def __init__(self):
super(CoreBrowser, self).__init__(parent=None, id=wx.ID_ANY,
title='CScience', size=(540, 380))
#hide the frame until the initial repo is loaded, to prevent flicker.
self.Show(False)
self.browser_view = SampleBrowserView()
self.core = None
self.CreateStatusBar()
self.create_menus()
self.create_widgets()
self.Bind(events.EVT_REPO_CHANGED, self.on_repository_altered)
self.Bind(wx.EVT_CLOSE, self.quit)
class CoreBrowser(MemoryFrame):
framename = 'samplebrowser'
def __init__(self):
super(CoreBrowser, self).__init__(parent=None, id=wx.ID_ANY,
title='CScience', size=(540, 380))
#hide the frame until the initial repo is loaded, to prevent flicker.
self.Show(False)
self.browser_view = SampleBrowserView()
self.core = None
self.CreateStatusBar()
self.create_menus()
self.create_widgets()
self.Bind(events.EVT_REPO_CHANGED, self.on_repository_altered)
self.Bind(wx.EVT_CLOSE, self.quit)
def create_menus(self):
menu_bar = wx.MenuBar()
#Build File menu
#Note: on a mac, the 'Quit' option is moved for platform nativity automatically
file_menu = wx.Menu()
item = file_menu.Append(wx.ID_OPEN, "Switch Repository\tCtrl-O",
"Switch to a different CScience Repository")
self.Bind(wx.EVT_MENU, self.change_repository, item)
file_menu.AppendSeparator()
item = file_menu.Append(wx.ID_SAVE, "Save Repository\tCtrl-S",
"Save changes to current CScience Repository")
self.Bind(wx.EVT_MENU, self.save_repository, item)
file_menu.AppendSeparator()
item = file_menu.Append(wx.ID_EXIT, "Quit CScience\tCtrl-Q",
"Quit CScience")
self.Bind(wx.EVT_MENU, self.quit, item)
edit_menu = wx.Menu()
item = edit_menu.Append(wx.ID_COPY, "Copy\tCtrl-C", "Copy selected samples.")
self.Bind(wx.EVT_MENU, self.OnCopy, item)
tool_menu = wx.Menu()
def bind_editor(name, edclass, menuname, tooltip):
menuitem = tool_menu.Append(wx.ID_ANY, menuname, tooltip)
hid_name = ''.join(('_', name))
def del_editor(event, *args, **kwargs):
setattr(self, hid_name, None)
def create_editor():
editor = getattr(self, hid_name, None)
if not editor:
#TODO: fix this hack!
editor = getattr(edclass, edclass.__name__.rpartition('.')[2])(self)
self.Bind(wx.EVT_CLOSE, del_editor, editor)
setattr(self, hid_name, editor)
return editor
def raise_editor(event, *args, **kwargs):
editor = create_editor()
editor.Show()
editor.Raise()
self.Bind(wx.EVT_MENU, raise_editor, menuitem)
return menuitem
bind_editor('filter_editor', FilterEditor, "Filter Editor\tCtrl-1",
"Create and Edit CScience Filters for use in the Sample Browser")
bind_editor('view_editor', ViewEditor, "View Editor\tCtrl-2",
"Edit the list of views that can filter the display of samples in CScience")
tool_menu.AppendSeparator()
bind_editor('attribute_editor', AttEditor, "Attribute Editor\tCtrl-3",
"Edit the list of attributes that can appear on samples in CScience")
tool_menu.AppendSeparator()
bind_editor('template_editor', TemplateEditor, "Template Editor\tCtrl-4",
"Edit the list of templates for the CScience Paleobase")
bind_editor('milieu_browser', MilieuBrowser, "Milieu Browser\tCtrl-5",
"Browse and Import Paleobase Entries")
tool_menu.AppendSeparator()
bind_editor('cplan_browser', ComputationPlanBrowser, "Computation Plan Browser\tCtrl-6",
"Browse Existing Computation Plans and Create New Computation Plans")
help_menu = wx.Menu()
item = help_menu.Append(wx.ID_ABOUT, "About CScience", "View Credits")
self.Bind(wx.EVT_MENU, self.show_about, item)
#Disallow save unless there's something to save :)
file_menu.Enable(wx.ID_SAVE, False)
#Disable copy when no rows are selected
edit_menu.Enable(wx.ID_COPY, False)
menu_bar.Append(file_menu, "&File")
menu_bar.Append(edit_menu, "&Edit")
menu_bar.Append(tool_menu, "&Tools")
menu_bar.Append(help_menu, "&Help")
self.SetMenuBar(menu_bar)
def create_action_buttons(self):
#TODO: These would make a lot more sense as menu & toolbar thingies.
