def test_all_files_are_created(self):
files = ['locations.txt', 'sites.txt', 'samples.txt', 'specimens.txt',
'measurements.txt', 'contribution.txt']
pmag.remove_files(files, self.download_dir)
ipmag.download_magic('magic_contribution_16533.txt',
dir_path=self.download_dir,
input_dir_path=self.download_dir)
output_files = os.listdir(self.download_dir)
for f in files:
self.assertIn(f, output_files)
def main():
"""
NAME
download_magic.py
DESCRIPTION
unpacks a magic formatted smartbook .txt file from the MagIC database into the
tab delimited MagIC format txt files for use with the MagIC-Py programs.
SYNTAX
download_magic.py command line options]
INPUT
takes either the upload.txt file created by upload_magic.py or a file
downloaded from the MagIC database (http://earthref.org/MagIC)
OPTIONS
-h prints help message and quits
-i allows interactive entry of filename
-f FILE specifies input file name
-sep write location data to separate subdirectories (Location_*), (default False)
-O do not overwrite duplicate Location_* directories while downloading
-DM data model (2 or 3, default 3)
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
# interactive entry
if '-i' in sys.argv:
infile = input("Magic txt file for unpacking? ")
dir_path = '.'
input_dir_path = '.'
# non-interactive
else:
infile = pmag.get_named_arg("-f", reqd=True)
# if -O flag is present, overwrite is False
overwrite = pmag.get_flag_arg_from_sys("-O", true=False, false=True)
# if -sep flag is present, sep is True
sep = pmag.get_flag_arg_from_sys("-sep", true=True, false=False)
data_model = pmag.get_named_arg("-DM", default_val=3, reqd=False)
dir_path = pmag.get_named_arg("-WD", default_val=".", reqd=False)
input_dir_path = pmag.get_named_arg("-ID", default_val=".", reqd=False)
#if '-ID' not in sys.argv and '-WD' in sys.argv:
# input_dir_path = dir_path
if "-WD" not in sys.argv and "-ID" not in sys.argv:
input_dir_path = os.path.split(infile)[0]
if not input_dir_path:
input_dir_path = "."
ipmag.download_magic(infile, dir_path, input_dir_path, overwrite, True,
data_model, sep)
def main():
"""
NAME
download_magic.py
DESCRIPTION
unpacks a magic formatted smartbook .txt file from the MagIC database into the
tab delimited MagIC format txt files for use with the MagIC-Py programs.
SYNTAX
download_magic.py command line options]
INPUT
takes either the upload.txt file created by upload_magic.py or a file
downloaded from the MagIC database (http://earthref.org/MagIC)
OPTIONS
-h prints help message and quits
-i allows interactive entry of filename
-f FILE specifies input file name
-sep write location data to separate subdirectories (Location_*), (default False)
-O do not overwrite duplicate Location_* directories while downloading
-DM data model (2 or 3, default 3)
"""
if '-h' in sys.argv:
print(main.__doc__)
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
# interactive entry
if '-i' in sys.argv:
infile=input("Magic txt file for unpacking? ")
dir_path = '.'
input_dir_path = '.'
# non-interactive
else:
infile = pmag.get_named_arg("-f", reqd=True)
# if -O flag is present, overwrite is False
overwrite = pmag.get_flag_arg_from_sys("-O", true=False, false=True)
# if -sep flag is present, sep is True
sep = pmag.get_flag_arg_from_sys("-sep", true=True, false=False)
data_model = pmag.get_named_arg("-DM", default_val=3, reqd=False)
dir_path = pmag.get_named_arg("-WD", default_val=".", reqd=False)
input_dir_path = pmag.get_named_arg("-ID", default_val=".", reqd=False)
#if '-ID' not in sys.argv and '-WD' in sys.argv:
# input_dir_path = dir_path
if "-WD" not in sys.argv and "-ID" not in sys.argv:
input_dir_path = os.path.split(infile)[0]
if not input_dir_path:
input_dir_path = "."
