def check_for_uncombined_files(self):
"""
Go through working directory and check for uncombined files.
(I.e., location1_specimens.txt and location2_specimens.txt but no specimens.txt.)
Show a warning if uncombined files are found.
Return True if no uncombined files are found OR user elects
to continue anyway.
"""
wd_files = os.listdir(self.WD)
ftypes = ['specimens.txt', 'samples.txt', 'sites.txt', 'locations.txt']
uncombined = set()
for ftype in ftypes:
if ftype not in wd_files:
for f in wd_files:
if f.endswith('_' + ftype):
uncombined.add(ftype)
if uncombined:
msg = 'It looks like you may have uncombined files of type(s) {} in your working directory.\nYou may want to go back to Step 1 and finish combining all files.\nIf you continue, the program will try to extract as much information as possible from your measurement file.'.format(
", ".join(list(uncombined)))
dlg = pw.ChooseOne(self,
'Continue anyway',
'Go back',
msg,
title="Warning!")
res = dlg.ShowModal()
if res == wx.ID_NO:
return
return True
def on_add_cols(self, event):
"""
Show simple dialog that allows user to add a new column name
"""
col_labels = self.grid.col_labels
dia = pw.ChooseOne(self, yes="Add single columns", no="Add groups")
result1 = dia.ShowModal()
if result1 == wx.ID_CANCEL:
return
elif result1 == wx.ID_YES:
items = [col_name for col_name in self.dm.index if col_name not in col_labels]
dia = pw.HeaderDialog(self, 'columns to add',
items1=list(items), groups=[])
dia.Centre()
result2 = dia.ShowModal()
else:
groups = self.dm['group'].unique()
dia = pw.HeaderDialog(self, 'groups to add',
items1=list(groups), groups=True)
dia.Centre()
result2 = dia.ShowModal()
new_headers = []
if result2 == 5100:
new_headers = dia.text_list
# if there is nothing to add, quit
if not new_headers:
return
if result1 == wx.ID_YES:
# add individual headers
errors = self.add_new_grid_headers(new_headers)
else:
# add header groups
errors = self.add_new_header_groups(new_headers)
if errors:
errors_str = ', '.join(errors)
pw.simple_warning('You are already using the following headers: {}\nSo they will not be added'.format(errors_str))
# problem: if widgets above the grid are too wide,
# the grid does not re-size when adding columns
# awkward solution (causes flashing):
if self.grid.GetWindowStyle() != wx.DOUBLE_BORDER:
self.grid.SetWindowStyle(wx.DOUBLE_BORDER)
self.main_sizer.Fit(self)
self.grid.SetWindowStyle(wx.NO_BORDER)
self.Centre()
self.main_sizer.Fit(self)
#
self.grid.changes = set(range(self.grid.GetNumberRows()))
dia.Destroy()
def on_remove_row(self, event, row_num=-1):
"""
Remove specified grid row.
If no row number is given, remove the last row.
"""
text = "Are you sure? If you select delete you won't be able to retrieve these rows..."
dia = pw.ChooseOne(self, "Yes, delete rows", "Leave rows for now", text)
dia.Centre()
result = dia.ShowModal()
if result == wx.ID_NO:
return
default = (255, 255, 255, 255)
if row_num == -1:
# unhighlight any selected rows:
for row in self.selected_rows:
attr = wx.grid.GridCellAttr()
attr.SetBackgroundColour(default)
self.grid.SetRowAttr(row, attr)
row_num = self.grid.GetNumberRows() - 1
self.deleteRowButton.Disable()
self.selected_rows = {row_num}
# remove row(s) from the contribution
df = self.contribution.tables[self.grid_type].df
row_nums = list(range(len(df)))
df = df.iloc[[i for i in row_nums if i not in self.selected_rows]]
self.contribution.tables[self.grid_type].df = df
# now remove row(s) from grid
# delete rows, adjusting the row # appropriately as you delete
for num, row in enumerate(self.selected_rows):
row -= num
if row < 0:
row = 0
self.grid.remove_row(row)
attr = wx.grid.GridCellAttr()
attr.SetBackgroundColour(default)
self.grid.SetRowAttr(row, attr)
# reset the grid
self.selected_rows = set()
self.deleteRowButton.Disable()
self.grid.Refresh()
self.main_sizer.Fit(self)
def on_btn_upload(self, event):
"""
Try to run upload_magic.
