    @Test
+    public void testGenericAssayPatientLevel() throws DaoException {
+
+        File dataFolder = new File("src/test/resources/incremental/generic_assay/");
+        File metaFile = new File(dataFolder, "meta_treatment_ic50_patient_level.txt");
+        File dataFile = new File(dataFolder, "data_treatment_ic50_patient_level.txt");
+
+        /**
+         * Test
+         */
+        assertThrows("Incremental upload for generic assay patient_level data is not supported. Please use sample level instead.",
+                RuntimeException.class, () -> {
+                    new ImportProfileData(new String[] {
+                            "--loadMode", "bulkLoad",
+                            "--meta", metaFile.getAbsolutePath(),
+                            "--data", dataFile.getAbsolutePath(),
+                            "--overwrite-existing",
+                    }).run();
+                });
+    }
+
     @Before
     public void setUp() throws DaoException {
         DaoCancerStudy.reCacheAll();
+
+        ic50Profile = DaoGeneticProfile.getGeneticProfileByStableId("study_tcga_pub_treatment_ic50");
+        assertNotNull(ic50Profile);
+
+        beforeResult = DaoGeneticAlteration.getInstance().getGeneticAlterationMapForEntityIds(ic50Profile.getGeneticProfileId(), null);
+        Set<Integer> beforeEntityIds = geneStableIdsToEntityIds(beforeStableIds);
+        assertPriorDataState(beforeResult, beforeEntityIds, beforeSampleIds);
     }
 
 }

src/test/resources/incremental/generic_assay/data_treatment_ic50_patient_level.txt

@@ -0,0 +1,8 @@
+ENTITY_STABLE_ID	NAME	DESCRIPTION	URL	TCGA-A1-A0SB	TCGA-A1-A0SD
+Erlotinib	Name of Erlotinib	Desc of Erlotinib	Url of Erlotinib	>8	7.5
+Irinotecan	Name of Irinotecan	Desc of Irinotecan	Url of Irinotecan		0.081
+# The database has this entity, but not the file
+#L-685458
+Lapatinib	Name of Lapatinib	Desc of Lapatinib	Url of Lapatinib	6.2	7.848
+#The entity will be added
+LBW242	Name of LBW242	Desc of LBW242	Url of LBW242	0.1	>~8

src/test/resources/incremental/generic_assay/meta_treatment_ic50_patient_level.txt

@@ -0,0 +1,13 @@
+cancer_study_identifier: study_tcga_pub
+genetic_alteration_type: GENERIC_ASSAY
+generic_assay_type: TREATMENT_RESPONSE
+datatype: LIMIT-VALUE
+stable_id: treatment_ic50
+profile_name: IC50 values of compounds on cellular phenotype readout
+profile_description: IC50 (compound concentration resulting in half maximal inhibition) of compounds on cellular phenotype readout of cultured mutant cell lines.
+data_filename: data_treatment_ic50_patient_level.txt
+show_profile_in_analysis_tab: true
+pivot_threshold_value: 0.1
+value_sort_order: ASC
+generic_entity_meta_properties: NAME,DESCRIPTION,URL
+patient_level: true