support output directories in TOPPAS

src/openms_gui/include/OpenMS/VISUAL/DIALOGS/TOPPASIOMappingDialog.h

@@ -57,9 +57,6 @@ public slots:
     /// The edge we are configuring
     TOPPASEdge * edge_;
 
-    /// Vector storing the mapping of the target input combobox indices to param indices of edges
-    QVector<int> target_input_param_indices_;
-
 protected slots:
 
     /// Called when OK is pressed; checks if the selected parameters are valid

src/openms_gui/include/OpenMS/VISUAL/TOPPASOutputFileListVertex.h

@@ -21,21 +21,12 @@ namespace OpenMS
       @ingroup TOPPAS_elements
   */
   class OPENMS_GUI_DLLAPI TOPPASOutputFileListVertex :
-    public TOPPASVertex
+    public TOPPASOutputVertex
   {
     Q_OBJECT
 
 public:
-
-    /// Default constructor
-    TOPPASOutputFileListVertex() = default;
-    /// Copy constructor
-    TOPPASOutputFileListVertex(const TOPPASOutputFileListVertex & rhs);
-    /// Destructor
-    ~TOPPASOutputFileListVertex() override = default;
-    /// Assignment operator
-    TOPPASOutputFileListVertex & operator=(const TOPPASOutputFileListVertex & rhs);
-    /// returns "OutputVertex"
+    /// returns "OutputFileVertex"
     String getName() const override;
     // documented in base class
     void paint(QPainter * painter, const QStyleOptionGraphicsItem * option, QWidget * widget) override;
@@ -66,21 +57,6 @@ namespace OpenMS
 public slots:
     //documented in base class
     void inEdgeHasChanged() override;
-
-signals:
-    /// Emitted when an output file was written
-    void outputFileWritten(const String& file);
-
-    /// Emitted when user has changed the output folder name (i.e. output dir needs to be newly created and packages updates)
-    void outputFolderNameChanged();
-
-protected:
-    /// custom output folder name
-    QString output_folder_name_;
-
-    // convenience members, not required for operation, but for progress during copying
-    int files_written_ = 0;   ///< files that were already written
-    int files_total_ = 0;     ///< total number of files from upstream
   };
 }
 

src/openms_gui/include/OpenMS/VISUAL/TOPPASOutputFolderVertex.h

@@ -0,0 +1,63 @@
+// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
+// SPDX-License-Identifier: BSD-3-Clause
+//
+// --------------------------------------------------------------------------
+// $Maintainer: Chris Bielow $
+// $Authors: Chris Bielow $
+// --------------------------------------------------------------------------
+
+#pragma once
+
+// OpenMS_GUI config
+#include <OpenMS/VISUAL/OpenMS_GUIConfig.h>
+
+#include <OpenMS/VISUAL/TOPPASVertex.h>
+
+namespace OpenMS
+{
+  /**
+      @brief A vertex representing an output folder
+
+      @ingroup TOPPAS_elements
+  */
+  class OPENMS_GUI_DLLAPI TOPPASOutputFolderVertex :
+    public TOPPASOutputVertex
+  {
+    Q_OBJECT
+
+public:
+    /// returns "OutputFolderVertex"
+    String getName() const override;
+    // documented in base class
+    void paint(QPainter * painter, const QStyleOptionGraphicsItem * option, QWidget * widget) override;
+    // documented in base class
+    QRectF boundingRect() const override;
+    // documented in base class
+    void reset(bool reset_all_files = false) override;
+    /// opens the folder containing the output data
+    void mouseDoubleClickEvent(QGraphicsSceneMouseEvent*) override;
+    /// Called when the parent node has finished execution
+    void run() override;
+    /// Returns the full directory (including preceding output path as selected by user)
+    String getFullOutputDirectory() const;
+    /// Returns the directory where the output files are stored
+    String getOutputDir() const;
+    /// Creates the output directory for this node
+    String createOutputDir() const;
+    /// Sets the topological sort number and removes invalidated tmp files
+    void setTopoNr(UInt nr) override;
+    /// Opens the folders of the output files
+    void openContainingFolder() const;
+    /// Sets a custom output folder name, which will be integrated into 'getOutputDir()' and 'getFullOutputDirectory()' calls.
+    /// @note The string is not checked for validity (avoid characters which are not allowed in directories, e.g. '{')
+    void setOutputFolderName(const QString& name);
+    /// return the output folder where results are written
+    const QString& getOutputFolderName() const;
+
+public slots:
+    //documented in base class
+    void inEdgeHasChanged() override;
+
+  };
+}
+

