def update_investigation_type(self, study, user, callback):
"""Updates the investigation type of a prep template
Parameters
----------
study : Study
The current study object
user : User
The current user object
callback : function
The callback function to call with the results once the processing
is done
"""
msg = "investigation type successfully updated"
msg_level = "success"
ppd_id = int(self.get_argument('ppd_id'))
prep_id = self.get_argument('prep_id')
edit_investigation_type = self.get_argument('edit-investigation-type',
None)
edit_user_defined_investigation_type = self.get_argument(
'edit-user-defined-investigation-type', None)
edit_new_investigation_type = self.get_argument(
'edit-new-investigation-type', None)
pt = PrepTemplate(prep_id)
investigation_type = self._process_investigation_type(
edit_investigation_type, edit_user_defined_investigation_type,
edit_new_investigation_type)
try:
pt.investigation_type = investigation_type
except QiitaDBColumnError as e:
msg = html_error_message % (", invalid investigation type: ",
investigation_type, str(e))
msg = convert_text_html(msg)
msg_level = "danger"
if ppd_id == 0:
top_tab = "prep_template_tab"
sub_tab = prep_id
prep_tab = None
else:
top_tab = "preprocessed_data_tab"
sub_tab = ppd_id
prep_tab = None
callback((msg, msg_level, top_tab, sub_tab, prep_tab))
def update_investigation_type(self, study, user, callback):
"""Updates the investigation type of a prep template
Parameters
----------
study : Study
The current study object
user : User
The current user object
callback : function
The callback function to call with the results once the processing
is done
"""
msg = "investigation type successfully updated"
msg_level = "success"
ppd_id = int(self.get_argument('ppd_id'))
prep_id = self.get_argument('prep_id')
edit_investigation_type = self.get_argument('edit-investigation-type',
None)
edit_user_defined_investigation_type = self.get_argument(
'edit-user-defined-investigation-type', None)
edit_new_investigation_type = self.get_argument(
'edit-new-investigation-type', None)
pt = PrepTemplate(prep_id)
investigation_type = self._process_investigation_type(
edit_investigation_type, edit_user_defined_investigation_type,
edit_new_investigation_type)
try:
pt.investigation_type = investigation_type
except QiitaDBColumnError as e:
msg = html_error_message % (", invalid investigation type: ",
investigation_type, str(e))
msg = convert_text_html(msg)
msg_level = "danger"
if ppd_id == 0:
top_tab = "prep_template_tab"
sub_tab = prep_id
prep_tab = None
else:
top_tab = "preprocessed_data_tab"
sub_tab = ppd_id
prep_tab = None
callback((msg, msg_level, top_tab, sub_tab, prep_tab))
def prep_template_patch_req(user_id, req_op, req_path, req_value=None,
req_from=None):
"""Modifies an attribute of the prep template
Parameters
----------
user_id : str
The id of the user performing the patch operation
req_op : str
The operation to perform on the prep information
req_path : str
The prep information and attribute to patch
req_value : str, optional
The value that needs to be modified
req_from : str, optional
The original path of the element
Returns
-------
dict of {str, str}
A dictionary with the following keys:
- status: str, whether if the request is successful or not
- message: str, if the request is unsuccessful, a human readable error
"""
req_path = [v for v in req_path.split('/') if v]
if req_op == 'replace':
# The structure of the path should be /prep_id/attribute_to_modify/
# so if we don't have those 2 elements, we should return an error
if len(req_path) != 2:
return {'status': 'error',
'message': 'Incorrect path parameter'}
prep_id = int(req_path[0])
attribute = req_path[1]
# Check if the user actually has access to the prep template
prep = PrepTemplate(prep_id)
access_error = check_access(prep.study_id, user_id)
if access_error:
return access_error
status = 'success'
msg = ''
if attribute == 'investigation_type':
prep.investigation_type = req_value
elif attribute == 'data':
fp = check_fp(prep.study_id, req_value)
if fp['status'] != 'success':
return fp
fp = fp['file']
job_id = safe_submit(user_id, update_prep_template, prep_id, fp)
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep_id,
dumps({'job_id': job_id}))
else:
# We don't understand the attribute so return an error
return {'status': 'error',
'message': 'Attribute "%s" not found. '
'Please, check the path parameter' % attribute}
return {'status': status, 'message': msg}
elif req_op == 'remove':
# The structure of the path should be /prep_id/{columns|samples}/name
if len(req_path) != 3:
return {'status': 'error',
'message': 'Incorrect path parameter'}
prep_id = int(req_path[0])
attribute = req_path[1]
attr_id = req_path[2]
# Check if the user actually has access to the study
pt = PrepTemplate(prep_id)
access_error = check_access(pt.study_id, user_id)
if access_error:
return access_error
# Offload the deletion of the column to the cluster
job_id = safe_submit(user_id, delete_sample_or_column, PrepTemplate,
prep_id, attribute, attr_id)
# Store the job id attaching it to the sample template id
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep_id,
dumps({'job_id': job_id}))
return {'status': 'success', 'message': ''}
