fix windows thread problem

CMakeLists.txt

@@ -81,7 +81,7 @@ if (WIN32)
     message(STATUS ">>> WIN32")
     set(ENV{LUA_DIR} "D:/libraries/lua-5.3.3/;C:/lua53/")
     message(STATUS "IN MINGW")
-    set(Qt5_DIR "C:/Qt/Qt5.7.0/5.7/mingw53_32;C:/Qt/5.7/mingw53_32")
+    set(Qt5_DIR "C:/Qt/5.8/mingw53_32;C:/Qt/5.8/mingw53_32")
     set(ENV{OPENSSL_ROOT_DIR} "C:/OpenSSL-Win32/lib/")
 
 endif()

doc/biogui_idea.rst

@@ -4,7 +4,7 @@
 How does bioGUI work?
 *********************
 
-*bioGUI* heavily relies on the philosophy that everything is a network.
+*bioGUI* relies on the philosophy that the visual appearance as well as the assembly of the command line arguments can be represented as a network.
 Especially templates are seen as network, both in their visual description but most importantly also in the execution model.
 
 .. _biogui_install_modules :
@@ -145,7 +145,7 @@ Finally we can send the template to *bioGUI*, if an IP address and port have bee
 
 Make sure to use ``nc`` to send the content, as this will not work on Mac OS otherwise.
 In order to customize the template inbetween the ``EOF``, bash variables to be replaced must be written as ``${var-name}``.
-This conflicts with how *bioGUI* expects variables. Therefore make sure to escape the backslaash where you want to access variables in the *bioGUI* template!
+This conflicts with how *bioGUI* expects variables. Therefore, make sure to escape the backslaash where you want to access variables in the *bioGUI* template!
 
 bioGUI Templates
 ================
@@ -248,7 +248,7 @@ The idea is again based on a network of predefined nodes.
 The nodes can either be visual components, accessed by their respective **id**, or :ref:`biogui_execution_nodes` .
 
 Upon starting an application with *bioGUI*, the execution network is responsible to construct the command line arguments with which the target application is called.
-Therefore all executable nodes in the ``<execution>`` part are searched and *evaluated* one after the other (if there exist several).
+Therefore, all executable nodes in the ``<execution>`` part are searched and *evaluated* one after the other (if there exist several).
 Since execution must be started via an ``action`` visual element, which can have a *program* attribute, this allows to specify which executable nodes are executed: if the ``program`` attribute is set, this must match with the ``program`` attribute of the executable node.
 
 Finally an executable node is executed. Upon this the command line arguments are assembled. This is shown exemplarily in the below figure:

doc/build_wsl.rst

@@ -29,7 +29,7 @@ Step 2: Setup WSL
 
 Despite the interest to hide any command line as much as possible from the user, the following initial setup can not be automised.
 First a Command Prompt or better PowerShell must be started.
-Therefore simply search for the *Windows PowerShell* in the start menu.
+Search for the *Windows PowerShell* in the start menu.
 
 .. image:: ./images/wsl/powershell.PNG
    :scale: 30
@@ -41,8 +41,8 @@ However, before the download starts, first the user has to acknowledge that he w
    :scale: 30
 
 Finally, after *WSL* has been downloaded and extracted, *WSL* has to create a linux user account.
-Therefore choose a username and password you can easily remember.
-Remembering the password is essential here it will be needed for any installation one is performing on *WSL*.
+It is recommended to choose a username and password you can easily remember.
+Remembering the password is essential here, as it will be needed for any installation one is performing on *WSL*.
 
 .. image:: ./images/wsl/powershell_setup_user.PNG
    :scale: 30

doc/user_guide.rst

@@ -33,7 +33,7 @@ Mac OS
 
 Download and open the provided dmg package. You can simply drag and drop the bioGUI.app into your Applications folder.
 In order to productively use bioGUI, it may be required to install the OSX command line tools as well as brew.
-Most (install) templates will require you to have wget and netcat install. Using brew installation is simple:
+Most (install) templates will require you to have wget and netcat installed. Using brew installation is simple:
 
 .. code:: bash
     
@@ -46,9 +46,10 @@ Downloading Templates
 
 
 Part of *bioGUI* is a user-friendly accessibility of templates for various programs.
-Therefore application developers and sophisticated users can upload their templates to our website in order to make their template available to other users.
+Therefore, application developers and sophisticated users can upload their templates to our website in order to make their template available to other users.
 The user has to submit his name, eMail address, a template name and the template itself.
 He can select whether he wants to be an anonymous user (user name is always hidden) and whether this is an installation script (which downloads and creates the \ac{GUI} template specifically for this installed application) or a regular template.
+Additionally, categories for the template can be supplied, e.g. whether this is a template for a sequencing tool, or proteomics.
 A screenshot of the template submission is shown below.
 