src/openms_gui/include/OpenMS/VISUAL/TOPPASScene.h

@@ -191,7 +191,7 @@ namespace OpenMS
     ///Connects the signals to slots
     void connectToolVertexSignals(TOPPASToolVertex * ttv);
     ///Connects the signals to slots
-    void connectOutputVertexSignals(TOPPASOutputFileListVertex * oflv);
+    void connectOutputVertexSignals(TOPPASOutputVertex * oflv);
     ///Connects the signals to slots
     void connectMergerVertexSignals(TOPPASMergerVertex * tmv);
     ///Connects the signals to slots

src/openms_gui/include/OpenMS/VISUAL/TOPPASToolVertex.h

@@ -63,7 +63,8 @@ namespace OpenMS
       enum IOType
       {
         IOT_FILE,
-        IOT_LIST
+        IOT_LIST,
+        IOT_DIR ///< output directory
       };
 
       /// Comparison operator
@@ -78,6 +79,11 @@ namespace OpenMS
           return param_name.compare(rhs.param_name) < 0;
         }
       }
+      /// Comparison operator
+      bool operator==(const IOInfo& rhs) const
+      {
+        return type == rhs.type && param_name == rhs.param_name;
+      }
 
       /// Assignment operator
       IOInfo& operator=(const IOInfo& rhs)
@@ -92,10 +98,9 @@ namespace OpenMS
       /// Is any of the input/output parameters a list?
       static bool isAnyList(const QVector<IOInfo>& params)
       {
-        for (QVector<IOInfo>::const_iterator it = params.begin();
-             it != params.end(); ++it)
+        for (const auto& p : params)
         {
-          if (it->type == IOT_LIST) return true;
+          if (p.type == IOT_LIST) return true;
         }
         return false;
       }
@@ -125,10 +130,8 @@ namespace OpenMS
     const String& getType() const;
     /// Returns input file/list parameters together with their valid types.
     QVector<IOInfo> getInputParameters() const;
-    /// Returns output file/list parameters together with their valid types.
+    /// Returns output file/list/dir parameters together with their valid types.
     QVector<IOInfo> getOutputParameters() const;
-    /// Returns 'output dir' parameters (if any)
-    QVector<IOInfo> getOutputDirParameters() const;
     // documented in base class
     void paint(QPainter* painter, const QStyleOptionGraphicsItem* option, QWidget* widget) override;
     // documented in base class

src/openms_gui/include/OpenMS/VISUAL/TOPPASVertex.h

@@ -131,12 +131,12 @@ namespace OpenMS
     /// indexing via "parameter_index" of adjacent edge (could later be param_name) -> filenames
     /// Index for input and output edges is (-1) implicitly, thus we need signed type
     /// warning: the index refers to either input OR output (depending on if this structure is used for input files storage or output files storage)
-    typedef std::map<Int, VertexRoundPackage> RoundPackage;
-    typedef RoundPackage::const_iterator RoundPackageConstIt;
-    typedef RoundPackage::iterator RoundPackageIt;
+    using RoundPackage        = std::map<Int, VertexRoundPackage>;
+    using RoundPackageConstIt = RoundPackage::const_iterator;
+    using RoundPackageIt      = RoundPackage::iterator;
 
     /// all information a node needs to process all rounds
-    typedef std::vector<RoundPackage> RoundPackages;
+    using RoundPackages = std::vector<RoundPackage>;
 
     /// The color of a vertex during depth-first search
     enum DFS_COLOR
@@ -346,5 +346,37 @@ public slots:
     }
 
   };
-}
+
+  /**
+  @brief A vertex representing an output, either folder or files(s)
+
+  @ingroup TOPPAS_elements
+  */
+  class OPENMS_GUI_DLLAPI TOPPASOutputVertex : public TOPPASVertex
+  {
+    Q_OBJECT
+  public:
+    /// Default C'tor
+    TOPPASOutputVertex() = default;
+    /// Copy constructor
+    TOPPASOutputVertex(const TOPPASOutputVertex& rhs);
+    /// Assignment operator
+    TOPPASOutputVertex& operator=(const TOPPASOutputVertex& rhs);
+
+  signals:
+    /// Emitted when an output file was written
+    void outputFileWritten(const String& file);
+
+    /// Emitted when user has changed the output folder name (i.e. output dir needs to be newly created and packages updates)
+    void outputFolderNameChanged();
+
+  protected:
+    /// custom output folder name
+    QString output_folder_name_;
+
+    // convenience members, not required for operation, but for progress during copying
+    int files_written_ = 0; ///< files that were already written
+    int files_total_ = 0;   ///< total number of files from upstream
+  };
+  }
 

src/openms_gui/include/OpenMS/VISUAL/sources.cmake

@@ -57,6 +57,7 @@ TOPPASEdge.h
 TOPPASInputFileListVertex.h
 TOPPASMergerVertex.h
 TOPPASOutputFileListVertex.h
+TOPPASOutputFolderVertex.h
 TOPPASResource.h
 TOPPASResources.h
 TOPPASScene.h

src/openms_gui/source/VISUAL/APPLICATIONS/TOPPASBase.cpp

@@ -74,6 +74,7 @@
 #include <QtWidgets/QVBoxLayout>
 #include <QtWidgets/QWhatsThis>
 #include <utility>
+#include <OpenMS/VISUAL/TOPPASOutputFolderVertex.h>
 
 
 using namespace std;
@@ -439,21 +440,18 @@ namespace OpenMS
     header_labels.append(QString("TOPP tools"));
     tools_tree_view->setHeaderLabels(header_labels);
 
