def make_file(self, binary=None):
"""Return readable and writable temporary file.
Arguments:
binary - unused. Here is only for backward compatibility
"""
if 'wsgi.file_callback' in self.environ:
return self.environ['wsgi.file_callback'](self.filename)
else:
return CgiFieldStorage.make_file(self)
def make_file(self, binary=None):
"""Return readable and writable temporary file.
Arguments:
binary - unused. Here is only for backward compatibility
"""
if 'wsgi.file_callback' in self.environ:
return self.environ['wsgi.file_callback'](self.filename)
else:
return CgiFieldStorage.make_file(self)
def _upload_test_data(self):
"""
Upload test datasets, which are defined in the <test></test>
section of the provided tool.
"""
if not self._tool.tests:
raise ValueError('Tests are not defined.')
self._test = self._tool.tests[0]
# All inputs with the type 'data'
self._data_inputs = {
x.name: x
for x in self._tool.input_params if x.type == 'data'
}
# Datasets from the <test></test> section
test_datasets = {
input_name: self._test.inputs[input_name][0]
for input_name in self._data_inputs.keys()
if input_name in self._test.inputs.keys()
}
# Conditional datasets
for name, value in self._test.inputs.items():
if '|' in name:
input_name = name.split('|')[1]
if input_name in self._data_inputs.keys():
test_datasets.update(
{input_name: self._test.inputs[name][0]})
if not test_datasets.keys():
not_supported_input_types = [
k for k, v in self._tool.inputs.items()
if v.type == 'repeat' or v.type == 'data_collection'
]
if not_supported_input_types:
raise ValueError('Not supported input types.')
else:
# Some tests don't have data inputs at all,
# so we can generate a tour without them
self._use_datasets = False
return
test_data_paths = [os.path.abspath('test-data')]
test_data_cache_dir = os.path.abspath(
os.environ.get('GALAXY_TEST_DATA_REPO_CACHE', 'test-data-cache'))
test_data_paths.extend(
[x[0] for x in os.walk(test_data_cache_dir) if '.git' not in x[0]])
if self._tool.tool_shed:
test_data_paths.append(
os.path.abspath(os.path.join(self._tool.tool_dir,
'test-data')))
# Upload all test datasets
for input_name, input in self._data_inputs.items():
if input_name in test_datasets.keys():
for i, data_path in enumerate(test_data_paths):
input_path = os.path.join(data_path,
test_datasets[input_name])
if os.path.exists(input_path):
break
elif i + 1 == len(test_data_paths): # the last path
raise ValueError('Test dataset "%s" doesn\'t exist.' %
input_name)
upload_tool = self._trans.app.toolbox.get_tool('upload1')
filename = os.path.basename(input_path)
with open(input_path, 'r') as f:
content = f.read()
headers = {
'content-disposition':
'form-data; name="{}"; filename="{}"'.format(
'files_0|file_data', filename),
}
input_file = FieldStorage(headers=headers)
input_file.file = input_file.make_file()
input_file.file.write(content)
inputs = {
'dbkey': '?', # is it always a question mark?
'file_type': input.extensions[0],
'files_0|type': 'upload_dataset',
'files_0|space_to_tab': None,
'files_0|to_posix_lines': 'Yes',
'files_0|file_data': input_file,
}
params = Params(inputs, sanitize=False)
incoming = params.__dict__
output = upload_tool.handle_input(self._trans,
incoming,
history=None)
job_errors = output.get('job_errors', [])
if job_errors:
# self._errors.extend(job_errors)
raise ValueError('Cannot upload a dataset.')
else:
self._hids.update(
{input_name: output['out_data'][0][1].hid})
def _upload_test_data(self):
"""
Upload test datasets, which are defined in the <test></test>
section of the provided tool.
"""
if not self._tool.tests:
raise ValueError('Tests are not defined.')
self._test = self._tool.tests[0]
# All inputs with the type 'data'
self._data_inputs = {x.name: x for x in self._tool.input_params if
x.type == 'data'}
# Datasets from the <test></test> section
test_datasets = {
input_name: self._test.inputs[input_name][0]
for input_name in self._data_inputs.keys()
if input_name in self._test.inputs.keys()
}
# Conditional datasets
for name, value in self._test.inputs.items():
if '|' in name:
input_name = name.split('|')[1]
if input_name in self._data_inputs.keys():
test_datasets.update({
input_name: self._test.inputs[name][0]
})
if not test_datasets.keys():
not_supported_input_types = [
k for k, v in self._tool.inputs.items() if
v.type == 'repeat' or v.type == 'data_collection'
]
if not_supported_input_types:
raise ValueError('Not supported input types.')
else:
# Some tests don't have data inputs at all,
# so we can generate a tour without them
self._use_datasets = False
return
test_data_paths = [os.path.abspath('test-data')]
test_data_cache_dir = os.path.abspath(
os.environ.get('GALAXY_TEST_DATA_REPO_CACHE', 'test-data-cache'))
test_data_paths.extend([
x[0] for x in os.walk(test_data_cache_dir) if '.git' not in x[0]])
if self._tool.tool_shed:
test_data_paths.append(os.path.abspath(os.path.join(
self._tool.tool_dir, 'test-data')))
# Upload all test datasets
for input_name, input in self._data_inputs.items():
if input_name in test_datasets.keys():
for i, data_path in enumerate(test_data_paths):
input_path = os.path.join(data_path,
test_datasets[input_name])
if os.path.exists(input_path):
break
elif i + 1 == len(test_data_paths): # the last path
raise ValueError('Test dataset "%s" doesn\'t exist.' %
input_name)
upload_tool = self._trans.app.toolbox.get_tool('upload1')
filename = os.path.basename(input_path)
with open(input_path, 'r') as f:
content = f.read()
headers = {
'content-disposition':
'form-data; name="{}"; filename="{}"'.format(
'files_0|file_data', filename
),
}
input_file = FieldStorage(headers=headers)
input_file.file = input_file.make_file()
input_file.file.write(content)
inputs = {
'dbkey': '?', # is it always a question mark?
'file_type': input.extensions[0],
'files_0|type': 'upload_dataset',
'files_0|space_to_tab': None,
'files_0|to_posix_lines': 'Yes',
'files_0|file_data': input_file,
}
params = Params(inputs, sanitize=False)
incoming = params.__dict__
output = upload_tool.handle_input(self._trans, incoming,
history=None)
job_errors = output.get('job_errors', [])
if job_errors:
# self._errors.extend(job_errors)
raise ValueError('Cannot upload a dataset.')
else:
self._hids.update({
input_name: output['out_data'][0][1].hid
})