Merge pull request #328 from ODM2/odm1_development

Odm1 development

Author: sreeder

doc/wxFormBuilder/frmCreateSource.fbp

@@ -4,14 +4,14 @@
 from odmtools.controller.logicPlotOptions import *
 from odmtools.controller.odmHighlightSTC import highlightSTC
 from odmtools.controller.olvSeriesSelector import clsSeriesTable
-
+# from odmtools.controller.pageSource import pageSource
 
 
 __all__ = [
     'EditTools',
     'OneSeriesPlotInfo',
     'highlightSTC',
     'clsSeriesTable',
-    'SeriesPlotInfo'
-
+    'SeriesPlotInfo',
+    # 'pageSource'
 ]

odmtools/controller/__init__.py

@@ -0,0 +1,75 @@
+"""Subclass of clsSource, which is generated by wxFormBuilder."""
+
+import wx
+from odmtools.view.clsCreateSource import clsSource
+from odmtools.odmdata import Source
+
+
+# Implementing clsSource
+class frmCreateSource(clsSource):
+    def __init__(self, parent, service_man, prev_src):
+        clsSource.__init__(self, parent)
+        self.service_man = service_man
+        self.prev = prev_src
+        self.source = None
+        self.series_service = self.service_man.get_series_service()
+        self.populate_meta()
+
+    def populate_meta(self):
+        self.meta_list = {}
+        metas = self.series_service.get_iso_metadata()
+        if metas is not None:
+            self.meta_list = {(x.title, x.id) for x in metas}
+            # {(key, value) for (key, value) in zip(key_list, value_list)}
+        self.meta_list["None"] = 0
+        self.chMeta.AppendItems(self.meta_list.keys())
+        self.chMeta.SetSelection(0)
+
+    def getSource(self):
+        return self.source
+
+    # Handlers for dlgCreateSource events.
+    def onOkClick(self, event):
+        self.source = self.createSource()
+
+        if self.all_fields_full():
+            self.EndModal(wx.ID_OK)
+        else:
+            wx.MessageDialog(None, "All required source fields must be completed.", " ", wx.OK).ShowModal()
+
+    def all_fields_full(self):
+        return (self.txtOrg.GetValue() != '') and \
+               (self.txtDescrip.GetValue() != '') and \
+               (self.txtName.GetValue() != '') and \
+               (self.txtPhone.GetValue() != '') and \
+               (self.txtEmail.GetValue() != '') and \
+               (self.txtAddress.GetValue() != '') and \
+               (self.txtCity.GetValue() != '') and \
+               (self.txtState.GetValue() != '') and \
+               (self.txtZip.GetValue() != '') and \
+               (self.txtCitation.GetValue() != '')
+
+    def createSource(self):
+        s = Source()
+
+        s.organization = self.txtOrg.GetValue() if self.txtOrg.GetValue() != u'' else None
+        s.description = self.txtDescrip.GetValue() if self.txtDescrip.GetValue() != u'' else None
+        s.link = self.txtLink.GetValue() if self.txtLink.GetValue() != u'' else None
+
+        s.contact_name = self.txtName.GetValue() if self.txtName.GetValue() != u'' else None
+        s.phone = self.txtPhone.GetValue() if self.txtPhone.GetValue() != u'' else None
+        s.email = self.txtEmail.GetValue() if self.txtEmail.GetValue() != u'' else None
+
+        s.address = self.txtAddress.GetValue() if self.txtAddress.GetValue() != u'' else None
+        s.city = self.txtCity.GetValue() if self.txtCity.GetValue() != u'' else None
+        s.state = self.txtState.GetValue() if self.txtState.GetValue() != u'' else None
+        s.zip_code = self.txtZip.GetValue() if self.txtZip.GetValue() != u'' else None
+
+        s.citation = self.txtCitation.GetValue() if self.txtCitation.GetValue() != u'' else None
+        s.iso_metadata_id = self.meta_list[self.chMeta.GetItems()[self.chMeta.GetSelection()]]
+        # s.iso_metadata_id = 0
+        return s
+
+    def onCancelClick(self, event):
+        # TODO: Implement onCancelClick
+        self.EndModal(wx.ID_CANCEL)

odmtools/controller/frmCreateSource.py

@@ -65,16 +65,16 @@ def getVariable(self):
 
     def all_fields_full(self):
         return (self.cbVarName.GetValue() is not None) and \
-            (self.txtVarCode.GetValue() <> '') and \
+            (self.txtVarCode.GetValue() != '') and \
             (self.cbVarUnits.GetValue() is not None)and \
             (self.cbTSUnits.GetValue() is not None) and \
             (self.cbSampleMedium.GetValue() is not None) and \
             (self.cbSpeciation.GetValue() is not None) and \
             (self.cbValueType.GetValue() is not None) and \
             (self.cbDataType.GetValue() is not None) and \
-            (self.txtNoDV.GetValue() <> '') and \
+            (self.txtNoDV.GetValue() != '') and \
             (self.cbGenCat.GetValue() is not None) and \
-            (self.txtTSValue.GetValue() <> '')
+            (self.txtTSValue.GetValue() != '')
 
 
     def OnBtnCreateButton(self, event):
@@ -89,24 +89,24 @@ def OnBtnCreateButton(self, event):
     def createVariable(self):
         v = Variable()
 
