Merge lp:~jon-hill/supertree-toolkit/bug_fixes into lp:supertree-toolkit

[Jon Hill]

Fixed 1387604 and 1387603

[Jon Hill (jon-hill)]

review: Approve

[lp:~jon-hill/supertree-toolkit/bug_fixes]

255. By Jon Hill on 2014-10-30

Fixes to export_trees and import_trees

=== modified file 'stk/supertree_toolkit.py'
--- stk/supertree_toolkit.py	2014-10-10 09:23:22 +0000
+++ stk/supertree_toolkit.py	2014-10-30 11:42:05 +0000
@@ -226,8 +226,11 @@
     for t in source.xpath("source_tree"):
         if 'name' in t.attrib and not t.attrib['name'] == "":
                 tree_count += 1
-
-    tree_name = source.attrib['name'] + "_" + str(tree_count)
+    try:
+        tree_name = source.attrib['name'] + "_" + str(tree_count)
+    except KeyError:
+        # no name set for source
+        tree_name = str(tree_count)
 
     return tree_name
 
 
=== modified file 'stk_gui/gui/gui.glade'
--- stk_gui/gui/gui.glade	2014-10-09 09:33:21 +0000
+++ stk_gui/gui/gui.glade	2014-10-30 11:42:05 +0000
@@ -1338,7 +1338,23 @@
             <property name="fill">True</property>
             <property name="position">2</property>
           </packing>
-        </child>
+       </child>
+       <child>
+        <widget class="GtkCheckButton" id="ignoreWarnings_checkbutton">
+            <property name="label" translatable="yes">Ignore Warnings</property>
+            <property name="visible">True</property>
+            <property name="can_focus">True</property>
+            <property name="receives_default">False</property>
+            <property name="use_action_appearance">False</property>
+            <property name="draw_indicator">True</property>
+          </widget>
+          <packing>
+            <property name="expand">True</property>
+            <property name="fill">True</property>
+            <property name="position">2</property>
+          </packing>
+
+       </child>
       </widget>
     </child>
   </widget>
 
=== modified file 'stk_gui/plugins/phyml/import_tree.py'
--- stk_gui/plugins/phyml/import_tree.py	2014-10-07 12:07:38 +0000
+++ stk_gui/plugins/phyml/import_tree.py	2014-10-30 11:42:05 +0000
@@ -39,8 +39,12 @@
     except TreeParseError as detail:
         msg = "Failed to import tree - can't parse tree.\n"+detail.msg
         dialogs.error(self.main_window,msg)
-    tree_name = stk.create_tree_name(xml,element.get_parent().get_parent())
+    source_tree_ele = element[0].getparent().getparent().getparent()
+    tree_name = stk.create_tree_name(xml,source_tree_ele)
+    print tree_name
     element[0].text = tree
+    source_tree_ele.attrib['name'] = tree_name
+
     
     stk_gui.interface.plugin_xml = etree.tostring(xml_root)
     stk_gui.interface.pluginSender.emit('plugin_changed_xml')
 
=== modified file 'stk_gui/stk_gui/interface.py'
--- stk_gui/stk_gui/interface.py	2014-10-13 07:47:23 +0000
+++ stk_gui/stk_gui/interface.py	2014-10-30 11:42:05 +0000
@@ -1951,9 +1951,9 @@
       ignoreWarnings = self.export_trees_gui.get_widget("ignoreWarnings_checkbutton").get_active()
 
       if (format_radio_1.get_active()):
-          format = 'Nexus'
+          format = 'nexus'
       elif (format_radio_2.get_active()):
-          format = 'Newick'
+          format = 'newick'
       elif (format_radio_3.get_active()):
           format = 'tnt'
       else:
@@ -1969,7 +1969,7 @@
       self.tree.write(f)
       XML = f.getvalue()
       try:
-        self.output_string = stk.amalgamate_trees(XML,format=format,anonymous=anonymous,ignoreWarnings=ignoreWarnings)
+            output_string = stk.amalgamate_trees(XML,format=format,anonymous=anonymous,ignoreWarnings=False)
       except NotUniqueError as detail:
             msg = "Failed to export trees.\n"+detail.msg
             dialogs.error(self.main_window,msg)
@@ -1987,7 +1987,8 @@
             dialogs.error(self.main_window,msg)
             return 
       except:
-            msg = "Failed to export trees due to an unknown error. Check the console output"
+            msg = "Failed to export trees due to an unknown error. Please report this a bug"
+            msg += "\n" + traceback.format_exc()
             dialogs.error(self.main_window,msg)
             return 
 
@@ -1996,8 +1997,10 @@
       # open file dialog
       filename = dialogs.get_filename(title = "Choose output trees fle", action = gtk.FILE_CHOOSER_ACTION_SAVE, filter_names_and_patterns = filter_names_and_patterns, folder_uri = self.file_path)
 
+      if (filename == None):
+          return # user cancelled save
       f = open(filename,"w")
-      f.write(self.output_string)
+      f.write(output_string)
       f.close()
 
       XML = stk.add_historical_event(XML, "Tree exported to: "+filename)
@@ -2107,6 +2110,7 @@
         return
     except:
         msg = "Failed to parse XML and obtain taxa. You probably have an unfinished dataset"
+        msg += "\n" + traceback.format_exc()
         dialogs.error(self.main_window,msg)
         return 
 
@@ -2307,7 +2311,8 @@
         dialogs.error(self.main_window,msg)
         return 
     except:
-        msg = "Failed to substitute taxa due to an unknown error. Check the console output"
+        msg = "Failed to substitute taxa due to an unknown error. Possibly a bug. PLease report on Launchpad."
+        msg += "\n" + traceback.format_exc()
         dialogs.error(self.main_window,msg)
         return 
 
@@ -2445,8 +2450,8 @@
         dialogs.error(self.main_window,msg)
         return 
      except:
-        msg = "Failed to clean data due to an unknown error. Check the console output"
-        traceback.print_exc()         
+        msg = "Failed to clean data due to an unknown error. Possibly a bug. Please report on Launchpad"
+        msg += "\n" + traceback.format_exc()     
         dialogs.error(self.main_window,msg)
         return 
 
@@ -2510,8 +2515,8 @@
         dialogs.error(self.main_window,msg)
         return 
      except:
-        msg = "Failed to replace generic taxa due to an unknown error. Check the console output"
-        traceback.print_exc()                 
+        msg = "Failed to replace generic taxa due to an unknown error. Possibly a bug. Please report on Launchpad"
+        msg += "\n" + traceback.format_exc()     
         dialogs.error(self.main_window,msg)
         return 
 
@@ -2722,8 +2727,8 @@
         dialogs.error(self.main_window,msg)
         return 
      except:
-        msg = "Failed to create subset due to an unknown error. Check the console output"
-        traceback.print_exc()     
+        msg = "Failed to create subset due to an unknown error. Possibly a bug. Please report on Launchpad"
+        msg += "\n" + traceback.format_exc()     
         dialogs.error(self.main_window,msg)
         return 
   
@@ -2768,7 +2773,8 @@
             dialogs.error(self.main_window,msg)
             return 
      except:
-            msg = "Failed to name trees due to an unknown error. Check the console output"
+            msg = "Failed to name trees due to an unknown error. Possibly a bug. Please report on Launchpad"
+            msg += "\n" + traceback.format_exc()     
             dialogs.error(self.main_window,msg)
             return