Rename upsertSampleProfiles to upsertSampleToProfileMapping

method in DaoSampleProfile
cBioPortal · Jun 21, 2024 · f120f5d · f120f5d
1 parent df8f7af
commit f120f5d
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Showing 9 changed files with 13 additions and 13 deletions.
diff --git a/src/main/java/org/mskcc/cbio/portal/dao/DaoSampleProfile.java b/src/main/java/org/mskcc/cbio/portal/dao/DaoSampleProfile.java
@@ -61,15 +61,15 @@ private DaoSampleProfile() {}
 
     private static final int NO_SUCH_PROFILE_ID = -1;
 
-    public static void upsertSampleProfiles(Collection<Integer> sampleIds, Integer geneticProfileId, Integer panelId) throws DaoException {
-        upsertSampleProfiles(
+    public static void upsertSampleToProfileMapping(Collection<Integer> sampleIds, Integer geneticProfileId, Integer panelId) throws DaoException {
+        upsertSampleToProfileMapping(
                 sampleIds.stream()
                         .map(sampleId -> new SampleProfileTuple(geneticProfileId, sampleId, panelId)).toList());
     }
 
     public record SampleProfileTuple(int geneticProfileId, int sampleId, Integer panelId) {}
 
-    public static void upsertSampleProfiles(Collection<SampleProfileTuple> idTuples) throws DaoException {
+    public static void upsertSampleToProfileMapping(Collection<SampleProfileTuple> idTuples) throws DaoException {
         if (idTuples.isEmpty()) {
             return;
         }

diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java
@@ -153,7 +153,7 @@ private void doImportData() throws Exception {
         orderedSampleList = newArrayList(toImport.eventsTable.columnKeySet());
         this.geneticAlterationGeneImporter = isIncrementalUpdateMode ?  new GeneticAlterationIncrementalImporter(geneticProfileId, orderedSampleList)
                 : new GeneticAlterationImporter(geneticProfileId, orderedSampleList);
-        DaoSampleProfile.upsertSampleProfiles(orderedSampleList, geneticProfileId, genePanelId);
+        DaoSampleProfile.upsertSampleToProfileMapping(orderedSampleList, geneticProfileId, genePanelId);
 
         for (Long entrezId : toImport.eventsTable.rowKeySet()) {
             boolean added = storeGeneticAlterations(toImport, entrezId);

diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java
@@ -474,7 +474,7 @@ public void importData() throws IOException, DaoException {
                 }
             }
         }
-        DaoSampleProfile.upsertSampleProfiles(internalSampleIds, geneticProfileId, genePanelId);
+        DaoSampleProfile.upsertSampleToProfileMapping(internalSampleIds, geneticProfileId, genePanelId);
 
         for (MutationEvent event : newEvents) {
             try {
@@ -611,7 +611,7 @@ private String processMAFHeader(BufferedReader buffer) throws IOException, DaoEx
             }
             line = buffer.readLine().trim();
         }
-        DaoSampleProfile.upsertSampleProfiles(internalSampleIds, geneticProfileId, genePanelId);
+        DaoSampleProfile.upsertSampleToProfileMapping(internalSampleIds, geneticProfileId, genePanelId);
         return line;
     }
 

diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportGenePanelProfileMap.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportGenePanelProfileMap.java
@@ -196,7 +196,7 @@ public void importData() throws Exception {
                 sampleProfileTuples.add(new DaoSampleProfile.SampleProfileTuple(geneticProfileId, sampleInternalId, genePanelId));
             }
 
-            DaoSampleProfile.upsertSampleProfiles(sampleProfileTuples);
+            DaoSampleProfile.upsertSampleToProfileMapping(sampleProfileTuples);
         }
     }
 

diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportGenericAssayPatientLevelData.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportGenericAssayPatientLevelData.java
@@ -122,7 +122,7 @@ public void importData() throws IOException, DaoException {
                 }
             }
             Integer genePanelID = (genePanel == null) ? null : GeneticProfileUtil.getGenePanelId(genePanel);
-            DaoSampleProfile.upsertSampleProfiles(orderedSampleList, geneticProfileId, genePanelID);
+            DaoSampleProfile.upsertSampleToProfileMapping(orderedSampleList, geneticProfileId, genePanelID);
 
             ProgressMonitor.setCurrentMessage(" --> total number of data lines:  " + (numLines-1));
 

diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportStructuralVariantData.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportStructuralVariantData.java
@@ -183,7 +183,7 @@ public void importData() throws IOException, DaoException {
             }
         }
 
-        DaoSampleProfile.upsertSampleProfiles(sampleIds, geneticProfileId, genePanelId);
+        DaoSampleProfile.upsertSampleToProfileMapping(sampleIds, geneticProfileId, genePanelId);
         if (isIncrementalUpdateMode) {
             DaoStructuralVariant.deleteStructuralVariants(geneticProfileId, sampleIds);
         }

diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java
@@ -386,7 +386,7 @@ private void doImportData() throws IOException, DaoException {
 
                 line = buf.readLine();
             }
-            DaoSampleProfile.upsertSampleProfiles(orderedSampleList, geneticProfileId, genePanelId);
+            DaoSampleProfile.upsertSampleToProfileMapping(orderedSampleList, geneticProfileId, genePanelId);
             geneticAlterationImporter.finalise();
             if (MySQLbulkLoader.isBulkLoad()) {
                 MySQLbulkLoader.flushAll();

diff --git a/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleProfile.java b/src/test/java/org/mskcc/cbio/portal/integrationTest/dao/TestDaoSampleProfile.java
@@ -106,7 +106,7 @@ public void testDaoSampleProfile() throws DaoException {
         Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(study.getInternalId(), "TCGA-12345");
         Sample sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-12345-01");
 
-        DaoSampleProfile.upsertSampleProfiles(List.of(
+        DaoSampleProfile.upsertSampleToProfileMapping(List.of(
                 new DaoSampleProfile.SampleProfileTuple(geneticProfileId, sample.getInternalId(), null)));
 
         boolean exists = DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId);
@@ -115,7 +115,7 @@ public void testDaoSampleProfile() throws DaoException {
         assertEquals(geneticProfileId, DaoSampleProfile.getProfileIdForSample(sample.getInternalId()));
 
         sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-123456-01");
-        DaoSampleProfile.upsertSampleProfiles(List.of(
+        DaoSampleProfile.upsertSampleToProfileMapping(List.of(
                 new DaoSampleProfile.SampleProfileTuple(geneticProfileId, sample.getInternalId(), genePanel.getInternalId())));
 
         boolean existsByPanelId = DaoSampleProfile.sampleProfileMappingExistsByPanel(genePanel.getInternalId());

diff --git a/...skcc/cbio/portal/integrationTest/incremental/TestIncrementalStructuralVariantsImport.java b/...skcc/cbio/portal/integrationTest/incremental/TestIncrementalStructuralVariantsImport.java
@@ -91,7 +91,7 @@ public void testIncrementalUpload() throws DaoException {
         structuralVariant.setComments("This record has to be overwritten");
         DaoStructuralVariant.addStructuralVariantToBulkLoader(structuralVariant);
         MySQLbulkLoader.flushAll();
-        DaoSampleProfile.upsertSampleProfiles(List.of(
+        DaoSampleProfile.upsertSampleToProfileMapping(List.of(
                 new DaoSampleProfile.SampleProfileTuple(svGeneticProfile.getGeneticProfileId(), svDataSample.getInternalId(), null)));
 
         File singleTcgaSampleFolder = new File("src/test/resources/incremental/structural_variants/");