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Flashpoint committed 7289883

The prototype widget for adding and removing custom gene sets

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Files changed (1)

_bioinformatics/widgets/prototypes/OWtest.py

+"""
+<name>test</name>
+<description>Import custom geneset files</description>
+
+"""
+import os
+from StringIO import StringIO
+
+import Orange
+
+from OWWidget import *
+import OWGUI
+
+from Orange.bio.obiGeneSets import loadGMT, list_local, register, local_path, remove_local
+
+class standard_icons(object):
+    def __init__(self, qwidget=None, style=None):
+        self.qwidget = qwidget
+        if qwidget is None:
+            self.style = QApplication.instance().style()
+        else:
+            self.style = qwidget.style()
+
+    @property
+    def dir_open_icon(self):
+        return self.style.standardIcon(QStyle.SP_DirOpenIcon)
+
+    @property
+    def reload_icon(self):
+        return self.style.standardIcon(QStyle.SP_BrowserReload)
+
+
+class OWCustomGeneSetUpload(OWWidget):
+    settingsList = ["recent_files"]
+
+    def __init__(self, parent=None, signalManager=None,
+                 title="Custom Geneset File (*.gmt) Import"):
+        OWWidget.__init__(self, parent, signalManager, title,
+                          wantMainArea=False)
+
+        self.inputs = []
+        self.outputs = []
+        self.new_geneset = set()
+
+        # List of recent opened files.
+        self.recent_files = []
+        self.loadSettings()
+        self.recent_files = filter(os.path.exists, self.recent_files)
+
+        layout = QHBoxLayout()
+        box = OWGUI.widgetBox(self.controlArea, "File", orientation=layout)
+
+        icons = standard_icons(self)
+
+        self.recent_combo = QComboBox(self, objectName="recent_combo",
+                                      toolTip="Recent files",
+                                      activated=self.on_select_recent)
+        self.recent_combo.addItems([os.path.basename(p) \
+                                    for p in self.recent_files])
+
+        self.browse_button = QPushButton("...", icon=icons.dir_open_icon,
+                                         toolTip="Browse filesystem",
+                                         clicked=self.on_open_dialog)
+
+        self.reload_button = QPushButton("Reload", icon=icons.reload_icon,
+                                         toolTip="Reload the selected file",
+                                         clicked=self.on_reload_file)
+
+        layout.addWidget(self.recent_combo, 2)
+        layout.addWidget(self.browse_button)
+        layout.addWidget(self.reload_button)
+       
+        ################
+        # File Preview #
+        ################
+        form = QFormLayout()
+        
+        box = OWGUI.widgetBox(self.controlArea, "Preview")
+        self.preview_view = QTableView()
+
+        box.layout().addWidget(self.preview_view)
+
+        OWGUI.button(self.controlArea, self, "Import", callback=self.import_data)
+
+        self.selected_file = None 
+
+        self.resize(450, 500)
+        if self.recent_files:
+            QTimer.singleShot(1,
+                    lambda: self.set_selected_file(self.recent_files[0])
+                    )
+
+    def on_select_recent(self, recent):
+        if isinstance(recent, int):
+            recent = self.recent_files[recent]
+
+        self.set_selected_file(recent)
+
+    def on_open_dialog(self):
+        last = os.path.expanduser("~/Documents")
+        path = QFileDialog.getOpenFileName(self, "Open File","" ,"geneset file *.gmt (*.gmt);;All files (*)", last)
+        path = unicode(path)
+        if path:
+            self.set_selected_file(path)
+
+    def on_reload_file(self):
+        if self.recent_files:
+            self.set_selected_file(self.recent_files[0])
+
+    def set_selected_file(self, filename):
+        basedir, name = os.path.split(filename)
+        self.selected_file = filename
+        self.genesetname = name
+        index_to_remove = None
+        if filename in self.recent_files:
+            index_to_remove = self.recent_files.index(filename)
+        elif self.recent_combo.count() > 6:
+            # Always keep 6 latest files in the list.
+            index_to_remove = self.recent_combo.count() - 1
+        self.recent_combo.insertItem(0, name)
+        self.recent_combo.setCurrentIndex(0)
+        self.recent_files.insert(0, filename)
+
+        if index_to_remove is not None:
+            self.recent_combo.removeItem(index_to_remove + 1)
+            self.recent_files.pop(index_to_remove + 1)
+ 
+        self.update_preview()
+
+
+    # Funkcija za brisanje fajla iz lokalnega repozitorija. Potrebno jo je še nekam zapakirat.
+    # remove_local(self.genesetname)
+
+    def update_preview(self):
+        pass
+        """ Leftovers from copying another widget
+        
+        self.error(0)
+        if self.selected_file:
+            head = StringIO("".join(self.selected_file_head))
+            hints = self.hints[self.selected_file]
+
+            # Save hints for the selected file
+            hints["quotechar"] = self.quote
+            hints["delimiter"] = self.delimiter or self.other_delimiter
+            hints["has_header"] = self.has_header
+            hints["has_orange_header"] = self.has_orange_header
+            hints["skipinitialspace"] = self.skipinitialspace
+            hints["DK"] = self.missing or None
+            try:
+                data = Orange.data.io.load_csv(head, delimiter=self.delimiter,
+                                   quotechar=self.quote,
+                                   has_header=self.has_header,
+                                   has_types=self.has_orange_header,
+                                   has_annotations=self.has_orange_header,
+                                   skipinitialspace=self.skipinitialspace,
+                                   DK=self.missing or None,
+                                   create_new_on=MakeStatus.OK)
+            except Exception, ex:
+                self.error(0, "Cannot parse (%r)" % ex)
+                data = None
+
+            if data is not None:
+                model = ExampleTableModel(data, None, self)
+            else:
+                model = None
+            self.preview_view.setModel(model)
+        """
+
+    def import_data(self):
+        self.error(0)     
+        if self.selected_file:
+            try:
+                self.new_geneset = loadGMT(open(self.selected_file, "rt").read(), self.genesetname)
+                geneset_split = self.new_geneset.split_by_hierarchy()
+                for geneset in geneset_split:
+                    register(geneset)
+            except Exception, ex:
+                self.error(0, "An error occurred while "
+                              "loading the file:\n\t%r" % self.selected_file
+                              )    
+        
+if __name__ == "__main__":
+    import sys
+    app = QApplication(sys.argv)
+    w = OWCustomGeneSetUpload()
+    w.show()
+    app.exec_()
+    w.saveSettings()