asl · asl · Jul 22, 2022 · Jul 22, 2022 · Jul 22, 2022 · Jul 22, 2022
diff --git a/blast/blastqueries.cpp b/blast/blastqueries.cpp
@@ -23,25 +23,15 @@
 #include "program/settings.h"
 #include <QTextStream>
 
-BlastQueries::BlastQueries() :
-    m_tempNuclFile(0), m_tempProtFile(0)
-{
-    m_presetColours = getPresetColours();
-}
-
+BlastQueries::BlastQueries()
+: m_presetColours{getPresetColours()} {}
 
 BlastQueries::~BlastQueries()
 {
     clearAllQueries();
 }
 
 
-void BlastQueries::createTempQueryFiles()
-{
-    m_tempNuclFile.reset(new QFile(g_blastSearch->m_tempDirectory + "nucl_queries.fasta"));
-    m_tempProtFile.reset(new QFile(g_blastSearch->m_tempDirectory + "prot_queries.fasta"));
-}
-
 BlastQuery * BlastQueries::getQueryFromName(QString queryName)
 {
     for (size_t i = 0; i < m_queries.size(); ++i)
@@ -63,7 +53,6 @@ void BlastQueries::addQuery(BlastQuery * newQuery)
     newQuery->setColour(m_presetColours[colourIndex]);
 
     m_queries.push_back(newQuery);
-    updateTempFiles();
 }
 
 
@@ -73,7 +62,6 @@ void BlastQueries::addQuery(BlastQuery * newQuery)
 QString BlastQueries::renameQuery(BlastQuery * newQuery, QString newName)
 {
     newQuery->setName(getUniqueName(newName));
-    updateTempFiles();
     return newQuery->getName();
 }
 
@@ -105,7 +93,6 @@ void BlastQueries::clearAllQueries()
     for (size_t i = 0; i < m_queries.size(); ++i)
         delete m_queries[i];
     m_queries.clear();
-    deleteTempFiles();
 }
 
 void BlastQueries::clearSomeQueries(std::vector<BlastQuery *> queriesToRemove)
@@ -115,47 +102,8 @@ void BlastQueries::clearSomeQueries(std::vector<BlastQuery *> queriesToRemove)
         m_queries.erase(std::remove(m_queries.begin(), m_queries.end(), queriesToRemove[i]), m_queries.end());
         delete queriesToRemove[i];
     }
-
-    updateTempFiles();
-}
-
-void BlastQueries::deleteTempFiles()
-{
-    if (tempNuclFileExists())
-        m_tempNuclFile->remove();
-    if (tempProtFileExists())
-        m_tempProtFile->remove();
-}
-
-void BlastQueries::updateTempFiles()
-{
-    deleteTempFiles();
-
-    if (getQueryCount(NUCLEOTIDE) > 0)
-        writeTempFile(m_tempNuclFile, NUCLEOTIDE);
-
-    if (getQueryCount(PROTEIN) > 0)
-        writeTempFile(m_tempProtFile, PROTEIN);
 }
 
-
-void BlastQueries::writeTempFile(QSharedPointer<QFile> file, QuerySequenceType sequenceType)
-{
-    file->open(QIODevice::Append | QIODevice::Text);
-    QTextStream out(file.data());
-    for (size_t i = 0; i < m_queries.size(); ++i)
-    {
-        if (m_queries[i]->getSequenceType() == sequenceType)
-        {
-            out << ">" << m_queries[i]->getName() << "\n";
-            out << m_queries[i]->getSequence();
-            out << "\n";
-        }
-    }
-    file->close();
-}
-
-
 void BlastQueries::searchOccurred()
 {
     for (size_t i = 0; i < m_queries.size(); ++i)
@@ -208,21 +156,6 @@ int BlastQueries::getQueryCount(QuerySequenceType sequenceType)
     return count;
 }
 
-
-bool BlastQueries::tempNuclFileExists()
-{
-    if (m_tempNuclFile.isNull())
-        return false;
-    return m_tempNuclFile->exists();
-}
-bool BlastQueries::tempProtFileExists()
-{
-    if (m_tempProtFile.isNull())
-        return false;
-    return m_tempProtFile->exists();
-}
-
-
 //This function looks to see if a query pointer is in the list
 //of queries.  The query pointer given may or may not still
 //actually exist, so it can't be dereferenced.

diff --git a/blast/blastqueries.h b/blast/blastqueries.h
@@ -26,12 +26,8 @@
 
 #include <vector>
 
-//This class manages all BLAST queries. It holds BlastQuery
-//objects itself, and it creates/modifies/deletes the temp
-//files which hold the queries for use in BLAST.
-//There are two separate temp files, one for nucleotide
-//queries (for blastn) and one for protein queries (for
-//tblasn).
+// This class manages all BLAST queries. It holds BlastQuery
+// objects
 
 class BlastQueries
 {
@@ -43,7 +39,6 @@ class BlastQueries
 
     BlastQuery * getQueryFromName(QString queryName);
 