-        v.code = self.txtVarCode.GetValue() if self.txtVarCode.GetValue() <> u'' else None
-        v.name = self.cbVarName.GetValue() if self.cbVarName.GetValue() <> u'' else None
-        v.speciation = self.cbSpeciation.GetValue() if self.cbSpeciation.GetValue() <> u'' else None
+        v.code = self.txtVarCode.GetValue() if self.txtVarCode.GetValue() != u'' else None
+        v.name = self.cbVarName.GetValue() if self.cbVarName.GetValue() != u'' else None
+        v.speciation = self.cbSpeciation.GetValue() if self.cbSpeciation.GetValue() != u'' else None
 
         v.variable_unit = self.series_service.get_unit_by_name( self.cbVarUnits.GetValue())
         v.variable_unit_id = v.variable_unit.id
 
-        v.sample_medium = self.cbSampleMedium.GetValue() if self.cbSampleMedium.GetValue() <> u'' else None
-        v.value_type = self.cbValueType.GetValue() if self.cbValueType.GetValue() <> u'' else None
-        v.is_regular = self.cbIsRegular.GetValue() if self.cbIsRegular.GetValue() <> u'' else None
-        v.time_support = self.txtTSValue.GetValue() if self.txtTSValue.GetValue() <> u'' else None
+        v.sample_medium = self.cbSampleMedium.GetValue() if self.cbSampleMedium.GetValue() != u'' else None
+        v.value_type = self.cbValueType.GetValue() if self.cbValueType.GetValue() != u'' else None
+        v.is_regular = self.cbIsRegular.GetValue() if self.cbIsRegular.GetValue() != u'' else None
+        v.time_support = self.txtTSValue.GetValue() if self.txtTSValue.GetValue() != u'' else None
 
         v.time_unit = self.series_service.get_unit_by_name(self.cbTSUnits.GetValue())
         v.time_unit_id = v.time_unit.id
 
-        v.data_type = self.cbDataType.GetValue() if self.cbDataType.GetValue() <> u'' else None
-        v.general_category = self.cbGenCat.GetValue() if self.cbGenCat.GetValue() <> u'' else None
-        v.no_data_value = self.txtNoDV.GetValue() if self.txtNoDV.GetValue() <> u'' else None
+        v.data_type = self.cbDataType.GetValue() if self.cbDataType.GetValue() != u'' else None
+        v.general_category = self.cbGenCat.GetValue() if self.cbGenCat.GetValue() != u'' else None
+        v.no_data_value = self.txtNoDV.GetValue() if self.txtNoDV.GetValue() != u'' else None
         return v
 
     def OnBtnCancelButton(self, event):

odmtools/controller/frmCreateVariable.py

@@ -68,7 +68,6 @@ def OnBtnTest(self, event):
 
 
     def OnBtnSave(self, event):
-
         self.parent.EndModal(wx.ID_OK)
 
 

odmtools/controller/frmDBConfig.py

@@ -234,7 +234,7 @@ def restore(self):
             self._script("edit_service.restore()\n", 'black')
             Publisher.sendMessage("scroll")
 
-    def saveFactory(self, var=None, method=None, qcl=None):
+    def saveFactory(self, var=None, method=None, qcl=None, source = None):
         """
 
         :param var:
@@ -247,17 +247,15 @@ def saveFactory(self, var=None, method=None, qcl=None):
         values['var'] = ("new_variable" if var else None)
         values['method'] = ("new_method" if method else None)
         values['qcl'] = ("new_qcl" if qcl else None)
+        values['source'] = ("new_source" if source else None)
         #values['override'] = override
-        return values['var'], values['method'], values['qcl']#, values['isSave']
+        return values['var'], values['method'], values['qcl'], values['source']#, values['isSave']
 
 
-    def save(self, var=None, method=None, qcl=None):
+    def save(self ):
         """
 
-        :param var:
-        :param method:
-        :param qcl:
-        :param override:
+
         :return:
         """
         result = self._edit_service.save()
@@ -269,25 +267,26 @@ def save(self, var=None, method=None, qcl=None):
             Publisher.sendMessage("scroll")
         return result
 
-    def save_as(self, var=None, method=None, qcl=None):
+    def save_as(self, var=None, method=None, qcl=None, source = None):
         """
 
