From 641450c2d738f2fef5d46ed867447764d187689f Mon Sep 17 00:00:00 2001
From: Ruslan Forostianov <ruslan@se4.bio>
Date: Fri, 12 Jul 2024 10:26:16 +0200
Subject: [PATCH] Use american english for method names

---
 .../cbio/portal/scripts/GeneticAlterationImporter.java    | 4 ++--
 .../scripts/GeneticAlterationIncrementalImporter.java     | 8 ++++----
 .../cbio/portal/scripts/ImportCnaDiscreteLongData.java    | 4 ++--
 .../org/mskcc/cbio/portal/scripts/ImportTabDelimData.java | 4 ++--
 4 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java
index a9cb4e63..e1d9a9f8 100644
--- a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java
+++ b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java
@@ -93,12 +93,12 @@ private void ensureNumberOfValuesIsCorrect(int valuesNumber) {
     }
 
 
-    public void initialise() {
+    public void initialize() {
         try {
             storeOrderedSampleList();
         } catch (DaoException e) {
             throw new RuntimeException(e);
         }
     }
-    public void finalise() { }
+    public void finalize() { }
 }
diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java
index 46585f48..4177420a 100644
--- a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java
+++ b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java
@@ -43,7 +43,7 @@ public boolean store(int geneticEntityId, String[] values) throws DaoException {
     }
 
     @Override
-    public void initialise() {
+    public void initialize() {
         try {
             this.geneticAlterationMap = daoGeneticAlteration.getGeneticAlterationMapForEntityIds(geneticProfileId, null);
             ArrayList <Integer> savedOrderedSampleList = DaoGeneticProfileSamples.getOrderedSampleList(this.geneticProfileId);
@@ -66,13 +66,13 @@ public void initialise() {
         } catch (DaoException e) {
             throw new RuntimeException(e);
         }
-        super.initialise();
+        super.initialize();
     }
 
     @Override
-    public void finalise() {
+    public void finalize() {
         expandRemainingGeneticEntityTabDelimitedRowsWithBlankValue();
-        super.finalise();
+        super.finalize();
     }
 
     private String[] extendValues(int geneticEntityId, String[] values) {
diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java
index bcad7ee8..e158f2d5 100644
--- 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);
-        geneticAlterationGeneImporter.initialise();
+        geneticAlterationGeneImporter.initialize();
         DaoSampleProfile.upsertSampleToProfileMapping(orderedSampleList, geneticProfileId, genePanelId);
 
         for (Long entrezId : toImport.eventsTable.rowKeySet()) {
@@ -171,7 +171,7 @@ private void doImportData() throws Exception {
 
         ProgressMonitor.setCurrentMessage(" --> total number of samples skipped (normal samples): " + getSamplesSkipped());
         buf.close();
-        geneticAlterationGeneImporter.finalise();
+        geneticAlterationGeneImporter.finalize();
         MySQLbulkLoader.flushAll();
     }
 
diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java
index a081ee35..75143ba3 100644
--- a/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java
+++ b/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java
@@ -305,7 +305,7 @@ private void doImportData() throws IOException, DaoException {
             this.geneticAlterationImporter = isIncrementalUpdateMode ? new GeneticAlterationIncrementalImporter(geneticProfileId, orderedSampleList)
                     : new GeneticAlterationImporter(geneticProfileId, orderedSampleList);
 
-            geneticAlterationImporter.initialise();
+            geneticAlterationImporter.initialize();
 
             //cache for data found in  cna_event' table:
             Set<CnaEvent.Event> existingCnaEvents = new HashSet<>();
@@ -389,7 +389,7 @@ private void doImportData() throws IOException, DaoException {
                 line = buf.readLine();
             }
             DaoSampleProfile.upsertSampleToProfileMapping(orderedSampleList, geneticProfileId, genePanelId);
-            geneticAlterationImporter.finalise();
+            geneticAlterationImporter.finalize();
             if (MySQLbulkLoader.isBulkLoad()) {
                 MySQLbulkLoader.flushAll();
             }