def sample_template_patch_request(user_id,
req_op,
req_path,
req_value=None,
req_from=None):
"""Modifies an attribute of the artifact
Parameters
----------
user_id : str
The id of the user performing the patch operation
req_op : str
The operation to perform on the artifact
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 == 'remove':
req_path = [v for v in req_path.split('/') if v]
if len(req_path) != 3:
return {'status': 'error', 'message': 'Incorrect path parameter'}
st_id = req_path[0]
attribute = req_path[1]
attr_id = req_path[2]
# Check if the user actually has access to the template
st = SampleTemplate(st_id)
access_error = check_access(st.study_id, user_id)
if access_error:
return access_error
# Offload the deletion of the sample or column to the cluster
job_id = safe_submit(user_id, delete_sample_or_column, SampleTemplate,
int(st_id), attribute, attr_id)
# Store the job id attaching it to the sample template id
r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % st_id,
dumps({'job_id': job_id}))
return {'status': 'success', 'message': ''}
else:
return {
'status':
'error',
'message':
'Operation "%s" not supported. '
'Current supported operations: remove' % req_op
}
def artifact_delete_req(artifact_id, user_id):
"""Deletes the artifact
Parameters
----------
artifact_id : int
Artifact being acted on
user_id : str
The user requesting the action
Returns
-------
dict
Status of action, in the form {'status': status, 'message': msg}
status: status of the action, either success or error
message: Human readable message for status
"""
pd = Artifact(int(artifact_id))
pt_id = pd.prep_templates[0].id
access_error = check_access(pd.study.id, user_id)
if access_error:
return access_error
job_id = safe_submit(user_id, delete_artifact, artifact_id)
r_client.set(PREP_TEMPLATE_KEY_FORMAT % pt_id, dumps({'job_id': job_id}))
return {'status': 'success', 'message': ''}
def artifact_post_req(user, artifact_id):
"""Deletes the artifact
Parameters
----------
user : qiita_db.user.User
The user requesting the action
artifact_id : int
Id of the artifact being deleted
"""
artifact_id = int(artifact_id)
artifact = Artifact(artifact_id)
check_artifact_access(user, artifact)
analysis = artifact.analysis
if analysis:
# Do something when deleting in the analysis part to keep track of it
redis_key = "analysis_%s" % analysis.id
else:
pt_id = artifact.prep_templates[0].id
redis_key = PREP_TEMPLATE_KEY_FORMAT % pt_id
job_id = safe_submit(user.id, delete_artifact, artifact_id)
r_client.set(redis_key, dumps({'job_id': job_id, 'is_qiita_job': False}))
def artifact_delete_req(artifact_id, user_id):
"""Deletes the artifact
Parameters
----------
artifact_id : int
Artifact being acted on
user_id : str
The user requesting the action
Returns
-------
dict
Status of action, in the form {'status': status, 'message': msg}
status: status of the action, either success or error
message: Human readable message for status
"""
pd = Artifact(int(artifact_id))
pt_id = pd.prep_templates[0].id
access_error = check_access(pd.study.id, user_id)
if access_error:
return access_error
job_id = safe_submit(user_id, delete_artifact, artifact_id)
r_client.set(PREP_TEMPLATE_KEY_FORMAT % pt_id,
dumps({'job_id': job_id}))
return {'status': 'success',
'message': ''}
def sample_template_delete_req(study_id, user_id):
"""Deletes the sample template attached to the study
Parameters
----------
study_id : int
The current study object id
user_id : str
The current user object id
Returns
-------
dict
results dictonary in the format
{'status': status,
'message': msg}
status can be success, warning, or error depending on result
message has the warnings or errors
"""
exists = _check_sample_template_exists(int(study_id))
if exists['status'] != 'success':
return exists
access_error = check_access(int(study_id), user_id)
if access_error:
return access_error
# Offload the deletion of the sample template to the cluster
job_id = safe_submit(user_id, delete_sample_template, int(study_id))
# Store the job id attaching it to the sample template id
r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
dumps({'job_id': job_id}))
return {'status': 'success', 'message': ''}
def sample_template_delete_req(study_id, user_id):
"""Deletes the sample template attached to the study
Parameters
----------
study_id : int
The current study object id
user_id : str
The current user object id
Returns
-------
dict
results dictonary in the format
{'status': status,
'message': msg}
status can be success, warning, or error depending on result
message has the warnings or errors
"""
exists = _check_sample_template_exists(int(study_id))
if exists['status'] != 'success':
return exists
access_error = check_access(int(study_id), user_id)
if access_error:
return access_error
