def on_upload_file(self, event):
wait = wx.BusyInfo('Validating data, please wait...')
wx.Yield()
res, error_message, has_problems, all_failing_items = ipmag.upload_magic3(dir_path=self.WD,
vocab=self.contribution.vocab)
self.failing_items = all_failing_items
if has_problems:
self.validation_mode = set(has_problems)
# highlighting doesn't work with Windows
if sys.platform in ['win32', 'win62']:
self.message.SetLabel('The following grid(s) have incorrect or incomplete data:\n{}'.format(', '.join(self.validation_mode)))
# highlighting does work with OSX
else:
for dtype in ["specimens", "samples", "sites", "locations", "ages"]:
wind = self.FindWindowByName(dtype + '_btn')
if dtype not in has_problems:
wind.Unbind(wx.EVT_PAINT, handler=self.highlight_button)
else:
wind.Bind(wx.EVT_PAINT, self.highlight_button)
self.Refresh()
self.message.SetLabel('Highlighted grids have incorrect or incomplete data')
self.bSizer_msg.ShowItems(True)
self.hbox.Fit(self)
if not has_problems:
self.validation_mode = set()
self.message.SetLabel('')
self.bSizer_msg.ShowItems(False)
self.hbox.Fit(self)
del wait
def on_btn_upload(self, event):
outstring = "upload_magic.py"
print "-I- running python script:\n %s" % (outstring)
wait = wx.BusyInfo("Please wait, working...")
wx.Yield()
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)
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 Your file: {} was generated in MagIC Project Directory.\nDrag and drop this file in the MagIC database.".format(
os.path.split(res)[1])
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/Command Prompt for details".format(
error_message)
dlg = wx.MessageDialog(self,
caption="Error",
message=text,
style=wx.OK)
result = dlg.ShowModal()
if result == wx.ID_OK:
dlg.Destroy()
def on_upload_file(self, event):
wait = wx.BusyInfo('Validating data, please wait...')
wx.Yield()
res, error_message, has_problems, all_failing_items = ipmag.upload_magic3(dir_path=self.WD,
vocab=self.contribution.vocab)
self.failing_items = all_failing_items
if has_problems:
self.validation_mode = set(has_problems)
# highlighting doesn't work with Windows
if sys.platform in ['win32', 'win62']:
self.message.SetLabel('The following grid(s) have incorrect or incomplete data:\n{}'.format(', '.join(self.validation_mode)))
# highlighting does work with OSX
else:
for dtype in ["specimens", "samples", "sites", "locations", "ages"]:
wind = self.FindWindowByName(dtype + '_btn')
if dtype not in has_problems:
wind.Unbind(wx.EVT_PAINT, handler=self.highlight_button)
else:
wind.Bind(wx.EVT_PAINT, self.highlight_button)
self.Refresh()
self.message.SetLabel('Highlighted grids have incorrect or incomplete data')
self.bSizer_msg.ShowItems(True)
self.hbox.Fit(self)
if not has_problems:
self.validation_mode = set()
self.message.SetLabel('')
self.bSizer_msg.ShowItems(False)
self.hbox.Fit(self)
del wait
def on_btn_upload(self, event):
outstring = "upload_magic.py"
print("-I- running python script:\n %s" % (outstring))
wait = wx.BusyInfo("Please wait, working...")
wx.Yield()
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 Your file: {} was generated in MagIC Project Directory.\nDrag and drop this file in the MagIC database.".format(
os.path.split(res)[1])
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)
result = dlg.ShowModal()
if result == wx.ID_OK:
dlg.Destroy()
if self.data_model_num == 3:
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_upload_file(self, event):
wait = wx.BusyInfo('Validating data, please wait...')