Open validation mode if the upload file has problems.
"""
if not self.check_for_uncombined_files():
return
outstring = "upload_magic.py"
print("-I- running python script:\n %s" % (outstring))
wait = wx.BusyInfo("Please wait, working...")
wx.SafeYield()
self.contribution.tables['measurements'].add_measurement_names()
if self.data_model_num == 3:
res, error_message, has_problems, all_failing_items = ipmag.upload_magic3(
dir_path=self.WD,
vocab=self.contribution.vocab,
contribution=self.contribution)
if self.data_model_num == 2:
res, error_message, errors = ipmag.upload_magic(
dir_path=self.WD, data_model=self.er_magic.data_model)
del wait
if res:
text = "You are ready to upload!\n{} was generated in {}".format(
os.path.split(res)[1],
os.path.split(res)[0])
dlg = pw.ChooseOne(self, "Go to MagIC for uploading",
"Not ready yet", text, "Saved")
del wait
#dlg = wx.MessageDialog(self, caption="Saved", message=text, style=wx.OK)
else:
text = "There were some problems with the creation of your upload file.\nError message: {}\nSee Terminal/message window for details".format(
error_message)
dlg = wx.MessageDialog(self,
caption="Error",
message=text,
style=wx.OK)
dlg.Centre()
result = dlg.ShowModal()
if result == wx.ID_OK:
dlg.Destroy()
if result == wx.ID_YES:
pw.on_database_upload(None)
if self.data_model_num == 3:
if not res:
from programs import magic_gui
self.Disable()
self.Hide()
self.magic_gui_frame = magic_gui.MainFrame(
self.WD,
dmodel=self.data_model,
title="Validations",
contribution=self.contribution)
self.magic_gui_frame.validation_mode = ['specimens']
self.magic_gui_frame.failing_items = all_failing_items
self.magic_gui_frame.change_dir_button.Disable()
self.magic_gui_frame.Centre()
self.magic_gui_frame.Show()
self.magic_gui_frame.highlight_problems(has_problems)
#
# change name of upload button to 'exit validation mode'
self.magic_gui_frame.bSizer2.GetStaticBox().SetLabel(
'return to main GUI')
self.magic_gui_frame.btn_upload.SetLabel(
"exit validation mode")
# bind that button to quitting magic gui and re-enabling Pmag GUI
self.magic_gui_frame.Bind(wx.EVT_BUTTON,
self.on_end_validation,
self.magic_gui_frame.btn_upload)
def on_btn_unpack(self, event):
"""
Create dialog to choose a file to unpack
with download magic.
Then run download_magic and create self.contribution.