self.button_panel = wx.Panel(self, wx.ID_ANY)
button_sizer = wx.BoxSizer(wx.HORIZONTAL)
imp_button = wx.Button(self.button_panel, wx.ID_ANY, "Import Samples...")
self.Bind(wx.EVT_BUTTON, self.import_samples, imp_button)
button_sizer.Add(imp_button, border=5, flag=wx.ALL)
calc_button = wx.Button(self.button_panel, wx.ID_APPLY, "Do Calculations...")
self.Bind(wx.EVT_BUTTON, self.OnDating, calc_button)
button_sizer.Add(calc_button, border=5, flag=wx.ALL)
calv_button = wx.Button(self.button_panel, wx.ID_ANY, "Analyze Ages...")
self.Bind(wx.EVT_BUTTON, self.OnRunCalvin, calv_button)
button_sizer.Add(calv_button, border=5, flag=wx.ALL)
self.del_button = wx.Button(self.button_panel, wx.ID_DELETE, "Delete Sample...")
self.Bind(wx.EVT_BUTTON, self.OnDeleteSample, self.del_button)
button_sizer.Add(self.del_button, border=5, flag=wx.ALL)
self.del_button.Disable()
self.strip_button = wx.Button(self.button_panel, wx.ID_ANY, "Strip Calculated Data...")
self.Bind(wx.EVT_BUTTON, self.OnStripExperiment, self.strip_button)
button_sizer.Add(self.strip_button, border=5, flag=wx.ALL)
self.strip_button.Disable()
exp_button = wx.Button(self.button_panel, wx.ID_ANY, "Export Samples...")
self.Bind(wx.EVT_BUTTON, self.OnExportView, exp_button)
button_sizer.Add(exp_button, border=5, flag=wx.ALL)
self.button_panel.SetSizer(button_sizer)
return self.button_panel
def create_widgets(self):
#NOTE: we can stick these in a panel if needed to prevent them showing
#up while asking to open the repository.
#TODO: investigate whether all these ComboBoxes should actually be Choices
#TODO: save & load these values using PersistentControls
self.selected_core = wx.ComboBox(self, wx.ID_ANY,
choices=['No Core Selected'],
style=wx.CB_READONLY)
self.selected_view = wx.ComboBox(self, wx.ID_ANY, choices=['All'],
style=wx.CB_READONLY)
self.selected_filter = wx.ComboBox(self, wx.ID_ANY, choices=['<No Filter>'],
style=wx.CB_READONLY)
self.filter_desc = wx.StaticText(self, wx.ID_ANY, "No Filter Selected")
self.Bind(wx.EVT_COMBOBOX, self.select_core, self.selected_core)
self.Bind(wx.EVT_COMBOBOX, self.select_view, self.selected_view)
self.Bind(wx.EVT_COMBOBOX, self.select_filter, self.selected_filter)
self.sselect_prim = wx.ComboBox(self, wx.ID_ANY, choices=["Not Sorted"],
style=wx.CB_DROPDOWN | wx.CB_READONLY | wx.CB_SORT)
self.sselect_sec = wx.ComboBox(self, wx.ID_ANY, choices=["Not Sorted"],
style=wx.CB_DROPDOWN | wx.CB_READONLY | wx.CB_SORT)
self.sdir_select = wx.ComboBox(self, wx.ID_ANY,
value=self.browser_view.get_direction(),
choices=["Ascending", "Descending"],
style=wx.CB_DROPDOWN | wx.CB_READONLY)
self.plotbutton = wx.Button(self, wx.ID_ANY, "Plot Attributes...")