wx.Yield()
res, error_message, has_problems, all_failing_items = ipmag.upload_magic3(
dir_path=self.WD, vocab=self.contribution.vocab)
self.failing_items = all_failing_items
if has_problems:
self.highlight_problems(has_problems)
if not has_problems:
self.validation_mode = set()
self.message.SetLabel('')
self.bSizer_msg.ShowItems(False)
self.hbox.Fit(self)
del wait
def test3_with_invalid_files(self):
dir_path = os.path.join(WD, 'data_files', '3_0', 'Megiddo')
outfile, error_message, errors, all_errors = ipmag.upload_magic3(dir_path=dir_path)
msg = "file validation has failed. You may run into problems if you try to upload this file."
self.assertEqual(error_message, msg)
# delete any upload file that was partially created
import re
pattern = re.compile('\w*[.]\w*[.]\w*[20]\d{2}\w*.txt$')
possible_files = os.listdir(dir_path)
files = []
for f in possible_files:
if pattern.match(f):
files.append(f)
pmag.remove_files(files, dir_path)
def test3_with_invalid_files(self):
dir_path = os.path.join(WD, 'data_files', '3_0', 'Megiddo')
outfile, error_message, errors, all_errors = ipmag.upload_magic3(
dir_path=dir_path)
msg = "file validation has failed. You may run into problems if you try to upload this file."
self.assertEqual(error_message, msg)
# delete any upload file that was partially created
import re
pattern = re.compile('\w*[.]\w*[.]\w*[20]\d{2}\w*.txt$')
possible_files = os.listdir(dir_path)
files = []
for f in possible_files:
if pattern.match(f):
files.append(f)
pmag.remove_files(files, dir_path)
def main():
"""
NAME
upload_magic.py
DESCRIPTION
This program will prepare your MagIC text files created by the programs nfo_magic.py,
zeq_magic.py, thellier_magic.py, mag_magic, specimens_results_magic.py and so on.
it will check for all the MagIC text files and skip the missing ones
SYNTAX
upload_magic.py
INPUT
MagIC txt files
OPTIONS
-h prints help message and quits
-all include all the measurement data, default is only those used in interpretations
-DM specify which MagIC data model number to use (2 or 3). Default is 3.
OUTPUT
upload file: file for uploading to MagIC database
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
else:
data_model_num = pmag.get_named_arg("-DM", 3)
dataframe = extractor.command_line_dataframe([['cat', False, 0], ['F', False, ''], ['f', False, '']])
checked_args = extractor.extract_and_check_args(sys.argv, dataframe)
dir_path, concat = extractor.get_vars(['WD', 'cat'], checked_args)
if data_model_num == 2:
ipmag.upload_magic(concat, dir_path)
else:
ipmag.upload_magic3(concat, dir_path)
def test3_with_contribution(self):
dir_path = os.path.join(WD, 'data_files', '3_0', 'Megiddo')
con = nb.Contribution(directory=dir_path)
outfile, error_message, errors, all_errors = ipmag.upload_magic3(contribution=con)
msg = "file validation has failed. You may run into problems if you try to upload this file."
self.assertEqual(error_message, msg)
# delete any upload file that was partially created
import re
pattern = re.compile('\A[^.]*\.[a-zA-Z]*\.\d{4}\_?\d*\.txt')
possible_files = os.listdir(dir_path)
files = []
for f in possible_files:
if pattern.match(f):
files.append(f)
pmag.remove_files(files, dir_path)
def main():
"""
NAME
upload_magic.py
DESCRIPTION
This program will prepare your PMAG text files created by the programs nfo_magic.py,
zeq_magic.py, thellier_magic.py, mag_magic, specimens_results_magic.py and so on.
it will check for all the MagIC text files and skip the missing ones
SYNTAX
upload_magic.py
INPUT
MagIC txt files
OPTIONS
-h prints help message and quits
-all include all the measurement data, default is only those used in interpretations
-DM specify which MagIC data model number to use (2 or 3). Default is 3.
