class ParseUploadTest(unittest.TestCase):
def setUp(self):
self.comm = Comm()
def test_successful(self):
self.comm.upload_output = 'SUCCESS 1234'
status = self.comm.parse_upload()
self.assertTrue(status)
self.assertEqual(self.comm.warnings, [])
self.assertEqual(self.comm.tree_id, '1234')
def test_successful_warnings(self):
self.comm.upload_output = "Warning 1\nWarning 2\nSUCCESS 1234"
status = self.comm.parse_upload()
self.assertTrue(status)
self.assertEqual(self.comm.warnings, ['Warning 1', 'Warning 2'])
self.assertEqual(self.comm.tree_id, '1234')
def test_fatal(self):
self.comm.upload_output = "ERR 1234"
status = self.comm.parse_upload()
self.assertFalse(status)
self.assertEqual(self.comm.warnings, ["ERR 1234"])
self.assertEqual(self.comm.tree_id, '')
def __init__(self):
"""
Initialize a few required variables
See http://itol.embl.de/help.cgi#bUpOpt for available params
"""
self.files = []
self.params = {
'uploadID': '',
'projectName': '',
'treeName': '',
'treeDescription': '',
}
self.comm = Comm()
def setUp(self):
self.tempfile = tempfile.TemporaryFile()
self.comm = Comm.Comm()
self.params = {'asdf': 'qwer'}
self.files = {'zxcv': self.tempfile}
self.all_params = self.params.copy()
self.all_params.update(self.files)
class UploadTreeTest(unittest.TestCase):
def setUp(self):
self.tempfile = tempfile.NamedTemporaryFile()
self.files = [self.tempfile.name]
self.comm = Comm()
self.params = {'treeName': 'asdf'}
def tearDown(self):
self.tempfile.close()
@patch('itolapi.comm.requests')
@patch('itolapi.Comm.parse_upload')
def test_upload_tree(self, mock_parse, mock_requests):
mock_requests.post().text = 'asdf'
mock_parse.return_value = 'qwer'
output = self.comm.upload_tree(self.files, self.params)
self.assertEqual(
mock_requests.post.call_args[0][0],
self.comm.upload_url
)
self.assertEqual(mock_requests.post.call_args[1]['data'], self.params)
self.assertTrue('zipFile' in mock_requests.post.call_args[1]['files'])
mock_parse.assert_called_once_with()
self.assertEqual(self.comm.upload_output, 'asdf')
self.assertEqual(output, 'qwer')
def test_tree_file_extension(self):
zip_file = Comm.create_zip_from_files([self.tempfile.name])
with open(zip_file.name, 'rb') as zip_file_handle:
with zipfile.ZipFile(zip_file_handle) as zip_handle:
files = zip_handle.namelist()
expected_tree_name = os.path.basename(self.tempfile.name)
self.assertIn(expected_tree_name, files)
zip_file.close()
class ExportImageTest(unittest.TestCase):
def setUp(self):
self.comm = Comm()
self.params = {'tree_id': '1234'}
@patch('itolapi.comm.requests')
def test_export_image(self, mock_requests):
mock_requests.post().content = 'asdf'
output = self.comm.export_image(self.params)
self.assertEqual(output, 'asdf')
def __init__(self):
"""
Initialize a few required variables
See http://itol.embl.de/help.cgi#bUpOpt for available params
"""
self.files = []
self.params = {
'uploadID': '',
'projectName': '',
'treeName': '',
'treeDescription': '',
}
self.comm = Comm()
class ItolExport:
EXPORT_FORMATS = ['png', 'svg', 'eps', 'ps', 'pdf', 'nexus', 'newick']
"""
Instantiate the itolexport class with empty params and empty server
"""
def __init__(self):
"""
Instantiate class
"""
self.params = dict({})
self.comm = Comm()
# Setting Export Parameters
def add_export_param_dict(self, param_dict):
"""
Add a dictionary of parameters to the parameters to be used when
exporting
@param: dictionary of parameters to be used
"""
self.params.update(param_dict)
def set_export_param_value(self, key, value):
"""
Add a value to the dictionary of parameters to be used when exporting
@param: dictionary of parameters to be used
"""
self.params[key] = value
def get_export_params(self):
"""
Get the dictionary of parameters to tbe used when exporting
@return: export the Parameters
"""
return self.params
# Do Exporting
def export(self, export_location):
"""
Call the export process
Calling this directly assumes that the export filetype is already set
in the export params
@param filelocation: the location to write the export to
@return: whether the export works
"""
output = self.comm.export_image(self.params)
file_handle = open(export_location, 'wb')
file_handle.write(output)
file_handle.close()
class ItolExport:
EXPORT_FORMATS = ['png', 'svg', 'eps', 'ps', 'pdf', 'nexus', 'newick']
"""
Instantiate the itolexport class with empty params and empty server
"""
def __init__(self):