"""
def magic_download_dia(warn=""):
dia = pw.TextDialog(
self, "Download from MagIC\nusing contribution id or DOI",
"MagIC id/DOI", warn)
res = dia.ShowModal()
magic_id = dia.text_ctrl.return_value()
if res == wx.ID_CANCEL:
return wx.ID_CANCEL
if res == wx.ID_OK:
return magic_id
else:
return False
dlg = pw.ChooseOne(
self,
"Download from MagIC",
"Unpack previous downloaded file",
text=
"You can unpack a downloaded file from MagIC, or download a file from MagIC directly using the contribution id or DOI.",
title="")
dlg.Centre()
res = dlg.ShowModal()
# try to download directly from MagIC
if res == wx.ID_YES:
magic_id = True
warning = ""
while magic_id:
magic_id = magic_download_dia(warning)
# if magic id was blank
if magic_id == "":
warning = "You must provide a MagIC contribution id or DOI"
magic_id = True
continue
# if user canceled the download
if magic_id == wx.ID_CANCEL:
return
# if everything looks good, try to download
if len(str(magic_id)) < 8: # use contribution id
status, stuff = ipmag.download_magic_from_id(magic_id)
f = "magic_contribution_{}.txt".format(magic_id)
else: # use DOI
status, stuff = ipmag.download_magic_from_doi(magic_id)
f = "magic_contribution.txt"
if not status:
warning = stuff
if status:
break
if not os.path.exists(os.path.join(self.WD, f)):
os.rename(os.path.join(os.getcwd(), f),
os.path.join(self.WD, f))
input_dir = self.WD
# try to unpack a previously downloaded file
if res == wx.ID_NO:
dlg = wx.FileDialog(
None,
message="choose txt file to unpack",
defaultDir=self.WD,
defaultFile="",
style=wx.FD_OPEN #| wx.FD_CHANGE_DIR
)
if dlg.ShowModal() == wx.ID_OK:
FILE = dlg.GetPath()
input_dir, f = os.path.split(FILE)
else:
return False
outstring = "download_magic.py -f {} -WD {} -ID {}".format(
f, self.WD, input_dir)
# run as module:
print("-I- running python script:\n %s" % (outstring))
wait = wx.BusyInfo("Please wait, working...")
wx.SafeYield()
ex = None
try:
if ipmag.download_magic(f,
self.WD,
input_dir,
overwrite=True,
data_model=self.data_model):
text = "Successfully ran download_magic.py program.\nMagIC files were saved in your working directory.\nSee Terminal/message window for details."
else:
text = "Something went wrong. Make sure you chose a valid file downloaded from the MagIC database and try again."
return
except Exception as ex:
text = "Something went wrong. Make sure you chose a valid file downloaded from the MagIC database and try again."
del wait
dlg = wx.MessageDialog(self,
caption="Saved",
message=text,
style=wx.OK)
result = dlg.ShowModal()
if result == wx.ID_OK:
dlg.Destroy()
if ex:
raise (ex)
return
self.contribution = cb.Contribution(self.WD)
# make a success pop-up
dlg = wx.MessageDialog(
self,
caption="Success",
message=
"You can now add orientation information or metadata, or open one of the analysis tools",
style=wx.OK)
dlg.ShowModal()
def on_btn_upload(self, event):
"""
Try to run upload_magic.
Open validation mode if the upload file has problems.
"""
if not self.check_for_uncombined_files():
return
outstring = "upload_magic.py"
print("-I- running python script:\n %s" % (outstring))
wait = wx.BusyInfo("Please wait, working...")
wx.SafeYield()
success_responses = ['200', 200, '201', 201, True]
if 'measurements' in self.contribution.tables:
self.contribution.tables['measurements'].add_measurement_names()
upload_file, val_response, dummy1, dummy2 = ipmag.upload_magic(
concat=False, input_dir_path=self.WD, dir_path=self.WD)
del wait
if val_response == "no 3.0 files found, upload file not created":
pw.simple_warning(
"No 3.0 files were found in your directory, so no upload could be created!"
)
return
status = val_response['status']
if not status:
pw.simple_warning(
"Oops, something went wrong with validating on the server.\n{}\nTry again later or submit a bug report."
