From b9b8c8ee2ee6a58b3745f0567700dd8f967f094c Mon Sep 17 00:00:00 2001
From: Eugene Melamud <eugene@calicolabs.com>
Date: Tue, 6 Feb 2018 11:29:36 -0800
Subject: [PATCH] when saving project in maven scans table is preserved

---
 src/maven/database.cpp          |  2 +-
 src/maven/projectDB.cpp         | 29 ++++++++++++++++++++++-------
 src/maven/projectDB.h           |  1 +
 src/maven/projectdockwidget.cpp |  5 -----
 4 files changed, 24 insertions(+), 13 deletions(-)

diff --git a/src/maven/database.cpp b/src/maven/database.cpp
index fa93b498..6dd194ee 100644
--- a/src/maven/database.cpp
+++ b/src/maven/database.cpp
@@ -162,7 +162,7 @@ void Database::loadCompoundsSQL(QString databaseName) {
         }
 
         sort(compoundsDB.begin(),compoundsDB.end(), Compound::compMass);
-        qDebug() << "loadCompoundSQL : " << compoundsDB.size();
+        qDebug() << "loadCompoundSQL : " << databaseName << compoundsDB.size();
         if(loadcount > 0 and databaseName != "ALL") loadedDatabase[databaseName] = 1;
 }
 
diff --git a/src/maven/projectDB.cpp b/src/maven/projectDB.cpp
index 8ca3fc48..1d046b0b 100644
--- a/src/maven/projectDB.cpp
+++ b/src/maven/projectDB.cpp
@@ -11,10 +11,9 @@ void ProjectDB::saveGroups(vector<PeakGroup>& allgroups, QString setName) {
 
 void ProjectDB::deleteAll() {
     QSqlQuery query(sqlDB);
-    query.exec("drop table peakgroups");
     query.exec("drop table samples");
+    query.exec("drop table peakgroups");
     query.exec("drop table peaks");
-    query.exec("drop table scans");
     query.exec("drop table rt_update_key");
 }
 
@@ -24,6 +23,18 @@ void ProjectDB::deleteGroups() {
     query.exec("drop table peaks");
 }
 
+
+void ProjectDB::deleteSearchResults(QString searchTable) {
+    QSqlQuery query(sqlDB);
+    query.prepare("delete from peaks where groupId in (select groupId from peakgroups where searchTableName = ?");
+    query.addBindValue(searchTable);
+    query.exec();
+
+    query.prepare("delete from peakgroups where searchTableName = ?");
+    query.addBindValue(searchTable);
+    query.exec();
+}
+
 void ProjectDB::assignSampleIds() {
     int maxSampleId = -1;
     for(mzSample* s: samples) if (s->getSampleId()>maxSampleId) maxSampleId=s->getSampleId();
@@ -59,7 +70,9 @@ void ProjectDB::saveScans(vector<mzSample *> &sampleSet) {
     QSqlQuery query0(sqlDB);
 
 	query0.exec("begin transaction");
-	if(!query0.exec("CREATE TABLE IF NOT EXISTS scans(\
+    query0.exec("drop table scans");
+
+    if(!query0.exec("CREATE TABLE IF NOT EXISTS scans(\
 				id INTEGER PRIMARY KEY   AUTOINCREMENT,\
 				sampleId     int       NOT NULL,\
 				scan    int       NOT NULL,\
@@ -532,7 +545,7 @@ void ProjectDB::loadGroupPeaks(PeakGroup* parent) {
      QSqlQuery query(sqlDB);
      query.prepare("select P.*, S.name as sampleName from peaks P, samples S where P.sampleId = S.sampleId and P.groupId = ?");
      query.bindValue(0,parent->groupId);
-     qDebug() << "loadin peaks for group " << parent->groupId;
+     //qDebug() << "loadin peaks for group " << parent->groupId;
      query.exec();
 
      while (query.next()) {
@@ -641,13 +654,15 @@ void ProjectDB::loadSamples() {
 		foreach(mzSample* loadedFile, samples) {
 			if (loadedFile->sampleName == sname.toStdString()) checkLoaded=true;
 			if (QString(loadedFile->fileName.c_str()) == fname) checkLoaded=true;
-		}
-	     	if(checkLoaded == true) continue;  // skip files that have been loaded already
+        }
+
+        if(checkLoaded == true) continue;  // skip files that have been loaded already
+
 
             	mzSample* s = new mzSample();
             	s->loadSample(fname.toLatin1());
                 s->fileName = fname.toStdString();
-                s->sampleId = sampleId;
+                s->setSampleId(sampleId);
                 s->setSampleOrder(sampleOrder);
                 s->isSelected = isSelected;
                 s->color[0]   = color_red;
diff --git a/src/maven/projectDB.h b/src/maven/projectDB.h
index 9213157c..fd56f2f3 100644
--- a/src/maven/projectDB.h
+++ b/src/maven/projectDB.h
@@ -30,6 +30,7 @@ class ProjectDB {
             void loadGroupPeaks(PeakGroup* group);
             void deleteAll();
             void deleteGroups();
+            void deleteSearchResults(QString searchTable);
             void deletePeakGroup(PeakGroup* g, QString tableName);
             void assignSampleIds();
             void saveAlignment();
diff --git a/src/maven/projectdockwidget.cpp b/src/maven/projectdockwidget.cpp
index 86a824c2..87f4bda5 100644
--- a/src/maven/projectdockwidget.cpp
+++ b/src/maven/projectdockwidget.cpp
@@ -508,8 +508,6 @@ void ProjectDockWidget::loadProjectSQLITE(QString fileName) {
         QString filepath   = query.value("filename").toString();
         QString sname   = query.value("name").toString();
 
-        qDebug() << "loadProjectSQLITE: " << sname << filepath;
-
         //skip files that have been loaded already
         bool checkLoaded=false;
         foreach(mzSample* loadedFile, _mainwindow->getSamples()) {
@@ -519,8 +517,6 @@ void ProjectDockWidget::loadProjectSQLITE(QString fileName) {
 
         if(checkLoaded == true) continue;  // skip files that have been loaded already
 
-        qDebug() << "Looking for sample: " << sname ;
-
         //locate file
         QString locatedpath = locateSample(filepath, pathlist);
         QFileInfo sampleFile(locatedpath);
@@ -624,7 +620,6 @@ void ProjectDockWidget::loadAllPeakTables() {
     for(int i=0; i < currentProject->allgroups.size(); i++ ) {
         PeakGroup* g = &(currentProject->allgroups[i]);
         currentProject->allgroups[i].groupStatistics();
-        qDebug() <<  "Loading peakgroup" << i;
 
         //put them in right place
         if(g->searchTableName.empty()) g->searchTableName="Bookmarks";