"""
Instantiate class
"""
self.params = dict({})
self.comm = Comm()
# Setting Export Parameters
def add_export_param_dict(self, param_dict):
"""
Add a dictionary of parameters to the parameters to be used when
exporting
@param: dictionary of parameters to be used
"""
self.params.update(param_dict)
def set_export_param_value(self, key, value):
"""
Add a value to the dictionary of parameters to be used when exporting
@param: dictionary of parameters to be used
"""
self.params[key] = value
def get_export_params(self):
"""
Get the dictionary of parameters to tbe used when exporting
@return: export the Parameters
"""
return self.params
# Do Exporting
def export(self, export_location):
"""
Call the export process
Calling this directly assumes that the export filetype is already set
in the export params
@param filelocation: the location to write the export to
@return: whether the export works
"""
output = self.comm.export_image(self.params)
file_handle = open(export_location, 'wb')
file_handle.write(output)
file_handle.close()
def __init__(self):
"""
Initialize a few required variables
"""
self.variables = dict()
self.comm = Comm.Comm()
class Itol:
"""
This class handles the main itol functionality
"""
def __init__(self):
"""
Initialize a few required variables
See http://itol.embl.de/help.cgi#bUpOpt for available params
"""
self.files = []
self.params = {
'uploadID': '',
'projectName': '',
'treeName': '',
'treeDescription': '',
}
self.comm = Comm()
def add_file(self, file_path):
"""
Add a file to be uploaded, tree or dataset
"""
if not os.path.isfile(file_path):
raise IOError('%s is not a file' % file_path)
self.files.append(file_path)
def upload(self):
"""
Upload the data to the iTOL server and return an ItolExport object
"""
good_upload = self.comm.upload_tree(self.files, self.params)
if good_upload:
return self.comm.tree_id
else:
self.comm.tree_id = 0
return False
def get_webpage(self):
"""
Get the web page where you can download the Itol tree
"""
webpage = "http://itol.embl.de/external.cgi?tree=" +\
str(self.comm.tree_id) + "&restore_saved=1"
return webpage
def get_itol_export(self):
"""
Returns an instance of ItolExport in preparation of exporting from the
generated tree
@return: instance of ItolExport
"""
itol_exporter = ItolExport()
itol_exporter.set_export_param_value('tree', self.comm.tree_id)
return itol_exporter
def print_variables(self):
"""
Print the files and params that have been set so far
"""
print('Files:')
pprint.pprint(self.files)
print('Parameters:')
pprint.pprint(self.params)
def setUp(self):
self.comm = Comm()
self.params = {'tree_id': '1234'}
def setUp(self):
self.comm = Comm()
def __init__(self):
"""
Instantiate class
"""
self.params = dict({})
self.comm = Comm.Comm()
class Itol:
"""
This class handles the main itol functionality
"""
def __init__(self):
"""
Initialize a few required variables
See http://itol.embl.de/help.cgi#bUpOpt for available params
"""
self.files = []
self.params = {
'uploadID': '',
'projectName': '',
'treeName': '',
'treeDescription': '',
}
self.comm = Comm()
def add_file(self, file_path):
"""
Add a file to be uploaded, tree or dataset
"""
if not os.path.isfile(file_path):
raise IOError('%s is not a file' % file_path)
self.files.append(file_path)
def upload(self):
"""
Upload the data to the iTOL server and return an ItolExport object
"""
good_upload = self.comm.upload_tree(self.files, self.params)
if good_upload:
return self.comm.tree_id
else:
self.comm.tree_id = 0
return False
def get_webpage(self):
"""
Get the web page where you can download the Itol tree
"""
webpage = "http://itol.embl.de/external.cgi?tree=" +\
str(self.comm.tree_id) + "&restore_saved=1"
return webpage
def get_itol_export(self):
"""
Returns an instance of ItolExport in preparation of exporting from the
generated tree
@return: instance of ItolExport
"""
itol_exporter = ItolExport()
itol_exporter.set_export_param_value('tree', self.comm.tree_id)
return itol_exporter
def print_variables(self):
"""
Print the files and params that have been set so far
"""
print('Files:')
pprint.pprint(self.files)
print('Parameters:')
pprint.pprint(self.params)
def __init__(self):
"""
Instantiate class
"""
self.params = dict({})
self.comm = Comm()
def setUp(self):
self.tempfile = tempfile.NamedTemporaryFile()
self.files = [self.tempfile.name]
self.comm = Comm()
self.params = {'treeName': 'asdf'}