# Offload the deletion of the sample template to the cluster
job_id = safe_submit(user_id, delete_sample_template, int(study_id))
# Store the job id attaching it to the sample template id
r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
dumps({'job_id': job_id}))
return {'status': 'success', 'message': ''}
def sample_template_post_req(study_id, user_id, data_type,
sample_template):
"""Creates the sample template from the given file
Parameters
----------
study_id : int
The current study object id
user_id : str
The current user object id
data_type : str
Data type for the sample template
sample_template : str
filename to use for creation
Returns
-------
dict
results dictonary in the format
{'status': status,
'message': msg,
'file': sample_template}
status can be success, warning, or error depending on result
message has the warnings or errors
file has the file name
"""
access_error = check_access(int(study_id), user_id)
if access_error:
return access_error
fp_rsp = check_fp(study_id, sample_template)
if fp_rsp['status'] != 'success':
# Unknown filepath, so return the error message
return fp_rsp
fp_rsp = fp_rsp['file']
# Define here the message and message level in case of success
msg = ''
status = 'success'
is_mapping_file = looks_like_qiime_mapping_file(fp_rsp)
if is_mapping_file and not data_type:
return {'status': 'error',
'message': 'Please, choose a data type if uploading a '
'QIIME mapping file',
'file': sample_template}
study = Study(int(study_id))
# Offload the creation of the sample template to the cluster
job_id = safe_submit(user_id, create_sample_template, fp_rsp, study,
is_mapping_file, data_type)
# Store the job id attaching it to the sample template id
r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study.id,
dumps({'job_id': job_id}))
return {'status': status,
'message': msg,
'file': sample_template}
def sample_template_post_req(study_id, user_id, data_type, sample_template):
"""Creates the sample template from the given file
Parameters
----------
study_id : int
The current study object id
user_id : str
The current user object id
data_type : str
Data type for the sample template
sample_template : str
filename to use for creation
Returns
-------
dict
results dictonary in the format
{'status': status,
'message': msg,
'file': sample_template}
status can be success, warning, or error depending on result
message has the warnings or errors
file has the file name
"""
access_error = check_access(int(study_id), user_id)
if access_error:
return access_error
fp_rsp = check_fp(study_id, sample_template)
if fp_rsp['status'] != 'success':
# Unknown filepath, so return the error message
return fp_rsp
fp_rsp = fp_rsp['file']
# Define here the message and message level in case of success
msg = ''
status = 'success'
is_mapping_file = looks_like_qiime_mapping_file(fp_rsp)
if is_mapping_file and not data_type:
return {
'status': 'error',
'message': 'Please, choose a data type if uploading a '
'QIIME mapping file',
'file': sample_template
}
study = Study(int(study_id))
# Offload the creation of the sample template to the cluster
job_id = safe_submit(user_id, create_sample_template, fp_rsp, study,
is_mapping_file, data_type)
# Store the job id attaching it to the sample template id
r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study.id,
dumps({'job_id': job_id}))
return {'status': status, 'message': msg, 'file': sample_template}
def post(self, job_id):
"""Updates the job to one of the completed statuses: 'success', 'error'
Parameters
----------
job_id : str
The job to complete
"""
with qdb.sql_connection.TRN:
job = _get_job(job_id)
if job.status != 'running':
raise HTTPError(403,
"Can't complete job: not in a running state")
payload = loads(self.request.body)
safe_submit(job.user.email, _job_completer, job_id, payload)
self.finish()
def post(self, job_id):
"""Updates the job to one of the completed statuses: 'success', 'error'
Parameters
----------
job_id : str
The job to complete
"""
with qdb.sql_connection.TRN:
job = _get_job(job_id)
if job.status != 'running':
raise HTTPError(
403, "Can't complete job: not in a running state")
payload = loads(self.request.body)
safe_submit(job.user.email, _job_completer, job_id, payload)
self.finish()
def sample_template_patch_request(user_id, req_op, req_path, req_value=None,
req_from=None):
"""Modifies an attribute of the artifact
Parameters
----------
user_id : str
The id of the user performing the patch operation
req_op : str
The operation to perform on the artifact
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 == 'remove':
req_path = [v for v in req_path.split('/') if v]
if len(req_path) != 3:
return {'status': 'error',
'message': 'Incorrect path parameter'}
st_id = req_path[0]
attribute = req_path[1]
attr_id = req_path[2]