-    QTreeWidgetItem* item = new QTreeWidgetItem((QTreeWidget*)nullptr);
-    item->setText(0, "<Input files>");
-    tools_tree_view->addTopLevelItem(item);
-    item = new QTreeWidgetItem((QTreeWidget*)nullptr);
-    item->setText(0, "<Output files>");
-    tools_tree_view->addTopLevelItem(item);
-    item = new QTreeWidgetItem((QTreeWidget*)nullptr);
-    item->setText(0, "<Merger>");
-    tools_tree_view->addTopLevelItem(item);
-    item = new QTreeWidgetItem((QTreeWidget*)nullptr);
-    item->setText(0, "<Collector>");
-    tools_tree_view->addTopLevelItem(item);
-    item = new QTreeWidgetItem((QTreeWidget*)nullptr);
-    item->setText(0, "<Splitter>");
-    tools_tree_view->addTopLevelItem(item);
+    auto add_list_item = [&tools_tree_view](const QString& node_name)
+      {
+      QTreeWidgetItem* item = new QTreeWidgetItem(tools_tree_view);
+      item->setText(0, node_name);
+      tools_tree_view->addTopLevelItem(item);
+    };
+    add_list_item("<Input files>");
+    add_list_item("<Output files>");
+    add_list_item("<Output folder>");
+    add_list_item("<Merger>");
+    add_list_item("<Collector>");
+    add_list_item("<Splitter>");
 
     //Param category_param = param_.copy("tool_categories:", true);
 
@@ -477,24 +475,24 @@ namespace OpenMS
 
     std::map<QString, QTreeWidgetItem*> category_map;
 
-    foreach(const QString &category, category_list)
+    for (const QString &category : category_list)
     {
-      item = new QTreeWidgetItem((QTreeWidget*)nullptr);
+      auto item = new QTreeWidgetItem((QTreeWidget*)nullptr);
       item->setText(0, category);
       tools_tree_view->addTopLevelItem(item);
       category_map[category] = item;
     }
 
-    for (ToolListType::iterator it = tools_list.begin(); it != tools_list.end(); ++it)
+    for (const auto& tool : tools_list)
     {
-      item = new QTreeWidgetItem(category_map[it->second.category.toQString()]);
-      item->setText(0, it->first.toQString());
+      auto item = new QTreeWidgetItem(category_map[tool.second.category.toQString()]);
+      item->setText(0, tool.first.toQString());
       QTreeWidgetItem* parent_item = item;
-      StringList types = ToolHandler::getTypes(it->first);
-      for (StringList::iterator types_it = types.begin(); types_it != types.end(); ++types_it)
+      StringList types = ToolHandler::getTypes(tool.first);
+      for (const auto& type : types)
       {
         item = new QTreeWidgetItem(parent_item);
-        item->setText(0, types_it->toQString());
+        item->setText(0, type.toQString());
       }
     }
     tools_tree_view->resizeColumnToContents(0);
@@ -1208,8 +1206,15 @@ namespace OpenMS
     {
       tv = new TOPPASOutputFileListVertex();
       TOPPASOutputFileListVertex* oflv = dynamic_cast<TOPPASOutputFileListVertex*>(tv);
-      connect(oflv, SIGNAL(outputFileWritten(const String &)), this, SLOT(outputVertexFinished(const String &)));
-      scene->connectOutputVertexSignals(oflv);
+      connect(tv, SIGNAL(outputFileWritten(const String &)), this, SLOT(outputVertexFinished(const String &)));
+      scene->connectOutputVertexSignals((TOPPASOutputVertex*)oflv);
+    }
+    else if (tool_name == "<Output folder>")
+    {
+      tv = new TOPPASOutputFolderVertex();
+      TOPPASOutputFolderVertex* oflv = dynamic_cast<TOPPASOutputFolderVertex*>(tv);
+      connect(tv, SIGNAL(outputFileWritten(const String&)), this, SLOT(outputVertexFinished(const String&)));
+      scene->connectOutputVertexSignals((TOPPASOutputVertex*)oflv);
     }
     else if (tool_name == "<Merger>")
     {