From 0e6ce2e2b83ab3d2bbf49343d27ac81373920ef1 Mon Sep 17 00:00:00 2001
From: Ruslan Forostianov <ruslan@se4.bio>
Date: Thu, 11 Jul 2024 20:58:23 +0200
Subject: [PATCH] Extract db communicating methods out of the constructor

introduce initialise() method
---
 .../scripts/GeneticAlterationImporter.java    | 11 ++++-
 .../GeneticAlterationIncrementalImporter.java | 49 +++++++++++--------
 .../scripts/ImportCnaDiscreteLongData.java    |  1 +
 .../portal/scripts/ImportTabDelimData.java    |  2 +
 4 files changed, 40 insertions(+), 23 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 c076a411..a9cb4e63 100644
--- a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java
+++ b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationImporter.java
@@ -25,10 +25,9 @@ protected GeneticAlterationImporter() {}
     public GeneticAlterationImporter(
         int geneticProfileId,
         List<Integer> orderedSampleList
-    ) throws DaoException {
+    ) {
         this.geneticProfileId = geneticProfileId;
         this.orderedSampleList = orderedSampleList;
-        storeOrderedSampleList();
     }
 
     protected void storeOrderedSampleList() throws DaoException {
@@ -93,5 +92,13 @@ private void ensureNumberOfValuesIsCorrect(int valuesNumber) {
         }
     }
 
+
+    public void initialise() {
+        try {
+            storeOrderedSampleList();
+        } catch (DaoException e) {
+            throw new RuntimeException(e);
+        }
+    }
     public void finalise() { }
 }
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 755ae0ee..b6164d0b 100644
--- a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java
+++ b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java
@@ -17,34 +17,15 @@ public class GeneticAlterationIncrementalImporter extends GeneticAlterationImpor
 
     private final List<Integer> fileOrderedSampleList;
     private final DaoGeneticAlteration daoGeneticAlteration = DaoGeneticAlteration.getInstance();
-    private final HashMap<Integer, HashMap<Integer, String>> geneticAlterationMap;
+    private HashMap<Integer, HashMap<Integer, String>> geneticAlterationMap;
 
     public GeneticAlterationIncrementalImporter(
             int geneticProfileId,
             List<Integer> fileOrderedSampleList
-    ) throws DaoException {
+    ) {
 
         this.geneticProfileId = geneticProfileId;
-        this.geneticAlterationMap = daoGeneticAlteration.getGeneticAlterationMapForEntityIds(geneticProfileId, null);
         this.fileOrderedSampleList = fileOrderedSampleList;
-
-        ArrayList <Integer> savedOrderedSampleList = DaoGeneticProfileSamples.getOrderedSampleList(this.geneticProfileId);
-        int initialOrderSampleListSize = savedOrderedSampleList.size();
-        geneticAlterationMap.forEach((geneticEntityId, sampleToValue) -> {
-            if (sampleToValue.size() != initialOrderSampleListSize) {
-                throw new IllegalStateException("Number of samples ("
-                        + sampleToValue.size() + ") for genetic entity with id "
-                        + geneticEntityId + " does not match with the number in the preexisting sample list ("
-                        + initialOrderSampleListSize + ").");
-            }
-        });
-        // add all new sample ids at the end
-        this.orderedSampleList = new ArrayList<>(savedOrderedSampleList);
-        List<Integer> newSampleIds = this.fileOrderedSampleList.stream().filter(sampleId -> !savedOrderedSampleList.contains(sampleId)).toList();
-        this.orderedSampleList.addAll(newSampleIds);
-        DaoGeneticProfileSamples.deleteAllSamplesInGeneticProfile(this.geneticProfileId);
-        this.storeOrderedSampleList();
-        daoGeneticAlteration.deleteAllRecordsInGeneticProfile(this.geneticProfileId);
     }
 
     @Override
@@ -60,6 +41,32 @@ public boolean store(int geneticEntityId, String[] values) throws DaoException {
         return super.store(geneticEntityId, expandedValues);
     }
 
+    @Override
+    public void initialise() {
+        try {
+            this.geneticAlterationMap = daoGeneticAlteration.getGeneticAlterationMapForEntityIds(geneticProfileId, null);
+            ArrayList <Integer> savedOrderedSampleList = DaoGeneticProfileSamples.getOrderedSampleList(this.geneticProfileId);
+            int initialOrderSampleListSize = savedOrderedSampleList.size();
+            geneticAlterationMap.forEach((geneticEntityId, sampleToValue) -> {
+                if (sampleToValue.size() != initialOrderSampleListSize) {
+                    throw new IllegalStateException("Number of samples ("
+                            + sampleToValue.size() + ") for genetic entity with id "
+                            + geneticEntityId + " does not match with the number in the preexisting sample list ("
+                            + initialOrderSampleListSize + ").");
+                }
+            });
+            // add all new sample ids at the end
+            this.orderedSampleList = new ArrayList<>(savedOrderedSampleList);
+            List<Integer> newSampleIds = this.fileOrderedSampleList.stream().filter(sampleId -> !savedOrderedSampleList.contains(sampleId)).toList();
+            this.orderedSampleList.addAll(newSampleIds);
+            DaoGeneticProfileSamples.deleteAllSamplesInGeneticProfile(this.geneticProfileId);
+            daoGeneticAlteration.deleteAllRecordsInGeneticProfile(this.geneticProfileId);
+        } catch (DaoException e) {
+            throw new RuntimeException(e);
+        }
+        super.initialise();
+    }
+
     @Override
     public void finalise() {
         expandRemainingGeneticEntityTabDelimitedRowsWithBlankValue();
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 765986b5..bcad7ee8 100644
--- a/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java
+++ b/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java
@@ -153,6 +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();
         DaoSampleProfile.upsertSampleToProfileMapping(orderedSampleList, geneticProfileId, genePanelId);
 
         for (Long entrezId : toImport.eventsTable.rowKeySet()) {
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 37736a96..a081ee35 100644
--- a/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java
+++ b/src/main/java/org/mskcc/cbio/portal/scripts/ImportTabDelimData.java
@@ -305,6 +305,8 @@ private void doImportData() throws IOException, DaoException {
             this.geneticAlterationImporter = isIncrementalUpdateMode ? new GeneticAlterationIncrementalImporter(geneticProfileId, orderedSampleList)
                     : new GeneticAlterationImporter(geneticProfileId, orderedSampleList);
 
+            geneticAlterationImporter.initialise();
+
             //cache for data found in  cna_event' table:
             Set<CnaEvent.Event> existingCnaEvents = new HashSet<>();
             if (isDiscretizedCnaProfile) {