.format(val_response['warnings']))
return
validation_errors = val_response['validation']
if (not validation_errors['warnings']) and (
not validation_errors['errors']):
text = "You are ready to upload!\n{} was generated in {}".format(
os.path.split(upload_file)[1], self.WD)
dlg = pw.ChooseOne(self, "Go to MagIC for uploading",
"Not ready yet", text, "Saved")
dlg.Centre()
result = dlg.ShowModal()
if result == wx.ID_OK:
dlg.Destroy()
if result == wx.ID_YES:
pw.on_database_upload(None)
return
# there were problems, so display validation
text = "There were some problems with the creation of your upload file.\nSee Terminal/message window for details"
dlg = wx.MessageDialog(self,
caption="Error",
message=text,
style=wx.OK)
dlg.Centre()
result = dlg.ShowModal()
# TODO: get the error-y business formatted into a dict of lists of dicts
from programs import magic_gui
self.Disable()
self.Hide()
self.magic_gui_frame = magic_gui.MainFrame(
self.WD,
dmodel=self.data_model,
title="Validations",
contribution=self.contribution,
errors=validation_errors['errors'])
self.magic_gui_frame.Centre()
self.magic_gui_frame.Show()
self.magic_gui_frame.highlight_problems()
# bind that button to quitting magic gui and re-enabling Pmag GUI
self.magic_gui_frame.Bind(wx.EVT_BUTTON, self.on_end_validation,
self.magic_gui_frame.return_btn)
# do binding so that closing/quitting re-opens the main frame
self.magic_gui_frame.Bind(wx.EVT_CLOSE, self.on_end_validation)
# this makes it work with only the validation window open
self.magic_gui_frame.Bind(
wx.EVT_MENU,
lambda event: self.menubar.on_quit(event, self.magic_gui_frame),
self.magic_gui_frame.menubar.file_quit)
# this makes it work if an additional grid is open
self.Bind(
wx.EVT_MENU,
lambda event: self.menubar.on_quit(event, self.magic_gui_frame),
self.magic_gui_frame.menubar.file_quit)
def onImport(self, event):
"""
Import a MagIC-format file
"""
if self.grid.changes:
print("-W- Your changes will be overwritten...")
wind = pw.ChooseOne(self, "Import file anyway", "Save grid first",
"-W- Your grid has unsaved changes which will be overwritten if you import a file now...")
wind.Centre()
res = wind.ShowModal()
# save grid first:
if res == wx.ID_NO:
self.onSave(None, alert=True, destroy=False)
# reset self.changes
self.grid.changes = set()
openFileDialog = wx.FileDialog(self, "Open MagIC-format file", self.WD, "",
"MagIC file|*.*", wx.FD_OPEN | wx.FD_FILE_MUST_EXIST)
result = openFileDialog.ShowModal()
if result == wx.ID_OK:
# get filename
filename = openFileDialog.GetPath()
# make sure the dtype is correct
f = open(filename)
line = f.readline()
if line.startswith("tab"):
delim, dtype = line.split("\t")
else:
delim, dtype = line.split("")
f.close()
dtype = dtype.strip()
if (dtype != self.grid_type) and (dtype + "s" != self.grid_type):
text = "You are currently editing the {} grid, but you are trying to import a {} file.\nPlease open the {} grid and then re-try this import.".format(self.grid_type, dtype, dtype)
pw.simple_warning(text)
return
# grab old data for concatenation
if self.grid_type in self.contribution.tables:
old_df_container = self.contribution.tables[self.grid_type]
else:
old_df_container = None
old_col_names = self.grid.col_labels
# read in new file and update contribution
df_container = nb.MagicDataFrame(filename, dmodel=self.dm,
columns=old_col_names)
# concatenate if possible
if not isinstance(old_df_container, type(None)):
df_container.df = pd.concat([old_df_container.df, df_container.df],
axis=0)
self.contribution.tables[df_container.dtype] = df_container
self.grid_builder = GridBuilder(self.contribution, self.grid_type,
self.panel, parent_type=self.parent_type,
reqd_headers=self.reqd_headers)
# delete old grid
self.grid_box.Hide(0)
self.grid_box.Remove(0)
# create new, updated grid
self.grid = self.grid_builder.make_grid()
self.grid.InitUI()
# add data to new grid
self.grid_builder.add_data_to_grid(self.grid, self.grid_type)
# add new grid to sizer and fit everything
self.grid_box.Add(self.grid, flag=wx.ALL, border=5)
self.main_sizer.Fit(self)
self.Centre()
# add any needed drop-down-menus
self.drop_down_menu = drop_down_menus.Menus(self.grid_type,
self.contribution,
self.grid)
# done!
return