Merge branch 'feature/cSubAssessment-Extension' into develop

datatypes/ext_cSubAssessment.JSON

+{
+"root-type":"ext:cSubAssessment",
+"comparison_data":{"identifier":["expt_id", "project"],"extra-source":"/projects/{project}/experiments/{expt_id}"},
+"fields":[
+{"label":"Subject-ID", "field":"ext:cSubAssessment/SUBJECT_ID", "required":false, "key": "subject_id"},
+{"label":"Experiment-ID", "field":"ext:cSubAssessment/EXPT_ID", "required":true, "key": "expt_id"},
+{"label":"Date", "field":"ext:cSubAssessment/DATE", "required":false, "key": "date"},
+{"label":"Age", "field":"ext:cSubAssessment/AGE", "required":false, "key": "age"},
+{"label":"Projects", "field":"ext:cSubAssessment/PROJECTS", "required":false, "key": "projects"},
+{"label":"Project", "field":"ext:cSubAssessment/PROJECT", "required":true, "key": "project"},
+{"label":"Label", "field":"ext:cSubAssessment/LABEL", "required":false, "key": "label"},
+{"label":"Insert Date", "field":"ext:cSubAssessment/INSERT_DATE", "required":false, "key": "insert_date"},
+{"label":"Insert User", "field":"ext:cSubAssessment/INSERT_USER", "required":false, "key": "insert_user"},
+{"label":"Datatype", "field":"ext:cSubAssessment/DATATYPE", "required":false, "key": "datatype"},
+{"label":"Datatype Category", "field":"ext:cSubAssessment/DATATYPE_CATEGORY", "required":false, "key": "datatype_category"},
+{"label":"Import Date", "field":"ext:cSubAssessment/IMPORT_DATE", "required":false, "key": "import_date"},
+{"label":"Project Protocol", "field":"ext:cSubAssessment/PROJECT_PROTOCOL", "required":false, "key": "project_protocol"},
+{"label":"Validation Method", "field":"ext:cSubAssessment/VALIDATION_METHOD", "required":false, "key": "validation_method"},
+{"label":"Validation Status", "field":"ext:cSubAssessment/VALIDATION_STATUS", "required":false, "key": "validation_status"}
+]
+}

datatypes/xnat_mrScanData.JSON

 {
 "root-type":"xnat:mrScanData",
+"comparison_data":{"identifier":["id","xnat_mrsessiondata_session_id"]},
 "REST-API":"/data/archive/projects/{xnat_mrsessiondata_project}/subjects/{xnat_mrsessiondata_subject_id}/experiments/{xnat_mrsessiondata_session_id}/scans/{id}/resources/DICOM/files?format=zip",
 "fields":[
 {"label":"Type", "field":"xnat:mrScanData/TYPE", "required":true, "key": "type"},

datatypes/xnat_mrSessionData.JSON

 {
 "root-type":"xnat:mrSessionData",
+"comparison_data":{"identifier":["session_id"]},
 "fields":[
 {"label":"Session-ID", "field":"xnat:mrSessionData/SESSION_ID", "required":false, "key": "session_id"},
 {"label":"Date", "field":"xnat:mrSessionData/DATE", "required":false, "key": "date"},

datatypes/xnat_projectData.JSON

-{"root-type":"xnat:projectData",
+{
+"root-type":"xnat:projectData",
+"comparison_data":{"identifier":["id"]},
 "fields":[
 {"label":"Project-ID", "field":"xnat:projectData/ID", "required":true, "key": "id"},
 {"label":"NAME", "field":"xnat:projectData/NAME", "required":false, "key": "name"},

datatypes/xnat_subjectData.JSON

-{"root-type":"xnat:subjectData",
+{
+"root-type":"xnat:subjectData",
+"comparison_data":{"identifier":["subject_id"]},
 "fields":[
 {"label":"Subject-ID", "field":"xnat:subjectData/SUBJECT_ID", "required":true, "key": "subject_id"},
 {"label":"Subject-Label", "field":"xnat:subjectData/SUBJECT_LABEL", "required":false, "key": "subject_label"},

xsa/datatypereader.py

@@ -39,6 +39,26 @@ def get_all(force=False):
     return get_all()
 get_all.cache = None
 