OUTPUT
upload.txt: file for uploading to MagIC database
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
else:
data_model_num = pmag.get_named_arg_from_sys("-DM", 3)
dataframe = extractor.command_line_dataframe([['cat', False, 0], ['F', False, ''], ['f', False, '']])
checked_args = extractor.extract_and_check_args(sys.argv, dataframe)
dir_path, concat = extractor.get_vars(['WD', 'cat'], checked_args)
if data_model_num == 2:
ipmag.upload_magic(concat, dir_path)
else:
ipmag.upload_magic3(concat, dir_path)
def test3_with_contribution(self):
dir_path = os.path.join(WD, 'data_files', '3_0', 'Megiddo')
con = cb.Contribution(directory=dir_path)
outfile, error_message, errors, all_errors = ipmag.upload_magic3(
contribution=con)
msg = "file validation has failed. You may run into problems if you try to upload this file."
self.assertEqual(error_message, msg)
# delete any upload file that was partially created
import re
pattern = re.compile('\A[^.]*\.[a-zA-Z]*\.\d{4}\_?\d*\.txt')
possible_files = os.listdir(dir_path)
files = []
for f in possible_files:
if pattern.match(f):
files.append(f)
pmag.remove_files(files, dir_path)
def on_btn_upload(self, event):
outstring="upload_magic.py"
print("-I- running python script:\n %s"%(outstring))
wait = wx.BusyInfo("Please wait, working...")
wx.Yield()
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 Your file: {} was generated in MagIC Project Directory.\nDrag and drop this file in the MagIC database.".format(os.path.split(res)[1])
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)
result = dlg.ShowModal()
if result == wx.ID_OK:
dlg.Destroy()
if self.data_model_num == 3:
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_upload_file(self, event):
wait = wx.BusyInfo('Validating data, please wait...')
wx.Yield()
res, error_message, has_problems, all_failing_items = ipmag.upload_magic3(dir_path=self.WD,
vocab=self.contribution.vocab)
self.failing_items = all_failing_items
if has_problems:
self.highlight_problems(has_problems)
if not has_problems:
self.validation_mode = set()
self.message.SetLabel('Validated!')
self.bSizer_msg.ShowItems(False)
self.hbox.Fit(self)
# do alert that your file passed
dlg = wx.MessageDialog(self,caption="Message:", message="Your contribution has passed validations!\nGo to https://www.earthref.org/MagIC to upload:\n{}".format(res), style=wx.OK)
dlg.ShowModal()
del wait
def test_depth_propagation(self):
dir_path = os.path.join(WD, 'data_files', 'core_depthplot')
#con = cb.Contribution(dir_path)
#self.assertNotIn('core_depth', con.tables['sites'].df.index)
#con.propagate_cols(['core_depth'], 'sites', 'samples', down=False)
#self.assertIn('core_depth', con.tables['sites'].df.columns)
#self.assertEqual(con.tables['sites'].df.loc['15-1-013', 'core_depth'], 55.23)
#
outfile, error_message, errors, all_errors = ipmag.upload_magic3(
dir_path=dir_path)
print('mv {} {}'.format(outfile, WD))
os.system('mv {} {}'.format(outfile, WD))
outfile = os.path.join(WD, os.path.split(outfile)[1])
ipmag.download_magic(outfile)
con = cb.Contribution(WD)
self.assertIn('core_depth', con.tables['sites'].df.columns)
self.assertEqual(con.tables['sites'].df.loc['15-1-013', 'core_depth'],
55.23)
def on_btn_upload(self, event):
outstring="upload_magic.py"
print "-I- running python script:\n %s"%(outstring)
wait = wx.BusyInfo("Please wait, working...")
wx.Yield()
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)
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 Your file: {} was generated in MagIC Project Directory.\nDrag and drop this file in the MagIC database.".format(os.path.split(res)[1])
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/Command Prompt for details".format(error_message)
dlg = wx.MessageDialog(self, caption="Error", message=text, style=wx.OK)
result = dlg.ShowModal()
if result == wx.ID_OK:
dlg.Destroy()
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)