else:
return {'status': 'error',
'message': 'Operation "%s" not supported. '
'Current supported operations: replace, remove'
% req_op}
def prep_template_patch_req(user_id, req_op, req_path, req_value=None,
req_from=None):
"""Modifies an attribute of the prep template
Parameters
----------
user_id : str
The id of the user performing the patch operation
req_op : str
The operation to perform on the prep information
req_path : str
The prep information and attribute to patch
req_value : str, optional
The value that needs to be modified
req_from : str, optional
The original path of the element
Returns
-------
dict of {str, str, str}
A dictionary with the following keys:
- status: str, whether if the request is successful or not
- message: str, if the request is unsuccessful, a human readable error
- row_id: str, the row_id that we tried to delete
"""
req_path = [v for v in req_path.split('/') if v]
if req_op == 'replace':
# The structure of the path should be /prep_id/attribute_to_modify/
# so if we don't have those 2 elements, we should return an error
if len(req_path) != 2:
return {'status': 'error',
'message': 'Incorrect path parameter'}
prep_id = int(req_path[0])
attribute = req_path[1]
# Check if the user actually has access to the prep template
prep = PrepTemplate(prep_id)
access_error = check_access(prep.study_id, user_id)
if access_error:
return access_error
status = 'success'
msg = ''
if attribute == 'investigation_type':
prep.investigation_type = req_value
elif attribute == 'data':
fp = check_fp(prep.study_id, req_value)
if fp['status'] != 'success':
return fp
fp = fp['file']
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('update_prep_template')
params = Parameters.load(
cmd, values_dict={'prep_template': prep_id, 'template_fp': fp})
job = ProcessingJob.create(User(user_id), params, True)
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep_id,
dumps({'job_id': job.id}))
job.submit()
elif attribute == 'name':
prep.name = req_value.strip()
else:
# We don't understand the attribute so return an error
return {'status': 'error',
'message': 'Attribute "%s" not found. '
'Please, check the path parameter' % attribute}
return {'status': status, 'message': msg}
elif req_op == 'remove':
# The structure of the path should be:
# /prep_id/row_id/{columns|samples}/name
if len(req_path) != 4:
return {'status': 'error',
'message': 'Incorrect path parameter'}
prep_id = int(req_path[0])
row_id = req_path[1]
attribute = req_path[2]
attr_id = req_path[3]
# Check if the user actually has access to the study
pt = PrepTemplate(prep_id)
access_error = check_access(pt.study_id, user_id)
if access_error:
return access_error
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('delete_sample_or_column')
params = Parameters.load(
cmd, values_dict={'obj_class': 'PrepTemplate',
'obj_id': prep_id,
'sample_or_col': attribute,
'name': attr_id})
job = ProcessingJob.create(User(user_id), params, True)
# Store the job id attaching it to the sample template id
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep_id,
dumps({'job_id': job.id}))
job.submit()
return {'status': 'success', 'message': '', 'row_id': row_id}
else:
return {'status': 'error',
'message': 'Operation "%s" not supported. '
'Current supported operations: replace, remove'
% req_op,
'row_id': '0'}
def prep_template_patch_req(user_id, req_op, req_path, req_value=None,
req_from=None):
"""Modifies an attribute of the prep template
Parameters
----------
user_id : str
The id of the user performing the patch operation
req_op : str
The operation to perform on the prep information
req_path : str
The prep information and attribute to patch
req_value : str, optional
The value that needs to be modified
req_from : str, optional
The original path of the element
Returns
-------
dict of {str, str}
A dictionary with the following keys:
- status: str, whether if the request is successful or not
- message: str, if the request is unsuccessful, a human readable error
"""
if req_op == 'replace':
req_path = [v for v in req_path.split('/') if v]
# The structure of the path should be /prep_id/attribute_to_modify/
# so if we don't have those 2 elements, we should return an error
if len(req_path) != 2:
return {'status': 'error',
'message': 'Incorrect path parameter'}
prep_id = int(req_path[0])
attribute = req_path[1]
# Check if the user actually has access to the prep template
prep = PrepTemplate(prep_id)
access_error = check_access(prep.study_id, user_id)
if access_error:
return access_error
status = 'success'
msg = ''
if attribute == 'investigation_type':
prep.investigation_type = req_value
elif attribute == 'data':
fp = check_fp(prep.study_id, req_value)
if fp['status'] != 'success':
return fp
fp = fp['file']
job_id = safe_submit(user_id, update_prep_template, prep_id, fp)
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep_id, job_id)
else:
# We don't understand the attribute so return an error
return {'status': 'error',
'message': 'Attribute "%s" not found. '
'Please, check the path parameter' % attribute}
return {'status': status, 'message': msg}
else:
return {'status': 'error',
'message': 'Operation "%s" not supported. '
'Current supported operations: replace' % req_op}
