def test_convert_fileobj(self, oldhepdata_file, oldhepdata_yaml_path):
# test fileobj
path = os.path.join(self.current_tmp, 'yaml')
hepdata_converter_ws_client.convert(self.get_server_url(), oldhepdata_file, path,
options={'input_format': 'oldhepdata'})
self.assertDirsEqual(oldhepdata_yaml_path, path)
def test_convert_no_extract(self, oldhepdata_path, oldhepdata_yaml_path):
output = BytesIO()
hepdata_converter_ws_client.convert(
self.get_server_url(),
oldhepdata_path,
output,
options={'input_format': 'oldhepdata'},
extract=False)
output.seek(0)
tmp_path = os.path.join(self.current_tmp, '1')
with tarfile.open(mode='r:gz', fileobj=output) as tar:
tar.extractall(tmp_path)
self.assertDirsEqual(os.path.join(tmp_path, ARCHIVE_NAME),
oldhepdata_yaml_path)
path = os.path.join(self.current_tmp, 'data.tar.gz')
hepdata_converter_ws_client.convert(
self.get_server_url(),
oldhepdata_path,
path,
options={'input_format': 'oldhepdata'},
extract=False)
tmp_path = os.path.join(self.current_tmp, '2')
with tarfile.open(path, mode='r:gz') as tar:
tar.extractall(tmp_path)
self.assertDirsEqual(os.path.join(tmp_path, ARCHIVE_NAME),
oldhepdata_yaml_path)
def test_convert_fileobj(self, oldhepdata_file, oldhepdata_yaml_path):
# test fileobj
path = os.path.join(self.current_tmp, 'yaml')
hepdata_converter_ws_client.convert(
self.get_server_url(),
oldhepdata_file,
path,
options={'input_format': 'oldhepdata'})
self.assertDirsEqual(oldhepdata_yaml_path, path)
def test_caching(self, oldhepdata_path, oldhepdata_yaml_path):
# test paths
path_1 = os.path.join(self.current_tmp, 'yaml', '1')
hepdata_converter_ws_client.convert(self.get_server_url(), oldhepdata_path, path_1,
options={'input_format': 'oldhepdata'}, id=1)
self.assertDirsEqual(oldhepdata_yaml_path, path_1)
path_2 = os.path.join(self.current_tmp, 'yaml', '2')
hepdata_converter_ws_client.convert(self.get_server_url(), oldhepdata_path, path_2,
options={'input_format': 'oldhepdata'}, id=1)
self.assertDirsEqual(oldhepdata_yaml_path, path_2)
self.assertDirsEqual(path_1, path_2)
def convert_zip_archive(input_archive, output_archive, options):
""" Convert a zip archive into a targz path with given options. """
input_root_dir = tempfile.mkdtemp()
with zipfile.ZipFile(input_archive, 'r') as zip_archive:
zip_archive.extractall(path=input_root_dir)
# Find the appropriate file/directory in the input archive
input = options.get('input_format', 'yaml')
validation = find_file_in_directory(
input_root_dir,
lambda x: x == 'submission.yaml' if input == 'yaml' else x.endswith('.oldhepdata')
)
if not validation:
return None
input_directory, input_file = validation
successful = convert(
CFG_CONVERTER_URL,
input_directory if input == 'yaml' else input_file,
output=output_archive,
options=options,
extract=False,
)
rmtree(input_root_dir)
# Error occurred, the output is a HTML file
if not successful:
output_file = output_archive[:-7] + '.html'
else:
output_file = output_archive
move(output_archive, output_file)
return output_file
def convert_zip_archive(input_archive, output_archive, options):
"""
Convert a zip archive into a targz path with given options.