-    void createTempQueryFiles();
     void addQuery(BlastQuery * newQuery);
     QString renameQuery(BlastQuery * newQuery, QString newName);
     void clearAllQueries();
@@ -60,16 +55,7 @@ class BlastQueries
     std::vector<QColor> m_presetColours;
 
 private:
-    QSharedPointer<QFile> m_tempNuclFile;
-    QSharedPointer<QFile> m_tempProtFile;
-
-    void deleteTempFiles();
-    void updateTempFiles();
-    bool tempNuclFileExists();
-    bool tempProtFileExists();
-    void writeTempFile(QSharedPointer<QFile> file, QuerySequenceType sequenceType);
     QString getUniqueName(QString name);
-
 };
 
 #endif // BLASTQUERIES_H
diff --git a/blast/blastsearch.cpp b/blast/blastsearch.cpp
@@ -32,14 +32,13 @@
 #include <QApplication>
 #include <cmath>
 
-BlastSearch::BlastSearch() :
-    m_blastQueries(), m_tempDirectory("bandage_temp/")
-{
-}
+BlastSearch::BlastSearch(const QDir &workDir) :
+    m_blastQueries(), m_tempDirectory(workDir.filePath("bandage_temp_XXXXXX")) {}
 
 BlastSearch::~BlastSearch()
 {
-    cleanUp();
+    clearBlastHits();
+    m_blastQueries.clearAllQueries();
 }
 
 void BlastSearch::clearBlastHits()
@@ -244,13 +243,7 @@ void BlastSearch::clearSomeQueries(std::vector<BlastQuery *> queriesToRemove)
 
 void BlastSearch::emptyTempDirectory() const
 {
-    //Safety checks
-    if (g_blastSearch->m_tempDirectory == "")
-        return;
-    if (!g_blastSearch->m_tempDirectory.contains("bandage_temp"))
-        return;
-
-    QDir tempDirectory(m_tempDirectory);
+    QDir tempDirectory(m_tempDirectory.path());
     tempDirectory.setNameFilters(QStringList() << "*.*");
     tempDirectory.setFilter(QDir::Files);
     foreach(QString dirFile, tempDirectory.entryList())

diff --git a/blast/blastsearch.h b/blast/blastsearch.h
@@ -21,23 +21,23 @@
 
 #include "blasthit.h"
 #include "blastqueries.h"
-#include "program/scinot.h"
 
-#include <QProcess>
 #include <QString>
-#include <QList>
-#include <QSharedPointer>
+#include <QDir>
+#include <QTemporaryDir>
 
 #include <vector>
 
 //This is a class to hold all BLAST search related stuff.
 //An instance of it is made available to the whole program
 //as a global.
 
+class QProcess;
+
 class BlastSearch
 {
 public:
-    BlastSearch();
+    explicit BlastSearch(const QDir &workDir = QDir::temp());
     ~BlastSearch();
 
     BlastQueries m_blastQueries;
@@ -46,7 +46,7 @@ class BlastSearch
     bool m_cancelRunBlastSearch{};
     QProcess *m_makeblastdb{};
     QProcess *m_blast{};
-    QString m_tempDirectory;
+    QTemporaryDir m_tempDirectory;
     std::vector<std::shared_ptr<BlastHit>> m_allHits;
 
     static QString getNodeNameFromString(const QString& nodeString);

diff --git a/blast/buildblastdatabaseworker.cpp b/blast/buildblastdatabaseworker.cpp
@@ -38,8 +38,11 @@ void BuildBlastDatabaseWorker::buildBlastDatabase()
 {
     g_blastSearch->m_cancelBuildBlastDatabase = false;
 
-    QFile file(g_blastSearch->m_tempDirectory + "all_nodes.fasta");
-    file.open(QIODevice::WriteOnly | QIODevice::Text);
+    QFile file(g_blastSearch->m_tempDirectory.filePath("all_nodes.fasta"));
+    if (!file.open(QIODevice::WriteOnly | QIODevice::Text)) {
+        emit finishedBuild("Failed to open: " + file.fileName());
+        return;
+    }
     QTextStream out(&file);
 
     for (auto &entry : g_assemblyGraph->m_deBruijnGraphNodes) {
@@ -72,7 +75,7 @@ void BuildBlastDatabaseWorker::buildBlastDatabase()
     }
 
     QStringList makeBlastdbOptions;
-    makeBlastdbOptions << "-in" << (g_blastSearch->m_tempDirectory + "all_nodes.fasta")
+    makeBlastdbOptions << "-in" << (g_blastSearch->m_tempDirectory.filePath("all_nodes.fasta"))
                        << "-dbtype" << "nucl";
 
     g_blastSearch->m_makeblastdb = new QProcess();

diff --git a/blast/runblastsearchworker.cpp b/blast/runblastsearchworker.cpp
@@ -22,6 +22,8 @@
 #include "program/globals.h"
 #include "program/settings.h"
 
+#include <QTemporaryFile>
+
 RunBlastSearchWorker::RunBlastSearchWorker(QString blastnCommand, QString tblastnCommand, QString parameters) :
     m_blastnCommand(blastnCommand), m_tblastnCommand(tblastnCommand), m_parameters(parameters)
 {
@@ -64,14 +66,36 @@ void RunBlastSearchWorker::runBlastSearch()
     emit finishedSearch(m_error);
 }
 