+def get_comparison_extra_source(root_type):
+    for data in get_all():
+        if data['root-type'] == root_type:
+            if not 'comparison_data' in data or not data['comparison_data']:
+                raise NoComparisonDataError("No comparison-data was defined for this datatype")
+            elif not 'extra-source' in data['comparison_data'] or not data['comparison_data']['extra-source']:
+                raise NoComparisonDataError("No Source of additional Data was defined for this datatype")
+            else:
+                return data['comparison_data']['extra-source']
+
+def get_comparison_identifier(root_type):
+    for data in get_all():
+        if data['root-type'] == root_type:
+            if not 'comparison_data' in data or not data['comparison_data']:
+                raise NoComparisonDataError("No comparison-data was defined for this datatype")
+            elif not 'identifier' in data['comparison_data'] or not data['comparison_data']['identifier']:
+                raise NoComparisonDataError("No Identifier for this datatype was defined")
+            else:
+                return data['comparison_data']['identifier']
+
 
 def get_rest(root_type):
     """Returns REST-API-Interface of a given Root-Type, defined in its json-file.
@@ -83,6 +103,18 @@ def get_labels(root_type):
     return []
 
 
+def get_keys(root_type):
+    """Returns a list of field-keys of a given root_type.
+
+    **Parameters**
+        :root_type: str, Root-Type of returned field-labels
+    """
+    fields = get_fields(root_type)
+    if fields is not None:
+        return list(f['key'] for f in fields)
+    return []
+
+
 def get_field_label_by_key(root_type, field_key):
     """Returns the label of the given field-key.
 

xsa/errors.py

@@ -38,6 +38,10 @@ class NoRestApiError(Error):
     """Should be raised when no REST-API was defined in the json-file of a root-type"""
     pass
 
+class NoComparisonDataError(Error):
+    """Should be raised when no comparision was defined in the json-file of a root-type"""
+    pass
+
 class CorruptedQueryError(Error):
     """Should be raised when the query-definition can not be loaded from file."""
     pass

xsa/queries.py

@@ -164,6 +164,28 @@ def disconnect_xnat_server():
         get_xnat_server_connection.cache = None
     except:
        return
+
+def query_for_additional_data(rest, result, host, creds):
+
+    import re
+    def subfunc(f):
+        key = f.group(0).strip("{}")
+        return result[key]
+    ret = re.sub('\{\w+\}', subfunc, rest)
+
+    user, passw = creds
+    central = get_xnat_server_connection(host=host, user=user, passw=passw)
+    exp = central.select(ret)
+
+    new_fields = exp.xpath("//xnat:field")
+    new_result = result.copy()
+    for f in new_fields:
+        fieldname = f.get("name")
+        value = exp.xpath("//xnat:field[@name='"+fieldname+"']/child::text()")
+        new_result[fieldname] = ''.join(value).replace("\n","")
+    return new_result
+
+
 def search_for(host, root_element, constraints, search_fields, user, passw):
     """
     Does a search for given values. raises xsa -Exceptions
@@ -182,6 +204,7 @@ def search_for(host, root_element, constraints, search_fields, user, passw):
         :xsa.errors.ResponseNotReady:
         :xsa.errors.QueryError:
 
+
     """
     import xsa.errors
 

xsagtk/main_controller.py

@@ -10,9 +10,14 @@ This module contains the controller that provides the communication between view
 import gtk
 import gobject
 
+import xsa.datatypereader
+
 class QueryController(gobject.GObject):
     """Provides communication between different views."""
 