:param input_archive:
:param output_archive:
:param options:
:return: output_file
"""
input = options.get('input_format', 'yaml')
with prepare_data_folder(input_archive, input) as validation:
if not validation:
return None
input_directory, input_file = validation
successful = convert(
CFG_CONVERTER_URL,
input_directory if input == 'yaml' else input_file,
output=output_archive,
options=options,
extract=False,
timeout=CFG_CONVERTER_TIMEOUT,
)
# Error occurred, the output is a HTML file
if not successful:
output_file = output_archive[:-7] + '.html'
else:
output_file = output_archive
move(output_archive, output_file)
return output_file
def convert_zip_archive(input_archive, output_archive, options):
""" Convert a zip archive into a targz path with given options. """
input_root_dir = tempfile.mkdtemp()
with zipfile.ZipFile(input_archive, 'r') as zip_archive:
zip_archive.extractall(path=input_root_dir)
# Find the appropriate file/directory in the input archive
input = options.get('input_format', 'yaml')
validation = find_file_in_directory(
input_root_dir,
lambda x: x == 'submission.yaml' if input == 'yaml' else x.endswith('.oldhepdata')
)
if not validation:
return None
input_directory, input_file = validation
successful = convert(
CFG_CONVERTER_URL,
input_directory if input == 'yaml' else input_file,
output=output_archive,
options=options,
extract=False,
)
rmtree(input_root_dir)
# Error occurred, the output is a HTML file
if not successful:
output_file = output_archive[:-7] + '.html'
else:
output_file = output_archive
move(output_archive, output_file)
return output_file
def test_convert_404(self, oldhepdata_file):
broken_url = self.get_server_url() + '/notavalidurl'
with self.assertRaises(hepdata_converter_ws_client.Error) as cm:
hepdata_converter_ws_client.convert(
broken_url,
oldhepdata_file,
self.current_tmp,
options={'input_format': 'oldhepdata'},
timeout=5)
self.assertEqual('Request to %s failed' % broken_url,
str(cm.exception))
self.assertTrue(
isinstance(cm.exception.__cause__, requests.exceptions.HTTPError))
self.assertTrue(
str(cm.exception.__cause__).startswith(
"404 Client Error: NOT FOUND for url: %s" % broken_url))
def test_return_value(self, oldhepdata_file, oldhepdata_yaml_path):
# test fileobj
path = os.path.join(self.current_tmp, 'yaml')
r = hepdata_converter_ws_client.convert(self.get_server_url(), oldhepdata_file,
options={'input_format': 'oldhepdata'})
with tarfile.open(mode='r:gz', fileobj=StringIO.StringIO(r)) as tar:
tar.extractall(path)
self.assertDirsEqual(oldhepdata_yaml_path, os.path.join(path, ARCHIVE_NAME))
def test_convert_timeout(self, oldhepdata_file):
broken_url = 'https://example.com:81'
with self.assertRaises(hepdata_converter_ws_client.Error) as cm:
hepdata_converter_ws_client.convert(
broken_url,
oldhepdata_file,
self.current_tmp,
options={'input_format': 'oldhepdata'},
timeout=5)
self.assertEqual('Request to %s failed' % broken_url,
str(cm.exception))
self.assertTrue(
isinstance(cm.exception.__cause__,
requests.exceptions.ConnectTimeout))
self.assertTrue(
str(cm.exception.__cause__).startswith(
"HTTPSConnectionPool(host='example.com', port=81): Max retries exceeded with url"
))
def test_convert_no_extract(self, oldhepdata_path, oldhepdata_yaml_path):
output = StringIO.StringIO()
hepdata_converter_ws_client.convert(self.get_server_url(), oldhepdata_path, output,
options={'input_format': 'oldhepdata'}, extract=False)
output.seek(0)
tmp_path = os.path.join(self.current_tmp, '1')
with tarfile.open(mode='r:gz', fileobj=output) as tar:
tar.extractall(tmp_path)
self.assertDirsEqual(os.path.join(tmp_path, ARCHIVE_NAME),
oldhepdata_yaml_path)
path = os.path.join(self.current_tmp, 'data.tar.gz')