 .. image:: ./images/templates/template_submission.png
@@ -63,7 +64,7 @@ Available templates are only shown and can be downloaded via the *bioGUI* applic
 Within *bioGUI*, clicking the *Download Templates* button, a new dialog window opens showing a list of available templates.
 Columns can be sorted by double clicking the header, and using the search only templates which contain the searched words are shown.
 Upon selecting one or multiple (keep ctrl-key down while clicking) rows and clicking the *Download* button, those templates are downloaded and available for the user.
-Since it is possible to copy or alter templates, new templates are created at all times (no information is lost).
+Since it is possible to copy or alter templates, *bioGUI* never overwrites existing templates, but will create a new copy.
 
 .. image:: ./images/templates/biogui_selection.png
    :scale: 50

install_templates/install_wsl_first.igui

@@ -8,7 +8,7 @@ echo "Dependencies: build-essential dos2unix"
 if [ ! "$2" = "" ]; then
 	echo "Installing dependencies"
 	echo $2 | sudo -S apt-get update
-	echo $2 | sudo -S apt-get -y install build-essential dos2unix
+	echo $2 | sudo -S apt-get -y install build-essential dos2unix unzip
 
 	echo "Enjoy bioGUI!"
 else

src/app/AdvancedStreamBox.h

@@ -257,8 +257,10 @@ Q_OBJECT
             {
 
                 ExtendedProcessBuffer* pBuffer = oIt->second.at(i);
-                pBuffer->transferText("\n");
 
+                LOGERROR("Deleting PROC Buffer: " + std::to_string((uint64_t) pBuffer));
+
+                pBuffer->transferText("\n");
                 pBuffer->deleteLater();
 
             }
@@ -272,7 +274,10 @@ Q_OBJECT
     void finishThread( ExecuteThread* pThread )
     {
 
-        std::cout << "finishing thread: " << pThread << std::endl;
+        LOGERROR("Finishing thread: " + std::to_string((uint64_t) pThread));
+
+        if (pThread == NULL)
+            return;
 
 
         std::map<ExecuteThread*, std::vector<ExtendedThreadBuffer*> >::iterator oJt = m_mThreadToBuffer.find(pThread);
@@ -466,7 +471,9 @@ protected slots:
     void receiveText(QString sString, QColor oColor, QString sStreamID)
     {
 
-        std::cout << "received: " << sString.toStdString() << " for stream " << sStreamID.toStdString()  << std::endl;
+        LOGERROR("AdvancedStreamBox received: " + std::to_string((uint64_t) this) + " for STREAM: " + sStreamID.toStdString());
+        LOGERROR( sString.toStdString() );
+        LOGERROR("RECEIVE END");
 
         AdvancedListWidgetItem* pLastStream = this->getLastItemForStream(&sStreamID);
 

src/app/ExtendedThreadBuffer.h

@@ -45,6 +45,7 @@ class ExtendedThreadBuffer : public ExtendedStdBuffer {
 
         if (this->m_pParentThread != NULL)
         {
+            m_pParentThread->pThread->deleteLater();
             delete m_pParentThread;
         }
 

src/app/ProcessLauncher.h

@@ -41,6 +41,7 @@
     #define __BIOGUI__64
 #endif
 
+/*
 
 class ProcessThread : public ExecuteThread
 {
@@ -118,6 +119,8 @@ Q_OBJECT
 
 };
 
+*/
+
 class ProcessLauncher : public QObject
 {
     Q_OBJECT
@@ -132,7 +135,7 @@ class ProcessLauncher : public QObject
         {
             m_pProcess = new QProcess();
         } else {
-            m_pThread = NULL;//new ProcessThread(m_sProgram + " " + m_sParam);
+            //m_pThread = NULL;//new ProcessThread(m_sProgram + " " + m_sParam);
             m_pProcess = new QProcess();
         }
     }
@@ -162,6 +165,8 @@ class ProcessLauncher : public QObject
         return m_pProcess;
     }
 
+    /*
+
     ExecuteThread* getThread()
     {
         return NULL;
@@ -172,6 +177,8 @@ class ProcessLauncher : public QObject
         return NULL;
     }
 