+
+    results = []
+
     _host = ""
     _user = ""
     _passw = ""
@@ -83,7 +88,6 @@ class QueryController(gobject.GObject):
         def on_search_query(host, credentials, root_type, query, fields):
             user, passw = credentials
 
-            import xsa.queries as queries
             import xsa.errors
 
             if passw =='' or user=='' or host=='':
@@ -104,7 +108,7 @@ class QueryController(gobject.GObject):
                 return
 
             try:
-                query_results = queries.search_for( host,
+                query_results = xsa.queries.search_for( host,
                                                     root_type,
                                                     query,
                                                     fields,
@@ -119,11 +123,12 @@ class QueryController(gobject.GObject):
                 md.run()
                 md.destroy()
                 self.results = []
-            except Exception:
+            except Exception as e:
                 md = gtk.MessageDialog( type=gtk.MESSAGE_WARNING,
                                         buttons=gtk.BUTTONS_OK,
-                                        message_format="An unexpected Error occured."
+                                        message_format="An unexpected Error occured:"
                                         )
+                md.format_secondary_text(e)
                 md.run()
                 md.destroy()
                 self.results = []
@@ -134,16 +139,28 @@ class QueryController(gobject.GObject):
             self.statusbar.push(0, "%s Results"%len(self.results))
             self.chartview.update_chart_view(self.results, root_type)
 
+            if self.results == []:
+                self.menuview.disable_download_button(False, "No Results for downloading")
+                self.menuview.disable_export_button(False, "No Results for exporting")
+                self.menuview.disable_adddata_button(False, "No Results for getting additional data")
+                return
+            else:
+                try:
+                    xsa.datatypereader.get_rest(root_type)
+                    self.menuview.disable_download_button(True, "Download selected items from result-table")
+                except xsa.errors.NoRestApiError as e:
+                    self.menuview.disable_download_button(False, str(e))
+
+                self.menuview.disable_adddata_button(True, "Get additional data")
+                self.menuview.disable_export_button(True, "Export Result-Table as csv-file")
+
+
         self.root=self.queryview.get_root_type()
         self.query=self.queryview.get_query()
         self.labels=self.queryview.get_fields()
 
-        import xsa.datatypereader as type_reader
-        fields = type_reader.get_fields_from_labels(self.labels,self.root)
-        on_search_query(self.host,                             self.credentials_tuple,
-                                self.root,
-                                self.query,
-                                fields)
+        fields = xsa.datatypereader.get_fields_from_labels(self.labels,self.root)
+        on_search_query(self.host, self.credentials_tuple, self.root, self.query, fields)
 
 
     def __init__(self, main, queryview, menuview, chartview, resultsview, statusbar):
@@ -167,6 +184,48 @@ class QueryController(gobject.GObject):
         self.resultsview = resultsview
         self.statusbar = statusbar
 
+        def callback_get_additional_data(*_):
+
+            rest = xsa.datatypereader.get_comparison_extra_source(self.root)
+
+            new_data_sets = []
+            for r in self.results:
+                new_data_sets.append(xsa.queries.query_for_additional_data(rest, r, self.host, self.credentials_tuple))
+
+            keys = []
+            for data_set in new_data_sets:
+                for key in data_set.keys():
+                    keys.append(key)
+
+            new_result = []
+            for data_set in new_data_sets:
+                dic = {}
+                for key in keys:
+                    try:
+                        dic[key] = data_set[key]
+                    except:
+                        dic[key] = "N/A"
+                new_result.append(dic)
+
+            from pyxnat.core.jsonutil import JsonTable
+            self.results = JsonTable(new_result)
+
+            self.resultsview.show_data(self.results, self.root)
+            self.chartview.update_chart_view(self.results, self.root)
+
+        def callback_export_csv(*_):
+            dialog = gtk.FileChooserDialog( "Save as...",
+                                            None,
+                                            gtk.FILE_CHOOSER_ACTION_SAVE,
+                                            (gtk.STOCK_CANCEL, gtk.RESPONSE_CANCEL,
+                                            gtk.STOCK_OPEN, gtk.RESPONSE_OK))
+            dialog.set_default_response(gtk.RESPONSE_CANCEL)
+
+            response = dialog.run()
+            if response == gtk.RESPONSE_OK:
+                self.results.dump_csv(dialog.get_filename())
+            dialog.destroy()
+
 
         def callback_edit_Server_Settings(*_):
             dialog = gtk.Dialog(    "Server Settings",
@@ -178,7 +237,7 @@ class QueryController(gobject.GObject):
             dialog.set_size_request(330, 180)
             hbox = gtk.HBox(False, 8)
             hbox.set_border_width(8)
-            dialog.vbox.pack_start(hbox, False, False, 0)
+            dialog.vbox.pack_start(hbox, True, True, 0)
 