hepdata_converter_ws_client.convert(self.get_server_url(), oldhepdata_path, path,
options={'input_format': 'oldhepdata'}, extract=False)
tmp_path = os.path.join(self.current_tmp, '2')
with tarfile.open(path, mode='r:gz') as tar:
tar.extractall(tmp_path)
self.assertDirsEqual(os.path.join(tmp_path, ARCHIVE_NAME),
oldhepdata_yaml_path)
def test_return_value(self, oldhepdata_file, oldhepdata_yaml_path):
# test fileobj
path = os.path.join(self.current_tmp, 'yaml')
r = hepdata_converter_ws_client.convert(
self.get_server_url(),
oldhepdata_file,
options={'input_format': 'oldhepdata'})
with tarfile.open(mode='r:gz', fileobj=BytesIO(r)) as tar:
tar.extractall(path)
self.assertDirsEqual(oldhepdata_yaml_path,
os.path.join(path, ARCHIVE_NAME))
def test_caching(self, oldhepdata_path, oldhepdata_yaml_path):
# test paths
path_1 = os.path.join(self.current_tmp, 'yaml', '1')
hepdata_converter_ws_client.convert(
self.get_server_url(),
oldhepdata_path,
path_1,
options={'input_format': 'oldhepdata'},
id=1)
self.assertDirsEqual(oldhepdata_yaml_path, path_1)
path_2 = os.path.join(self.current_tmp, 'yaml', '2')
hepdata_converter_ws_client.convert(
self.get_server_url(),
oldhepdata_path,
path_2,
options={'input_format': 'oldhepdata'},
id=1)
self.assertDirsEqual(oldhepdata_yaml_path, path_2)
self.assertDirsEqual(path_1, path_2)
def convert_oldhepdata_to_yaml(input_path, output_path):
""" Converts the data on the server from oldhepdata format to the new one. """
options = {
'input_format': 'oldhepdata',
'output_format': 'yaml',
}
successful = convert(
CFG_CONVERTER_URL,
input_path,
output=output_path,
options=options
)
return successful
def convert_oldhepdata_to_yaml(input_path, output_path):
""" Converts the data on the server from oldhepdata format to the new one. """
options = {
'input_format': 'oldhepdata',
'output_format': 'yaml',
}
successful = convert(
CFG_CONVERTER_URL,
input_path,
output=output_path,
options=options
)
return successful
def download_datatable(data_resource, file_format, *args, **kwargs):
record_path, table_name = os.path.split(data_resource.file_location)
filename = 'HEPData-{0}'.format(kwargs.pop('submission_id'))
if 'table_name' in kwargs:
filename += '-' + kwargs.pop('table_name').replace(' ', '')
output_path = os.path.join(current_app.config['CFG_TMPDIR'], filename)
if file_format == 'yaml':
return send_file(
data_resource.file_location,
as_attachment=True,
)
options = {
'input_format': 'yaml',
'output_format': file_format,
'table': table_name,
'filename': table_name.split('.')[0],
}
if not os.path.exists(output_path):
successful = convert(
CFG_CONVERTER_URL,
record_path,
output=output_path + '-dir',
options=options,
extract=False,
)
else:
successful = True
# Error occurred, the output is a HTML file
if successful:
new_path = output_path + "." + file_format
new_path = extract(filename + ".tar.gz", output_path + '-dir', new_path)
file_to_send = get_file_in_directory(new_path, file_format)
else:
file_to_send = output_path + '-dir'
file_format = 'html'
return send_file(file_to_send, as_attachment=True,
attachment_filename=filename + '.' + file_format)
def convert_oldhepdata_to_yaml(input_path, output_path):
"""
Converts the data on the server from oldhepdata format to the new YAML format.
:param input_path:
:param output_path:
:return: whether conversion was successful
"""
options = {
'input_format': 'oldhepdata',
'output_format': 'yaml',
}
successful = convert(
CFG_CONVERTER_URL,
input_path,
output=output_path,
options=options
)
return successful
def download_datatable(datasubmission, file_format, *args, **kwargs):
"""
Download a particular data table given a ``datasubmission``.