self.Bind(wx.EVT_COMBOBOX, self.OnChangeSort, self.sselect_prim)
self.Bind(wx.EVT_COMBOBOX, self.OnChangeSort, self.sselect_sec)
self.Bind(wx.EVT_COMBOBOX, self.OnSortDirection, self.sdir_select)
self.Bind(wx.EVT_BUTTON, self.do_plot, self.plotbutton)
self.search_box = wx.TextCtrl(self, wx.ID_ANY, size=(300, -1))
self.exact_box = wx.CheckBox(self, wx.ID_ANY, "Use Exact Match")
self.Bind(wx.EVT_TEXT, self.OnTextSearchUpdate, self.search_box)
self.Bind(wx.EVT_CHECKBOX, self.OnTextSearchUpdate, self.exact_box)
self.grid = grid.LabelSizedGrid(self, wx.ID_ANY)
self.table = SampleGridTable(self.grid)
self.grid.SetSelectionMode(wx.grid.Grid.SelectRows)
self.grid.AutoSize()
self.grid.EnableEditing(False)
self.create_action_buttons()
sizer = wx.BoxSizer(wx.VERTICAL)
row_sizer = wx.BoxSizer(wx.HORIZONTAL)
row_sizer.Add(wx.StaticText(self, wx.ID_ANY, "Viewing Core:"), border=5, flag=wx.ALL)
row_sizer.Add(self.selected_core, border=5, flag=wx.ALL)
row_sizer.AddStretchSpacer()
row_sizer.Add(wx.StaticText(self, wx.ID_ANY, "View:"), border=5, flag=wx.ALL)
row_sizer.Add(self.selected_view, border=5, flag=wx.ALL)
row_sizer.Add(wx.StaticText(self, wx.ID_ANY, "Filter:"), border=5, flag=wx.ALL)
row_sizer.Add(self.selected_filter, border=5, flag=wx.ALL)
row_sizer.Add(self.filter_desc, border=5, flag=wx.ALL)
sizer.Add(row_sizer, flag=wx.EXPAND)
row_sizer = wx.BoxSizer(wx.HORIZONTAL)
row_sizer.Add(wx.StaticText(self, wx.ID_ANY, "Sort by"), border=5, flag=wx.ALL)
row_sizer.Add(self.sselect_prim, border=5, flag=wx.ALL)
row_sizer.Add(wx.StaticText(self, wx.ID_ANY, "and then by"), border=5, flag=wx.ALL)
row_sizer.Add(self.sselect_sec, border=5, flag=wx.ALL)
row_sizer.Add(self.sdir_select, border=5, flag=wx.ALL)
row_sizer.Add(self.plotbutton, border=5, flag=wx.ALL)
sizer.Add(row_sizer, flag=wx.EXPAND)
sizer.Add(self.grid, proportion=1, flag=wx.EXPAND)
row_sizer = wx.BoxSizer(wx.HORIZONTAL)
row_sizer.Add(wx.StaticText(self, wx.ID_ANY, "Search:"), border=5, flag=wx.ALL)
row_sizer.Add(self.search_box, border=5, flag=wx.ALL)
row_sizer.Add(self.exact_box, border=5, flag=wx.ALL)
sizer.Add(row_sizer, flag=wx.EXPAND)
sizer.Add(self.button_panel)
self.SetSizer(sizer)
def show_about(self, event):
dlg = AboutBox(self)
dlg.ShowModal()
dlg.Destroy()
def quit(self, event):
self.close_repository()
wx.Exit()
def on_repository_altered(self, event):
"""
Used to cause the File->Save Repo menu option to be enabled only if
there is new data to save.
"""
if 'views' in event.changed:
view_name = self.browser_view.get_view()
# get list of views
self.selected_view.SetItems(datastore.views.keys())
# if current view has been deleted, then switch to "All" view
if view_name not in datastore.views:
self.selected_view.SetValue('All')
else:
self.selected_view.SetValue(view_name)
if event.value and view_name == event.value:
#update the currently viewed view, if that's the one that
#was changed.
self.select_view(None)
elif 'filters' in event.changed:
filter_name = self.browser_view.get_filter()
# get list of filters
self.selected_filter.SetItems(['<No Filter>'] +
sorted(datastore.filters.keys()))
# if current filter has been deleted, then switch to "None" filter
if filter_name not in datastore.filters:
self.selected_filter.SetValue('<No Filter>')
else:
self.selected_filter.SetValue(filter_name)
if event.value and filter_name == event.value:
#if we changed the currently selected filter, we should
#re-filter the current view.