ipmag.download_magic(infile, dir_path, input_dir_path, overwrite, True, data_model, sep)
def test_all_files_are_created(self):
files = [
'locations.txt', 'sites.txt', 'samples.txt', 'specimens.txt',
'measurements.txt', 'contribution.txt'
]
pmag.remove_files(files, self.download_dir)
ipmag.download_magic('magic_contribution_15143.txt',
dir_path=self.download_dir,
input_dir_path=self.download_dir)
output_files = os.listdir(self.download_dir)
for f in files:
self.assertIn(f, output_files)
def on_unpack(self, event):
dlg = wx.FileDialog(
None, message = "choose txt file to unpack",
defaultDir=self.WD,
defaultFile="",
style=wx.OPEN #| wx.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.Yield()
ex = None
try:
if ipmag.download_magic(f, self.WD, input_dir, overwrite=True):
text = "Successfully ran download_magic.py program.\nMagIC files were saved in your working directory.\nSee Terminal/Command Prompt for details."
else:
text = "Something went wrong. Make sure you chose a valid file downloaded from the MagIC database and try again."
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)
def on_unpack(self, event):
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.Yield()
ex = None
try:
if ipmag.download_magic(f, self.WD, input_dir, overwrite=True):
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."
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)
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_magic(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 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 main():
"""
NAME
download_magic.py
DESCRIPTION
unpacks a magic formatted smartbook .txt file from the MagIC database into the
tab delimited MagIC format txt files for use with the MagIC-Py programs.
SYNTAX
download_magic.py command line options]
INPUT
takes either the upload.txt file created by upload_magic.py or the file
exported by the MagIC v2.2 console software (downloaded from the MagIC database
or output by the Console on your PC).
OPTIONS
-h prints help message and quits
-i allows interactive entry of filename
-f FILE specifies input file name
-O do not overwrite duplicate Location_* directories while downloading
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind = sys.argv.index('-WD')
dir_path = sys.argv[ind + 1]
# interactive entry
if '-i' in sys.argv:
infile = raw_input("Magic txt file for unpacking? ")
dir_path = '.'
input_dir_path = '.'
# non-interactive
else:
dataframe = extractor.command_line_dataframe([['O', False, True]])
checked_args = extractor.extract_and_check_args(sys.argv, dataframe)
infile, dir_path, input_dir_path, overwrite = extractor.get_vars(
['f', 'WD', 'ID', 'O'], checked_args)
data_model = float(pmag.get_named_arg_from_sys("-DM", 2.5))
ipmag.download_magic(infile, dir_path, input_dir_path, overwrite,
data_model)
def main():
"""
NAME
download_magic.py
DESCRIPTION
unpacks a magic formatted smartbook .txt file from the MagIC database into the
tab delimited MagIC format txt files for use with the MagIC-Py programs.
SYNTAX
download_magic.py command line options]
INPUT
takes either the upload.txt file created by upload_magic.py or the file
exported by the MagIC v2.2 console software (downloaded from the MagIC database
or output by the Console on your PC).
OPTIONS
-h prints help message and quits
-i allows interactive entry of filename
-f FILE specifies input file name
-O do not overwrite duplicate Location_* directories while downloading
"""
if '-h' in sys.argv:
print main.__doc__
sys.exit()
if '-WD' in sys.argv:
ind=sys.argv.index('-WD')
dir_path=sys.argv[ind+1]
# interactive entry
if '-i' in sys.argv:
infile=raw_input("Magic txt file for unpacking? ")
dir_path = '.'
input_dir_path = '.'
# non-interactive
else:
dataframe = extractor.command_line_dataframe([['O', False, True]])
checked_args = extractor.extract_and_check_args(sys.argv, dataframe)
infile, dir_path, input_dir_path, overwrite = extractor.get_vars(['f', 'WD', 'ID', 'O'], checked_args)
data_model = float(pmag.get_named_arg_from_sys("-DM", 2.5))
ipmag.download_magic(infile, dir_path, input_dir_path, overwrite, data_model)
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()