:param datasubmission:
:param file_format:
:param args:
:param kwargs:
:return: display_error or send_file depending on success of conversion
"""
if file_format == 'json':
return redirect('/record/data/{0}/{1}/{2}'.format(
datasubmission.publication_recid, datasubmission.id,
datasubmission.version))
elif file_format not in CFG_SUPPORTED_FORMATS:
return display_error(
title="The " + file_format + " output format is not supported",
description="This output format is not supported. " +
"Currently supported formats: " + str(CFG_SUPPORTED_FORMATS),
)
dataresource = DataResource.query.filter_by(
id=datasubmission.data_file).one()
record_path, table_name = os.path.split(dataresource.file_location)
filename = 'HEPData-{0}-v{1}'.format(kwargs.pop('submission_id'),
datasubmission.version)
if 'table_name' in kwargs:
filename += '-' + kwargs.pop('table_name').replace(' ', '_').replace(
'/', '_').replace('$', '').replace('\\', '')
output_path = os.path.join(current_app.config['CFG_TMPDIR'], filename)
if file_format == 'yaml':
return send_file(dataresource.file_location,
as_attachment=True,
attachment_filename=filename + '.yaml')
options = {
'input_format': 'yaml',
'output_format': file_format,
'table': table_name,
'filename': table_name.split('.')[0],
'validator_schema_version': '0.1.0',
}
hepsubmission = HEPSubmission.query.filter_by(
publication_recid=datasubmission.publication_recid,
version=datasubmission.version).first()
if datasubmission.doi and hepsubmission.overall_status != 'sandbox':
options['hepdata_doi'] = datasubmission.doi.rsplit(
'/', 1)[0].encode('ascii')
if file_format == 'yoda':
rivet_analysis_name = kwargs.pop('rivet_analysis_name', '')
if rivet_analysis_name:
options['rivet_analysis_name'] = rivet_analysis_name
elif datasubmission.publication_inspire_id:
record = get_record_contents(datasubmission.publication_recid)
if record:
# Check if this record has a Rivet analysis, then extract the Rivet analysis name from the URL.
if 'analyses' in record:
for analysis in record['analyses']:
if analysis['type'] == 'rivet':
options['rivet_analysis_name'] = analysis[
'analysis'].split('/')[-1]
# Otherwise guess the Rivet analysis name using the collaboration name,
# the creation year of the INSPIRE record, and the INSPIRE ID.
if 'rivet_analysis_name' not in options:
try:
year = parse(record['creation_date']).year
except:
year = record['year'] # publication year
options['rivet_analysis_name'] = '{0}_{1}_I{2}'.format(
''.join(record['collaborations']).upper(), year,
datasubmission.publication_inspire_id)
successful = convert(
CFG_CONVERTER_URL,
record_path,
output=output_path + '-dir',
options=options,
extract=False,
)
if successful:
new_path = output_path + "." + file_format
new_path = extract(output_path + '-dir', new_path)
os.remove(output_path + '-dir')
file_to_send = get_file_in_directory(new_path, file_format)
else:
# Error occurred, the output is a HTML file
file_to_send = output_path + '-dir'
file_format = 'html'
return send_file(file_to_send,
as_attachment=True,
attachment_filename=filename + '.' + file_format)
def download_datatable(datasubmission, file_format, *args, **kwargs):
"""
Download a particular data table given a ``datasubmission``.