self.select_filter(None)
else:
#TODO: select new core on import, & stuff.
self.show_new_core()
datastore.data_modified = True
self.GetMenuBar().Enable(wx.ID_SAVE, True)
event.Skip()
def change_repository(self, event):
self.close_repository()
#Close all other editors, as the repository is changing...
for window in self.Children:
if window.IsTopLevel():
window.Close()
self.open_repository()
self.SetTitle(' '.join(('CScience:', datastore.data_source)))
def open_repository(self, repo_dir=None):
if not repo_dir:
dialog = wx.DirDialog(None, "Choose a Repository",
style=wx.DD_DEFAULT_STYLE | wx.DD_DIR_MUST_EXIST | wx.DD_CHANGE_DIR)
if dialog.ShowModal() == wx.ID_OK:
repo_dir = dialog.GetPath()
dialog.Destroy()
else:
#end the app, if the user doesn't want to open a repo dir
self.Close()
return
elif not os.path.exists(repo_dir):
raise datastore.RepositoryException('Previously saved repository no longer exists.')
try:
datastore.set_data_source(repo_dir)
except Exception as e:
import traceback
print repr(e)
print traceback.format_exc()
raise datastore.RepositoryException('Error while loading selected repository.')
else:
self.selected_core.SetItems(sorted(datastore.cores.keys()) or
['No Cores -- Import Samples to Begin'])
self.selected_core.SetSelection(0)
self.selected_view.SetItems([v for v in datastore.views])
self.selected_view.SetStringSelection(self.browser_view.get_view())
self.selected_filter.SetItems(['<No Filter>'] + sorted(datastore.filters.keys()))
self.selected_filter.SetStringSelection(self.browser_view.get_filter())
self.show_new_core()
wx.CallAfter(self.Raise)
def close_repository(self):
if datastore.data_modified:
if wx.MessageBox('You have modified this repository. '
'Would you like to save your changes?', "Unsaved Changes",
wx.YES_NO | wx.ICON_EXCLAMATION) == wx.YES:
self.save_repository(None)
#just in case, for now
datastore.data_modified = False
def save_repository(self, event):
datastore.save_datastore()
def OnCopy(self, event):
samples = [self.displayed_samples[index] for index in self.grid.SelectedRowset]
view = datastore.views[self.browser_view.get_view()]
#views are guaranteed to give attributes as id, then computation_plan, then
#remaining atts in order when iterated.
result = os.linesep.join(['\t'.join([
datastore.sample_attributes.format_value(att, sample[att])
for att in view]) for sample in samples])
result = os.linesep.join(['\t'.join(view), result])
data = wx.TextDataObject()
data.SetText(result)
if wx.TheClipboard.Open():
wx.TheClipboard.SetData(data)
wx.TheClipboard.Close()
def show_new_core(self):
self.samples = []
if self.core is not None:
for vc in self.core.virtualize():
self.samples.extend(vc)
self.filter_samples()
def filter_samples(self):
self.displayed_samples = None
filter_name = self.browser_view.get_filter()
try:
filt = datastore.filters[filter_name]
except KeyError:
self.browser_view.set_filter('<No Filter>')
self.selected_filter.SetStringSelection('<No Filter>')
self.filter_desc.SetLabel('No Filter Selected')
filtered_samples = self.samples[:]
else:
self.filter_desc.SetLabel(filt.description)
filtered_samples = filter(filt.apply, self.samples)
self.search_samples(filtered_samples)
def search_samples(self, filtered_samples=[]):
value = self.search_box.GetValue()
if value:
if not self.exact_box.IsChecked() and self.displayed_samples and \
self.previous_query in value:
samples_to_search = self.displayed_samples
else:
samples_to_search = filtered_samples
self.previous_query = value
view = datastore.views[self.browser_view.get_view()]
self.displayed_samples = [s for s in samples_to_search if
s.search(value, view, self.exact_box.IsChecked())]
else:
self.displayed_samples = filtered_samples
self.previous_query = ''
self.display_samples()
def display_samples(self):
