def _get_study_and_check_access(self, study_id):
"""Checks if the current user has access to the study
First tries to instantiate the study object. Then it checks if the
current user has access to such study.
Parameters
----------
study_id : str or int
The current study
Returns
-------
The study object, the current user object and a boolean indicating if
the user has full access to the study or only to public data
Raises
------
HTTPError
If study_id does not correspond to any study in the system
"""
user = self.current_user
try:
study = Study(_to_int(study_id))
except (QiitaDBUnknownIDError, HTTPError):
# Study not in database so fail nicely
raise HTTPError(404, "Study %s does not exist" % study_id)
else:
check_access(user, study, raise_error=True)
full_access = (user.level == 'admin' or
study.id in user.user_studies | user.shared_studies)
return study, user, full_access
def _get_sudy_and_check_access(self, study_id):
"""Checks if the current user has access to the study
First tries to instantiate the study object. Then it checks if the
current user has access to such study.
Parameters
----------
study_id : str or int
The current study
Returns
-------
The study object and the current user object
Raises
------
HTTPError
If study_id does not correspond to any study in the system
"""
user = User(self.current_user)
try:
study = Study(_to_int(study_id))
except (QiitaDBUnknownIDError, HTTPError):
# Study not in database so fail nicely
raise HTTPError(404, "Study %s does not exist" % study_id)
else:
check_access(user, study, raise_error=True)
return study, user
def _get_study_and_check_access(self, study_id):
"""Checks if the current user has access to the study
First tries to instantiate the study object. Then it checks if the
current user has access to such study.
Parameters
----------
study_id : str or int
The current study
Returns
-------
The study object and the current user object
Raises
------
HTTPError
If study_id does not correspond to any study in the system
"""
user = self.current_user
try:
study = Study(_to_int(study_id))
except (QiitaDBUnknownIDError, HTTPError):
# Study not in database so fail nicely
raise HTTPError(404, "Study %s does not exist" % study_id)
else:
check_access(user, study, raise_error=True)
return study, user
def _get_study_and_check_access(self, study_id):
"""Checks if the current user has access to the study
First tries to instantiate the study object. Then it checks if the
current user has access to such study.
Parameters
----------
study_id : str or int
The current study
Returns
-------
The study object, the current user object and a boolean indicating if
the user has full access to the study or only to public data
Raises
------
HTTPError
If study_id does not correspond to any study in the system
"""
user = self.current_user
try:
study = Study(_to_int(study_id))
except (QiitaDBUnknownIDError, HTTPError):
# Study not in database so fail nicely
raise HTTPError(404, "Study %s does not exist" % study_id)
else:
check_access(user, study, raise_error=True)
full_access = (user.level == 'admin'
or study in user.user_studies | user.shared_studies)
return study, user, full_access
def _check_study_exists_and_user_access(self, study_id):
try:
study = Study(int(study_id))
except QiitaDBUnknownIDError:
# Study not in database so fail nicely
raise HTTPError(404, "Study %s does not exist" % study_id)
# We need to check if the user has access to the study
check_access(self.current_user, study)
return study
def _check_study_exists_and_user_access(self, study_id):
try:
study = Study(int(study_id))
except QiitaDBUnknownIDError:
# Study not in database so fail nicely
raise HTTPError(404, "Study %s does not exist" % study_id)
# We need to check if the user has access to the study
check_access(self.current_user, study)
return study
def _get_template_variables(self, preprocessed_data_id, callback):
"""Generates all the variables needed to render the template
Parameters
----------
preprocessed_data_id : int
The preprocessed data identifier
callback : function
The callback function to call with the results once the processing
is done
Raises
------
HTTPError
If the preprocessed data does not have a log file
"""
# Get the objects and check user privileges
ppd = Artifact(preprocessed_data_id)
study = ppd.study
check_access(self.current_user, study, raise_error=True)
# Get the return address
back_button_path = self.get_argument(
'back_button_path',
'/study/description/%d?top_tab=preprocessed_data_tab&sub_tab=%s' %
(study.id, preprocessed_data_id))
# Get all the filepaths attached to the preprocessed data
files_tuples = ppd.filepaths
# Group the files by filepath type
files = defaultdict(list)
for _, fp, fpt in files_tuples:
files[fpt].append(fp)
try:
log_path = files['log'][0]
except KeyError:
raise HTTPError(
500, "Log file not found in preprocessed data %s" %
preprocessed_data_id)
with open(log_path, 'U') as f:
contents = f.read()
contents = contents.replace('\n', '<br/>')
contents = contents.replace('\t', ' ')
title = 'Preprocessed Data: %d' % preprocessed_data_id
callback((title, contents, back_button_path))
def _get_template_variables(self, preprocessed_data_id, callback):
"""Generates all the variables needed to render the template
Parameters
----------
preprocessed_data_id : int
The preprocessed data identifier
callback : function
The callback function to call with the results once the processing
is done
Raises
------
HTTPError
If the preprocessed data does not have a log file
"""
# Get the objects and check user privileges
ppd = PreprocessedData(preprocessed_data_id)
study = Study(ppd.study)
check_access(self.current_user, study, raise_error=True)
# Get the return address
back_button_path = self.get_argument(
'back_button_path',
'/study/description/%d?top_tab=preprocessed_data_tab&sub_tab=%s'
% (study.id, preprocessed_data_id))
# Get all the filepaths attached to the preprocessed data
files_tuples = ppd.get_filepaths()
# Group the files by filepath type
files = defaultdict(list)
for _, fp, fpt in files_tuples:
files[fpt].append(fp)
try:
log_path = files['log'][0]
except KeyError:
raise HTTPError(500, "Log file not found in preprocessed data %s"
% preprocessed_data_id)
with open(log_path, 'U') as f:
contents = f.read()
contents = contents.replace('\n', '<br/>')
contents = contents.replace('\t', ' ')
title = 'Preprocessed Data: %d' % preprocessed_data_id
callback((title, contents, back_button_path))
def get(self):
study_id = int(self.get_argument('study_id'))
study = Study(study_id)
check_access(self.current_user, study, no_public=True,
raise_error=True)
selected = self.get_argument('selected', None)
deselected = self.get_argument('deselected', None)
if selected is not None:
yield Task(self._share, study, selected)
if deselected is not None:
yield Task(self._unshare, study, deselected)
users, links = yield Task(self._get_shared_for_study, study)
self.write(dumps({'users': users, 'links': links}))
def get(self):
study_id = int(self.get_argument('id'))
study = Study(study_id)
check_access(self.current_user, study, no_public=True,
raise_error=True)
selected = self.get_argument('selected', None)
deselected = self.get_argument('deselected', None)
if selected is not None:
yield Task(self._share, study, selected)
if deselected is not None:
yield Task(self._unshare, study, deselected)
users, links = yield Task(self._get_shared_for_study, study)
self.write(dumps({'users': users, 'links': links}))