+    */
+
     QString startBlocking(uint32_t iWaitMSec = 10000)
     {
         this->start();
@@ -259,23 +266,23 @@ class ProcessLauncher : public QObject
         this->connect(m_pProcess, static_cast<void(QProcess::*)(int, QProcess::ExitStatus)>(&QProcess::finished),
                            [pProcess, this](int exitCode, QProcess::ExitStatus exitStatus){
 
-                               std::cerr << "Exit Code: " << exitCode << std::endl;
-                               std::cerr << "Exit Status: " << exitStatus << std::endl;
-
-                               std::string sError = pProcess->errorString().toStdString();
-                               std::cerr << "Error: " << sError << std::endl;
-
-                               std::string sProgram = pProcess->program().toStdString();
-                               std::cerr << "Program: " << sProgram << std::endl;
+                                LOGERROR( "Exit Code: " + std::to_string(exitCode) );
+                                LOGERROR( "Exit Status: " + std::to_string(exitStatus) );
+                                LOGERROR( "Error: " + pProcess->errorString().toStdString() );
+                                LOGERROR( "Program: " + pProcess->program().toStdString() );
 
                                for (int i = 0; i < pProcess->arguments().size(); ++i)
                                {
                                    std::string sArgument = pProcess->arguments().at(i).toStdString();
 
                                    std::cerr << "Argument " << i << " : " << sArgument << std::endl;
+
+                                   LOGERROR( "Argument " + std::to_string(i) + ": " + pProcess->arguments().at(i).toStdString() );
+
                                }
 
-                               std::cout << "finished: " << pProcess << std::endl;
+                               LOGERROR( "Process ID: " + std::to_string(pProcess->processId()) );
+                               LOGERROR( "Process: " + std::to_string((uint64_t) pProcess) );
 
                                emit this->finished();
                            });
@@ -294,8 +301,10 @@ public slots:
 
     void executionFinished()
     {
+        /*
         if (m_pThread != NULL)
             m_pThread->deleteLater();
+            */
 
         if (m_pProcess != NULL)
             m_pProcess->deleteLater();
@@ -389,7 +398,7 @@ public slots:
 
 
     QProcess* m_pProcess = NULL;
-    ProcessThread* m_pThread = NULL;
+    //ProcessThread* m_pThread = NULL;
     bool m_bWindowsProcNoHandle = false;
     QString m_sProgram;
     QString m_sParam;

src/app/TCPExtendedBuffer.h

@@ -77,7 +77,7 @@ class TCPExtendedBuffer : public ExtendedThreadBuffer
     ~TCPExtendedBuffer()
     {
 
-        this->stopTransmissions();
+        //this->stopTransmissions();
 
         m_pServer->deleteLater();
 

src/bioGUIapp.h

@@ -259,21 +259,38 @@ class bioGUIapp : public QApplication {
     {
 
         ExecutionNetwork* pNetwork = NULL;
-        ExecutionRunThread* pThread = NULL;
+
+        if (m_pExecThread != NULL)
+        {
+            LOGERROR("QUIT");
+            m_pExecThread->quit();
+            LOGERROR("WAIT");
+            m_pExecThread->wait();
+            LOGERROR("DELETE");
+            m_pExecThread->deleteLater();
+
+            m_pExecThread = NULL;
+        }
+
 
         this->disableActions();
 
         XMLParserExecution* pParseExecution = new XMLParserExecution();
         std::string sCurrentFilePath = m_pWindowParser->getCurrentDocumentPath();
         pParseExecution->initializeFile(sCurrentFilePath);
 
-        pThread = new ExecutionRunThread(m_pWindowParser, pParseExecution, sProgramToRun);
+        m_pExecThread = new ExecutionRunThread(m_pWindowParser, pParseExecution, sProgramToRun);
+        bioGUIapp* pApp = this;
 
-        this->connect(pThread, &QThread::started, pThread, &ExecutionRunThread::startExecution);
-        this->connect(pThread, &ExecutionRunThread::executionFinished, this, &bioGUIapp::programFinished);
-        this->connect(pThread, &ExecutionRunThread::executionFinished, pThread, &ExecutionRunThread::deleteLater);
+        this->connect(m_pExecThread, &QThread::started, m_pExecThread, &ExecutionRunThread::startExecution);
+        this->connect(m_pExecThread, &ExecutionRunThread::executionFinished, [pApp] () {
 