def sort_none_last(x, y):
def cp_none(x, y):
if x is None and y is None:
return 0
elif x is None:
return 1
elif y is None:
return -1
else:
return cmp(x, y)
for a, b in zip(x, y):
val = cp_none(a, b)
if val:
return val
return 0
self.displayed_samples.sort(cmp=sort_none_last,
key=lambda s: (s[self.browser_view.get_primary()],
s[self.browser_view.get_secondary()]),
reverse=self.GetSortDirection())
self.table.view = datastore.views[self.browser_view.get_view()]
self.table.samples = self.displayed_samples
def OnTextSearchUpdate(self, event):
self.search_samples()
def OnExportView(self, event):
view_name = self.browser_view.get_view()
view = datastore.views[view_name]
# add header labels -- need to use iterator to get computation_plan/id correct
rows = [att for att in view]
rows.extend([[sample[att] for att in view] for sample in self.displayed_samples])
wildcard = "CSV Files (*.csv)|*.csv|" \
"All files (*.*)|*.*"
dlg = wx.FileDialog(self, message="Save view in ...", defaultDir=os.getcwd(), defaultFile="view.csv", wildcard=wildcard, style=wx.SAVE | wx.CHANGE_DIR | wx.OVERWRITE_PROMPT)
dlg.SetFilterIndex(0)
if dlg.ShowModal() == wx.ID_OK:
path = dlg.GetPath()
tmp = open(path, "wb")
writer = csv.writer(tmp)
writer.writerows(rows)
tmp.flush()
tmp.close()
the_dir = os.path.dirname(path)
os.chdir(the_dir)
dlg.Destroy()
def do_plot(self, event):
#TODO: let user select all those pretty plotting options!
options = PlotOptions('depth')
pw = PlotWindow(self, self.displayed_samples, options)
pw.Show()
pw.Raise()
def import_samples(self, event):
dialog = wx.FileDialog(None,
"Please select a CSV File containing Samples to be Imported or Updated:",
defaultDir=os.getcwd(), wildcard="CSV Files (*.csv)|*.csv|All Files|*.*",
style=wx.OPEN | wx.DD_CHANGE_DIR)
result = dialog.ShowModal()
path = dialog.GetPath()
#destroy the dialog now so no problems happen on early return
dialog.Destroy()
if result == wx.ID_OK:
with open(path, 'rU') as input_file:
#allow whatever sane csv formats we can manage, here
sniffer = csv.Sniffer()
dialect = sniffer.sniff(input_file.read(1024))
dialect.skipinitialspace = True
input_file.seek(0)
reader = csv.DictReader(input_file, dialect=dialect)
if not reader.fieldnames:
wx.MessageBox("Selected file is empty.", "Operation Cancelled",
wx.OK | wx.ICON_INFORMATION)
return
#strip extra spaces, since that was apparently a problem before?
reader.fieldnames = [name.strip() for name in reader.fieldnames]
if 'depth' not in reader.fieldnames:
wx.MessageBox("Selected file is missing the required attribute 'depth'.",
"Operation Cancelled", wx.OK | wx.ICON_INFORMATION)
return
rows = []
for index, line in enumerate(reader, 1):
#do appropriate type conversions...
for key, value in line.iteritems():
try:
line[key] = datastore.sample_attributes.convert_value(key, value)
except ValueError:
wx.MessageBox("%s on row %i has an incorrect type."
"Please update the csv file and try again." % (key, index),
"Operation Cancelled", wx.OK | wx.ICON_INFORMATION)
return
rows.append(line)
if not rows:
wx.MessageBox("Selected file appears to contain no data.",
"Operation Cancelled", wx.OK | wx.ICON_INFORMATION)
return
dialog = DisplayImportedSamples(self, os.path.basename(path),
reader.fieldnames, rows)
if dialog.ShowModal() == wx.ID_OK:
if dialog.source_name:
for item in rows:
item['source'] = dialog.source_name
cname = dialog.core_name
core = datastore.cores.get(cname, None)
if core is None:
core = Core(cname)
datastore.cores[cname] = core
for item in rows:
s = Sample('input', item)
core.add(s)
wx.MessageBox('Core %s imported/updated' % cname, "Import Results",
wx.OK | wx.CENTRE)
events.post_change(self, 'samples')
dialog.Destroy()
def OnRunCalvin(self, event):
"""
Runs Calvin on all highlighted samples, or all samples if none are
highlighted.