             stock = gtk.image_new_from_stock(
                     gtk.STOCK_DIALOG_AUTHENTICATION,
@@ -221,6 +280,16 @@ class QueryController(gobject.GObject):
             if response == gtk.RESPONSE_OK:
                 self.credentials_tuple = (entry_user.get_text(),entry_passw.get_text())
                 self.host = entry_host.get_text()
+                import xsa.queries
+                try:
+                    xsa.queries.get_xnat_server_connection(force=True, host=self.host, user=self.credentials_tuple[0], passw=self.credentials_tuple[1])
+                except Exception as e:
+                    md = gtk.MessageDialog( type=gtk.MESSAGE_WARNING,
+                                            buttons=gtk.BUTTONS_OK,
+                                            message_format=str(e)
+                                            )
+                    md.run()
+                    md.destroy()
 
             dialog.destroy()
 
@@ -232,9 +301,6 @@ class QueryController(gobject.GObject):
             if self.resultsview.get_selected_items() == []:
                 return
 
-            import xsa.queries as queries
-            import xsa.datatypereader as type_reader
-
             dialog = gtk.FileChooserDialog( "Open..",
                                             None,
                                             gtk.FILE_CHOOSER_ACTION_SELECT_FOLDER,
@@ -244,7 +310,7 @@ class QueryController(gobject.GObject):
 
             response = dialog.run()
             if response == gtk.RESPONSE_OK:
-                rest = type_reader.get_rest(self.root)
+                rest = xsa.datatypereader.get_rest(self.root)
                 enabled = (d for d in self.resultsview.get_store() if d[0])
                 for d in enabled:
                     def stop_spinner(_row):
@@ -252,7 +318,7 @@ class QueryController(gobject.GObject):
                         _row[0] = False # Checkbox to false
                     d[3] = 0
                     d[2] = True # Show Spinner
-                    queries.download_async( d[1],
+                    xsa.queries.download_async( d[1],
                                             self.host,
                                             self.credentials_tuple,
                                             rest,
@@ -262,9 +328,6 @@ class QueryController(gobject.GObject):
                                             )
             dialog.destroy()
 
-        def disable_download_button(_, is_enable, text):
-            self.menuview.disable_download_button(is_enable, text)
-
         root_key = 'root'
         query_key = 'query'
         labels_key = 'labels'
@@ -314,15 +377,13 @@ class QueryController(gobject.GObject):
                                             query = f[query_key],
                                             field_labels = f[labels_key]
                                             )
-
             dialog.destroy()
 
-
         self.menuview.connect("spawn-connection-dialog", callback_edit_Server_Settings)
         self.menuview.connect("send-query", self.send_query)
         self.menuview.connect("toggle-selection", event_clicked_toggle_selection)
         self.menuview.connect("download-selection", event_clicked_download)
         self.menuview.connect("save-query", save_query)
         self.menuview.connect("load-query", load_query)
-
-        self.queryview.connect("rest-api", disable_download_button)
+        self.menuview.connect("get-additional-data",callback_get_additional_data)
+        self.menuview.connect("export-csv", callback_export_csv)

xsagtk/menu_view.py

@@ -13,6 +13,16 @@ import gobject
 class MenuView(gtk.Toolbar):
     """A ToolBar containing Buttons"""
 
+    def disable_export_button(self, is_enable, text):
+        """Disables export-button and sets given text as tooltip.
+
+        **Parameters**
+            :is_enable: bool: true for enabling and false for disabling export-button
+            :text: str, that will be set as tooltip
+        """
+        self.tb_export.set_tooltip_text(text)
+        self.tb_export.set_sensitive(is_enable)
+
     def disable_download_button(self, is_enable, text):
         """Disables download-button and sets given text as tooltip.
 
@@ -23,6 +33,16 @@ class MenuView(gtk.Toolbar):
         self.tb_downl.set_tooltip_text(text)
         self.tb_downl.set_sensitive(is_enable)
 
+    def disable_adddata_button(self, is_enable, text):
+        """Disables get-additional-data-button and sets given text as tooltip.
+
+        **Parameters**
+            :is_enable: bool: true for enabling and false for disabling button
+            :text: str, that will be set as tooltip
+        """
+        self.tb_adddata.set_tooltip_text(text)
+        self.tb_adddata.set_sensitive(is_enable)
+
     def __init__(self, *args, **kwargs):
         """Creates buttons for this Toolbar and defines signals when this buttons will be pressed.
 