+static void writeQueryFile(QFile *file,
+                           const BlastQueries &queries,
+                           QuerySequenceType sequenceType) {
 
-QString RunBlastSearchWorker::runOneBlastSearch(QuerySequenceType sequenceType, bool * success)
-{
+    QTextStream out(file);
+    for (const auto *query: queries.m_queries) {
+        if (query->getSequenceType() != sequenceType)
+            continue;
+
+        out << '>' << query->getName() << '\n'
+            << query->getSequence()
+            << '\n';
+    }
+}
+
+QString RunBlastSearchWorker::runOneBlastSearch(QuerySequenceType sequenceType, bool * success) {
     QStringList blastOptions;
 
-    blastOptions << "-query" << (g_blastSearch-> m_tempDirectory +
-                                 (sequenceType == NUCLEOTIDE ? "nucl_queries.fasta" : "prot_queries.fasta"))
-                 << "-db" << (g_blastSearch->m_tempDirectory + "all_nodes.fasta")
+    QTemporaryFile tmpFile(g_blastSearch->m_tempDirectory.filePath(sequenceType == NUCLEOTIDE ?
+                                            "nucl_queries.XXXXXX.fasta" : "prot_queries.XXXXXX.fasta"));
+    if (!tmpFile.open()) {
+        m_error = "Failed to create temporary query file";
+        *success = false;
+        return "";
+    }
+
+    writeQueryFile(&tmpFile, g_blastSearch->m_blastQueries, sequenceType);
+
+    blastOptions << "-query" << tmpFile.fileName()
+                 << "-db" << (g_blastSearch->m_tempDirectory.filePath("all_nodes.fasta"))
                  << "-outfmt" << "6";
     blastOptions << m_parameters.split(" ", Qt::SkipEmptyParts);
 

diff --git a/command_line/commoncommandlinefunctions.cpp b/command_line/commoncommandlinefunctions.cpp
@@ -1189,28 +1189,6 @@ void getCommonHelp(QStringList * text)
 
 
 
-bool createBlastTempDirectory()
-{
-    //Running from the command line, it makes more sense to put the temp
-    //directory in the current directory.
-    g_blastSearch->m_tempDirectory = "bandage_temp-" + QString::number(QApplication::applicationPid()) + "/";
-
-    if (!QDir().mkdir(g_blastSearch->m_tempDirectory))
-        return false;
-
-    g_blastSearch->m_blastQueries.createTempQueryFiles();
-    return true;
-}
-
-void deleteBlastTempDirectory()
-{
-    if (g_blastSearch->m_tempDirectory != "" &&
-            QDir(g_blastSearch->m_tempDirectory).exists() &&
-            QDir(g_blastSearch->m_tempDirectory).dirName().contains("bandage_temp"))
-        QDir(g_blastSearch->m_tempDirectory).removeRecursively();
-}
-
-
 
 QString getElapsedTime(const QDateTime& start, const QDateTime& end)
 {

diff --git a/command_line/commoncommandlinefunctions.h b/command_line/commoncommandlinefunctions.h
@@ -73,9 +73,6 @@ void parseSettings(QStringList arguments);
 void getCommonHelp(QStringList * text);
 void getSettingsUsage(QStringList *text);
 
-bool createBlastTempDirectory();
-void deleteBlastTempDirectory();
-
 QString getElapsedTime(const QDateTime& start, const QDateTime& end);
 
 void getGraphScopeOptions(QStringList * text);

diff --git a/command_line/image.cpp b/command_line/image.cpp
@@ -119,9 +119,9 @@ int bandageImage(QStringList arguments)
 
     if (blastUsed)
     {
-        if (!createBlastTempDirectory())
+        if (!g_blastSearch->m_tempDirectory.isValid())
         {
-            err << "Error creating temporary directory for BLAST files" << Qt::endl;
+            err << "Error creating temporary directory for BLAST files: " << g_blastSearch->m_tempDirectory.errorString() << Qt::endl;
             return 1;
         }
 
@@ -227,8 +227,6 @@ int bandageImage(QStringList arguments)
     else
         returnCode = 0;
 
-    if (blastUsed)
-        deleteBlastTempDirectory();
 
     return returnCode;
 }

diff --git a/command_line/querypaths.cpp b/command_line/querypaths.cpp
@@ -118,9 +118,9 @@ int bandageQueryPaths(QStringList arguments)
         return 1;
     out << "done" << Qt::endl;
 
-    if (!createBlastTempDirectory())
+    if (!g_blastSearch->m_tempDirectory.isValid())
     {
-        err << "Error creating temporary directory for BLAST files" << Qt::endl;
+        err << "Error creating temporary directory for BLAST files: " << g_blastSearch->m_tempDirectory.errorString() << Qt::endl;
         return 1;
     }
 
@@ -261,7 +261,6 @@ int bandageQueryPaths(QStringList arguments)
 
     out << Qt::endl << "Elapsed time: " << getElapsedTime(startTime, QDateTime::currentDateTime()) << Qt::endl;
 
-    deleteBlastTempDirectory();
     return 0;
 }