"""
if not self.grid.SelectedRowset:
samples = self.displayed_samples
else:
indexes = list(self.grid.SelectedRowset)
samples = [self.displayed_samples[index] for index in indexes]
calvin.argue.analyzeSamples(samples)
def select_core(self, event):
try:
self.core = datastore.cores[self.selected_core.GetStringSelection()]
except KeyError:
self.core = None
self.show_new_core()
def select_filter(self, event):
self.browser_view.set_filter(self.selected_filter.GetStringSelection())
self.filter_samples()
def select_view(self, event):
view_name = self.selected_view.GetStringSelection()
try:
view = datastore.views[view_name]
except KeyError:
view_name = 'All'
view = datastore.views['All']
self.selected_view.SetStringSelection('All')
self.browser_view.set_view(view_name)
self.sselect_prim.SetItems(view)
self.sselect_sec.SetItems(view)
previous_primary = self.browser_view.get_primary()
previous_secondary = self.browser_view.get_secondary()
if previous_primary in view:
self.sselect_prim.SetStringSelection(previous_primary)
else:
self.sselect_prim.SetStringSelection("depth")
self.browser_view.set_primary("depth")
if previous_secondary in view:
self.sselect_sec.SetStringSelection(previous_secondary)
else:
self.sselect_sec.SetStringSelection("computation plan")
self.browser_view.set_secondary("computation plan")
self.filter_samples()
def GetSortDirection(self):
# return true for descending, else return false
# this corresponds to the expected value for the reverse parameter of the sort() method
if self.browser_view.get_direction() == "Descending":
return True
return False
def OnSortDirection(self, event):
self.browser_view.set_direction(self.sdir_select.GetStringSelection())
self.display_samples()
def OnChangeSort(self, event):
self.browser_view.set_primary(self.sselect_prim.GetStringSelection())
self.browser_view.set_secondary(self.sselect_sec.GetStringSelection())
self.display_samples()
def OnDating(self, event):
dlg = ComputationDialog(self, self.core)
ret = dlg.ShowModal()
plan = dlg.plan
# depths = dlg.depths
dlg.Destroy()
if ret != wx.ID_OK:
return
computation_plan = datastore.computation_plans[plan]
workflow = datastore.workflows[computation_plan['workflow']]
vcore = self.core.new_computation(plan)
aborting = wx.lib.delayedresult.AbortEvent()
self.button_panel.Disable()
self.plotbutton.Disable()
dialog = WorkflowProgress(self, "Applying Computation '%s'" % plan)
wx.lib.delayedresult.startWorker(self.OnDatingDone, workflow.execute,
wargs=(computation_plan, vcore, aborting),
cargs=(plan, self.core, dialog))
if dialog.ShowModal() != wx.ID_OK:
aborting.set()
self.core.strip_experiment(plan)
dialog.Destroy()
def OnDatingDone(self, dresult, planname, core, dialog):
try:
result = dresult.get()
except Exception as exc:
core.strip_experiment(planname)
print exc
wx.MessageBox("There was an error running the requested computation."
" Please contact support.")
else:
dialog.EndModal(wx.ID_OK)
events.post_change(self, 'samples')
finally:
self.button_panel.Enable()
self.plotbutton.Enable()
def OnStripExperiment(self, event):
indexes = list(self.grid.SelectedRowset)
samples = [self.displayed_samples[index] for index in indexes]
dialog = wx.MessageDialog(None, 'This operation will strip all performed computations from the selected samples. (Note: Input cannot be deleted.) Are you sure you want to do this?', "Are you sure?", wx.YES_NO | wx.ICON_EXCLAMATION)
if dialog.ShowModal() == wx.ID_YES:
for sample in samples:
for exp in sample.keys():
if exp != 'input':
del sample[exp]
self.grid.ClearSelection()
events.post_change(self, 'samples')
def OnDeleteSample(self, event):
indexes = self.grid.SelectedRowset
samples = [self.displayed_samples[index] for index in indexes]
ids = [sample['id'] for sample in samples]
dialog = wx.MessageDialog(None, 'Are you sure that you want to delete the following samples: %s' % (ids), "Are you sure?", wx.YES_NO | wx.ICON_EXCLAMATION)
if dialog.ShowModal() == wx.ID_YES:
for s_id in ids:
del self.core[depth]
self.grid.ClearSelection()
events.post_change(self, 'samples')
