def fetch_nexson(self, study_id, output_filepath=None, store_raw=False):
'''Calls export_gzipNexSON URL and unzips response.
Raises HTTP error, gzip module error, or RuntimeError
'''
if study_id.startswith('pg_'):
study_id = study_id[3:] #strip pg_ prefix
uri = self.domain + '/study/export_gzipNexSON.json/' + study_id
_LOG.debug('Downloading %s using "%s"\n', study_id, uri)
resp = requests.get(uri,
headers=GZIP_REQUEST_HEADERS,
allow_redirects=True)
resp.raise_for_status()
try:
uncompressed = gzip.GzipFile(mode='rb',
fileobj=StringIO(
resp.content)).read()
results = uncompressed
except:
raise
if is_str_type(results):
if output_filepath is None:
return anyjson.loads(results)
else:
if store_raw:
write_to_filepath(results, output_filepath)
else:
write_as_json(anyjson.loads(results), output_filepath)
return True
raise RuntimeError(
'gzipped response from phylografter export_gzipNexSON.json, but not a string is:',
results)
def fetch_nexson(self, study_id, output_filepath=None, store_raw=False):
'''Calls export_gzipNexSON URL and unzips response.
Raises HTTP error, gzip module error, or RuntimeError
'''
if study_id.startswith('pg_'):
study_id = study_id[3:] #strip pg_ prefix
uri = self.domain + '/study/export_gzipNexSON.json/' + study_id
_LOG.debug('Downloading %s using "%s"\n', study_id, uri)
resp = requests.get(uri,
headers=GZIP_REQUEST_HEADERS,
allow_redirects=True)
resp.raise_for_status()
try:
uncompressed = gzip.GzipFile(mode='rb',
fileobj=StringIO(resp.content)).read()
results = uncompressed
except:
raise
if is_str_type(results):
if output_filepath is None:
return anyjson.loads(results)
else:
if store_raw:
write_to_filepath(results, output_filepath)
else:
write_as_json(anyjson.loads(results), output_filepath)
return True
raise RuntimeError('gzipped response from phylografter export_gzipNexSON.json, but not a string is:', results)
def _write_master_branch_resource(self, content, fn, commit_msg, is_json=False):
'''This will force the current branch to master! '''
#TODO: we might want this to push, but currently it is only called in contexts in which
# we are about to push any way (study creation)
with self._master_branch_repo_lock:
ga = self._create_git_action_for_global_resource()
with ga.lock():
ga.checkout_master()
if is_json:
write_as_json(content, fn)
else:
write_to_filepath(content, fn)
ga._add_and_commit(fn, self._infrastructure_commit_author, commit_msg)
def _write_master_branch_resource(self, content, fn, commit_msg, is_json=False):
'''This will force the current branch to master! '''
#TODO: we might want this to push, but currently it is only called in contexts in which
# we are about to push any way (study creation)
with self._master_branch_repo_lock:
ga = self._create_git_action_for_global_resource()
with ga.lock():
ga.checkout_master()
if is_json:
write_as_json(content, fn)
else:
write_to_filepath(content, fn)
ga._add_and_commit(fn, self._infrastructure_commit_author, commit_msg)