         :param var:
         :param method:
         :param qcl:
+        :param source:
         :param override:
         :return:
         """
-        result = self._edit_service.save_as(var=var, method=method, qcl=qcl)
+        result = self._edit_service.save_as(var=var, method=method, qcl=qcl, source = source)
         if self._record:
             self._script(
-                "edit_service.save_as(%s, %s, %s)\n" % (self.saveFactory(var, method, qcl)),
+                "edit_service.save_as(%s, %s, %s, %s)\n" % (self.saveFactory(var, method, qcl, source)),
                 'black')
             #self._script("edit_service.save(%s, %s, %s, saveAs=%s)\n" % (var, method, qcl, isSave), 'black')
             Publisher.sendMessage("scroll")
         return result
 
-    def save_appending(self, var = None, method =None, qcl = None, overwrite = False):
+    def save_appending(self, var = None, method =None, qcl = None, source = None,  overwrite = False):
         """
 
         :param var:
@@ -296,14 +295,14 @@ def save_appending(self, var = None, method =None, qcl = None, overwrite = False
         :param override:
         :return:
         """
-        result = self._edit_service.save_appending(var=var, method=method, qcl=qcl, overwrite= overwrite)
+        result = self._edit_service.save_appending(var=var, method=method, qcl=qcl, source = source, overwrite= overwrite)
         if result:
             print "Save worked!"
 
             if self._record:
 
                 self._script(
-                    "edit_service.save_appending(%s, %s, %s, " % self.saveFactory(var, method, qcl)+str(overwrite )+")\n",
+                    "edit_service.save_appending(%s, %s, %s, %s " % self.saveFactory(var, method, qcl, source)+str(overwrite )+")\n",
                     'black')
                 #self._script("edit_service.save(%s, %s, %s, saveAs=%s)\n" % (var, method, qcl, isSave), 'black')
                 Publisher.sendMessage("scroll")
@@ -314,7 +313,7 @@ def save_appending(self, var = None, method =None, qcl = None, overwrite = False
         return result
 
 
-    def save_existing(self, var=None, method=None, qcl=None):
+    def save_existing(self, var=None, method=None, qcl=None, source =None):
         """
 
         :param var:
@@ -323,14 +322,14 @@ def save_existing(self, var=None, method=None, qcl=None):
         :param override:
         :return:
         """
-        result = self._edit_service.save_existing(var=var, method=method, qcl=qcl)
+        result = self._edit_service.save_existing(var=var, method=method, qcl=qcl, source = source)
         if result:
             print "Save worked!"
 
             if self._record:
 
                 self._script(
-                    "edit_service.save_existing(%s, %s, %s)\n" % (self.saveFactory(var, method, qcl)),
+                    "edit_service.save_existing(%s, %s, %s, %s)\n" % (self.saveFactory(var, method, qcl, source)),
                     'black')
                 #self._script("edit_service.save(%s, %s, %s, saveAs=%s)\n" % (var, method, qcl, isSave), 'black')
                 Publisher.sendMessage("scroll")
@@ -369,6 +368,13 @@ def get_qcl(self, q):
             Publisher.sendMessage("scroll")
 
         return qcl
+    def get_source(self, s):
+        src = self._edit_service.get_source(s.id)
+        if self._record:
+            self._script('new_src = series_service.get_src_by_id(%s)\n' % (src.id))
+            Publisher.sendMessage("scroll")
+
+        return src
 
     def get_method(self, m):
         method = self._edit_service.get_method(m.id)
@@ -434,6 +440,14 @@ def create_variable(self, v):
 
         return var
 
+    def create_source(self, src):
+        src = self._edit_service.create_source(src)
+        if self._record:
+            self._script('new_variable = series_service.get_soource(%s)\n' % (src))
+            Publisher.sendMessage("scroll")
+
+        return src
+
     def write_header(self):
         self._script("#Uncomment the following commands when running outside ODMTools\n", 'black')
         self._script("#from odmtools.odmservices import EditService, SeriesService\n", 'black')

odmtools/controller/logicEditTools.py

@@ -483,7 +483,9 @@ def calculateIntervalsOnGroups(self, interval):
             data_median = np.median(datavalue)
             data_std = math.sqrt(np.var(datavalue))
             data_sqrt = math.sqrt(len(interval))
-            data_deviation = data_std / data_sqrt
+            if data_sqrt != 0:
+                data_deviation = data_std / data_sqrt
+            else: data_deviation = 1
 
             ci = stats.norm.interval(.95, data_mean, scale=10*data_deviation)
             cl = stats.norm.interval(.95, data_median, scale=data_deviation)

odmtools/controller/logicPlotOptions.py

@@ -67,7 +67,7 @@ def enableButtons(self, isEnabled):
 
     def getSeries(self):
         selectedObject = self.pnlExisting.olvSeriesList.GetSelectedObject()
-        return selectedObject.method, selectedObject.quality_control_level, selectedObject.variable
+        return selectedObject.method, selectedObject.quality_control_level, selectedObject.variable, selectedObject.source
 
     def initTable(self, dbservice, site_id):
         """Set up columns and objects to be used in the objectlistview to be visible in the series selector"""