-        pThread->start();
+            pApp->programFinished();
+
+        });
+        //this->connect(pThread, &ExecutionRunThread::executionFinished, pThread, &ExecutionRunThread::deleteLater);
+
+        m_pExecThread->start();
 
     }
 
@@ -380,6 +397,10 @@ public slots:
     QString m_sDownloadServerLocation = "";
 
 
+    /** TEST PLAYGROUND **/
+    ExecutionRunThread* m_pExecThread = NULL;
+
+
 };
 
 

src/parsing/nodes/ExecutionExecuteNode.h

@@ -137,12 +137,12 @@ class ExecutionExecuteNode : public ExecutionExecutableNode {
 
         ProcessLauncher* pLauncher = new ProcessLauncher(QString(sProgram.c_str()), QString(sCLArg.c_str()), bWSL);
 
-        this->evaluateChildren(pID2Node, pInputID2Value, pInputID2FunctionWidget, pLauncher->getProcess(), pLauncher->getThread(), false);
+        this->evaluateChildren(pID2Node, pInputID2Value, pInputID2FunctionWidget, pLauncher->getProcess(), NULL, false); //
 
         pLauncher->connect(pLauncher, &ProcessLauncher::finished,
                 [pLauncher, pID2Node, pInputID2Value, pInputID2FunctionWidget, bEmitSignal, this](){
 
-                    this->evaluateChildren(pID2Node, pInputID2Value, pInputID2FunctionWidget, pLauncher->getProcess(), pLauncher->getThread(), true);
+                    this->evaluateChildren(pID2Node, pInputID2Value, pInputID2FunctionWidget, pLauncher->getProcess(), NULL, true);
                     pLauncher->deleteLater();
 
                     // calculation finished!

src/parsing/nodes/ExecutionIfNode.h

@@ -155,9 +155,10 @@ class ExecutionIfNode : public ExecutionExecutableNode {
          * Any method that needs value2
          *
          */
-        std::cerr << "Val 1: " << sValue1 << std::endl;
-        std::cerr << "Val 2: " << sValue2 << std::endl;
-        std::cerr << "Evaluating else node: " << m_bEvaluateElse << std::endl;
+        LOGERROR("IF ID: " + m_sID);
+        LOGERROR("Val 1: " + sValue1);
+        LOGERROR("Val 2: " + sValue2);
+        LOGERROR("Go into Else? " + std::to_string(m_bEvaluateElse));
 
         sReturn = this->evaluateChildren(pID2Node, pInputID2Value, pInputID2FunctionWidget, bEmitSignal);
 

src/parsing/nodes/ExecutionNetwork.h

@@ -132,6 +132,8 @@ class ExecutionNetwork : public QObject{
 
         if (oIt == m_vExecNodes.end())
         {
+            LOGERROR("EXECUTION FINISHED!")
+
             emit executionFinished();
             return 0;
         }

src/parsing/nodes/ExecutionOutputNode.h

@@ -223,6 +223,8 @@ class ExecutionOutputNode : public ExecutionDeferredNode {
 
             } else {
 
+                LOGERROR("Deferred Output Node");
+
                 pTextEdit->finishProcess(pProcess);
                 pTextEdit->finishThread(pThread);
 

templates/WSL_install.gui

@@ -84,14 +84,14 @@
 <const>&quot;</const>
 </add>
 <value from="addtopath"/>
-<if comp="EQUALS" value1="templpath_sel" value2="true" sep=" ">
+<if id="templpath_sel_if" comp="EQUALS" value1="templpath_sel" value2="true" sep=" ">
 <value from="localip"/>
 <const>33333</const>
 </if>
 </add>
 
 <add id="template_path" sep="">
-<if comp="EQUALS" value1="templpath_sel" value2="true">
+<if id="script_else" comp="EQUALS" value1="templpath_sel" value2="true">
 <script argv="${templpath},${loc_appdir}">
 <![CDATA[
 function evaluate(gvnPath, appdir)
@@ -121,7 +121,7 @@ end
     <output id="outcout" type="COUT" color="green" to="outputstream1" />
 	<output id="outcout2" type="CERR" color="red" to="outputstream2" />
 	<output type="TCP" host="" port="33333" color="blue" to="savetemplate" />
-	<output deferred="true" type="FILE" from="template_path" to="savetemplate" />
+	<output deferred="true" type="FILE" from="${template_path}" to="savetemplate" />
   </execute>
 
 </execution>