@@ -41,6 +61,11 @@ class MenuView(gtk.Toolbar):
                             gobject.SIGNAL_RUN_FIRST,
                             gobject.TYPE_NONE,
                             ())
+        gobject.signal_new( "get-additional-data",
+                            MenuView,
+                            gobject.SIGNAL_RUN_FIRST,
+                            gobject.TYPE_NONE,
+                            ())
         gobject.signal_new( "send-query",
                             MenuView,
                             gobject.SIGNAL_RUN_FIRST,
@@ -66,6 +91,11 @@ class MenuView(gtk.Toolbar):
                             gobject.SIGNAL_RUN_FIRST,
                             gobject.TYPE_NONE,
                             ())
+        gobject.signal_new("export-csv",
+                            MenuView,
+                            gobject.SIGNAL_RUN_FIRST,
+                            gobject.TYPE_NONE,
+                            ())
 
         tb_savequery = gtk.ToolButton()
         tb_savequery.set_label("Save Query")
@@ -109,3 +139,23 @@ class MenuView(gtk.Toolbar):
         self.tb_downl.set_stock_id(gtk.STOCK_SAVE)
         self.tb_downl.connect("clicked",lambda *_: self.emit("download-selection"))
         self.insert(self.tb_downl, 6)
+
+        self.tb_export = gtk.ToolButton()
+        self.tb_export.set_label("Export As CSV")
+        self.tb_export.set_stock_id(gtk.STOCK_CONVERT)
+        self.tb_export.connect("clicked",lambda *_: self.emit("export-csv"))
+        self.insert(self.tb_export, 7)
+
+        self.insert(gtk.SeparatorToolItem(), 8)
+
+        self.tb_adddata = gtk.ToolButton()
+        self.tb_adddata.set_label("Get Additional Data")
+        self.tb_adddata.set_stock_id(gtk.STOCK_INDEX)
+        self.tb_adddata.connect("clicked",lambda *_: self.emit("get-additional-data"))
+        self.insert(self.tb_adddata, 9)
+
+
+
+        self.disable_download_button(False, "No Results")
+        self.disable_adddata_button(False, "No Results")
+        self.disable_export_button(False, "No Results")

xsagtk/query_view.py

@@ -13,7 +13,7 @@ class QueryView(gtk.VBox):
     """Contains all widgets for creating the query"""
 
     def __init__(self, *args, **kwargs):
-        """Creates signal "rest-api". Creates all query-view-widgets.
+        """Creates all query-view-widgets.
 
         **Parameters**
             :\*args: same as gtk.VBox
@@ -22,13 +22,6 @@ class QueryView(gtk.VBox):
 
         super(QueryView, self).__init__(*args, **kwargs)
 
-        import gobject
-        gobject.signal_new( "rest-api",
-                            QueryView,
-                            gobject.SIGNAL_RUN_FIRST,
-                            gobject.TYPE_NONE,
-                            (bool,str))
-
         # root-type
 
         hBox_root_type = gtk.HBox()
@@ -42,13 +35,6 @@ class QueryView(gtk.VBox):
             import xsa.datatypereader as type_reader
             import xsa.errors
             selected =  combobox.get_active_text()
-            try:
-                type_reader.get_rest(selected)
-            except xsa.errors.NoRestApiError as e:
-                self.emit("rest-api", False, e)
-            else:
-                self.emit("rest-api", True, "Download selected items from result-table")
-
             self.treeView_search.set_root_type(selected)
             self.treeView_fields.reset_fields(selected)
 

xsagtk/xsa_app_main.py

@@ -75,7 +75,6 @@ class XsaApp(gtk.Window):
         vpaned.add1(self.resultsview)
 
         # chart
-
         from xsagtk.chart_view import ChartView
         self.chartview = ChartView()
         vpaned.add2(self.chartview)