:param datasubmission:
:param file_format:
:param args:
:param kwargs:
:return: display_error or send_file depending on success of conversion
"""
if file_format == 'json':
return redirect('/record/data/{0}/{1}/{2}'.format(datasubmission.publication_recid,
datasubmission.id, datasubmission.version))
elif file_format not in CFG_SUPPORTED_FORMATS:
return display_error(
title="The " + file_format + " output format is not supported",
description="This output format is not supported. " +
"Currently supported formats: " + str(CFG_SUPPORTED_FORMATS),
)
dataresource = DataResource.query.filter_by(id=datasubmission.data_file).one()
record_path, table_name = os.path.split(dataresource.file_location)
filename = 'HEPData-{0}-v{1}'.format(kwargs.pop('submission_id'), datasubmission.version)
if 'table_name' in kwargs:
filename += '-' + kwargs.pop('table_name').replace(' ', '_').replace('/', '_').replace('$', '').replace('\\','')
output_path = os.path.join(current_app.config['CFG_TMPDIR'], filename)
if file_format == 'yaml' or file_format == 'original':
return send_file(
dataresource.file_location,
as_attachment=True,
attachment_filename=filename + '.yaml'
)
options = {
'input_format': 'yaml',
'output_format': file_format,
'table': table_name,
'filename': table_name.split('.')[0],
'validator_schema_version': '0.1.0',
}
hepsubmission = HEPSubmission.query.filter_by(publication_recid=datasubmission.publication_recid,
version=datasubmission.version).first()
if datasubmission.doi and not hepsubmission.overall_status.startswith('sandbox'):
options['hepdata_doi'] = datasubmission.doi.rsplit('/', 1)[0]
if file_format == 'yoda':
rivet_analysis_name = kwargs.pop('rivet_analysis_name', '')
if not rivet_analysis_name:
rivet_analysis_name = guess_rivet_analysis_name(hepsubmission)
if rivet_analysis_name:
options['rivet_analysis_name'] = rivet_analysis_name
try:
successful = convert(
CFG_CONVERTER_URL,
record_path,
output=output_path + '-dir',
options=options,
extract=False,
timeout=CFG_CONVERTER_TIMEOUT,
)
except Error as error: # hepdata_converter_ws_client.Error
return display_error(title='Report concerns to [email protected]', description=str(error))
if successful:
new_path = output_path + "." + file_format
new_path = extract(output_path + '-dir', new_path)
os.remove(output_path + '-dir')
file_to_send = get_file_in_directory(new_path, file_format)
else:
# Error occurred, the output is a HTML file
file_to_send = output_path + '-dir'
file_format = 'html'
return send_file(file_to_send, as_attachment=True,
attachment_filename=filename + '.' + file_format)
def download_datatable(datasubmission, file_format, *args, **kwargs):
if file_format == 'json':
return redirect('/record/data/{0}/{1}/{2}'.format(
datasubmission.publication_recid, datasubmission.id,
datasubmission.version))
elif file_format not in CFG_SUPPORTED_FORMATS:
return display_error(
title="The " + file_format + " output format is not supported",
description="This output format is not supported. " +
"Currently supported formats: " + str(CFG_SUPPORTED_FORMATS),
)
dataresource = DataResource.query.filter_by(
id=datasubmission.data_file).one()
record_path, table_name = os.path.split(dataresource.file_location)
filename = 'HEPData-{0}-v{1}'.format(kwargs.pop('submission_id'),
datasubmission.version)
if 'table_name' in kwargs:
filename += '-' + kwargs.pop('table_name').replace(' ', '')
output_path = os.path.join(current_app.config['CFG_TMPDIR'], filename)
if file_format == 'yaml':
return send_file(dataresource.file_location,
as_attachment=True,
attachment_filename=filename + '.yaml')
options = {
'input_format': 'yaml',
'output_format': file_format,
'table': table_name,
'filename': table_name.split('.')[0],
}
if datasubmission.doi:
options['hepdata_doi'] = datasubmission.doi.rsplit(
'/', 1)[0].encode('ascii')
if datasubmission.publication_inspire_id and file_format == 'yoda':
record = get_record_contents(datasubmission.publication_recid)
if record:
options['rivet_analysis_name'] = '{0}_{1}_I{2}'.format(
''.join(record['collaborations']).upper(), record['year'],
datasubmission.publication_inspire_id)
if not os.path.exists(output_path):
successful = convert(
CFG_CONVERTER_URL,
record_path,
output=output_path + '-dir',
options=options,
extract=False,
)
else:
successful = True
# Error occurred, the output is a HTML file
if successful:
new_path = output_path + "." + file_format
new_path = extract(filename + ".tar.gz", output_path + '-dir',
new_path)
file_to_send = get_file_in_directory(new_path, file_format)
else:
file_to_send = output_path + '-dir'
file_format = 'html'
return send_file(file_to_send,
as_attachment=True,
attachment_filename=filename + '.' + file_format)