# Check if the user actually has access to the template
st = SampleTemplate(st_id)
access_error = check_access(st.study_id, user_id)
if access_error:
return access_error
# Offload the deletion of the sample or column to the cluster
job_id = safe_submit(user_id, delete_sample_or_column, SampleTemplate,
int(st_id), attribute, attr_id)
# Store the job id attaching it to the sample template id
r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % st_id,
dumps({'job_id': job_id}))
return {'status': 'success', 'message': ''}
else:
return {'status': 'error',
'message': 'Operation "%s" not supported. '
'Current supported operations: remove' % req_op}
def sample_template_put_req(study_id, user_id, sample_template):
"""Updates a sample template using the given file
Parameters
----------
study_id : int
The current study object id
user_id : str
The current user object id
sample_template : str
filename to use for updating
Returns
-------
dict
results dictonary in the format
{'status': status,
'message': msg,
'file': sample_template}
status can be success, warning, or error depending on result
message has the warnings or errors
file has the file name
"""
exists = _check_sample_template_exists(int(study_id))
if exists['status'] != 'success':
return exists
access_error = check_access(int(study_id), user_id)
if access_error:
return access_error
fp_rsp = check_fp(study_id, sample_template)
if fp_rsp['status'] != 'success':
# Unknown filepath, so return the error message
return fp_rsp
fp_rsp = fp_rsp['file']
msg = ''
status = 'success'
# Offload the update of the sample template to the cluster
job_id = safe_submit(user_id, update_sample_template, int(study_id),
fp_rsp)
# Store the job id attaching it to the sample template id
r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
dumps({'job_id': job_id}))
return {'status': status,
'message': msg,
'file': sample_template}
def sample_template_put_req(study_id, user_id, sample_template):
"""Updates a sample template using the given file
Parameters
----------
study_id : int
The current study object id
user_id : str
The current user object id
sample_template : str
filename to use for updating
Returns
-------
dict
results dictonary in the format
{'status': status,
'message': msg,
'file': sample_template}
status can be success, warning, or error depending on result
message has the warnings or errors
file has the file name
"""
exists = _check_sample_template_exists(int(study_id))
if exists['status'] != 'success':
return exists
access_error = check_access(int(study_id), user_id)
if access_error:
return access_error
fp_rsp = check_fp(study_id, sample_template)
if fp_rsp['status'] != 'success':
# Unknown filepath, so return the error message
return fp_rsp
fp_rsp = fp_rsp['file']
msg = ''
status = 'success'
# Offload the update of the sample template to the cluster
job_id = safe_submit(user_id, update_sample_template, int(study_id),
fp_rsp)
# Store the job id attaching it to the sample template id
r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
dumps({'job_id': job_id}))
return {'status': status, 'message': msg, 'file': sample_template}
def artifact_post_req(user_id,
filepaths,
artifact_type,
name,
prep_template_id,
artifact_id=None):
"""Creates the initial artifact for the prep template
Parameters
----------
user_id : str
User adding the atrifact
filepaths : dict of str
Comma-separated list of files to attach to the artifact,
keyed by file type
artifact_type : str
The type of the artifact
name : str
Name to give the artifact
prep_template_id : int or str castable to int
Prep template to attach the artifact to
artifact_id : int or str castable to int, optional
The id of the imported artifact
Returns
-------
dict of objects
A dictionary containing the new artifact ID
{'status': status,
'message': message,
'artifact': id}
"""
prep = PrepTemplate(int(prep_template_id))
study_id = prep.study_id
# First check if the user has access to the study
access_error = check_access(study_id, user_id)
if access_error:
return access_error
if artifact_id:
# if the artifact id has been provided, import the artifact
job_id = safe_submit(user_id, copy_raw_data, prep, artifact_id)
else:
uploads_path = get_mountpoint('uploads')[0][1]
path_builder = partial(join, uploads_path, str(study_id))
cleaned_filepaths = []
for ftype, file_list in viewitems(filepaths):
# JavaScript sends us this list as a comma-separated list
for fp in file_list.split(','):
# JavaScript will send this value as an empty string if the
# list of files was empty. In such case, the split will
# generate a single element containing the empty string. Check
# for that case here and, if fp is not the empty string,
# proceed to check if the file exists
if fp:
# Check if filepath being passed exists for study
full_fp = path_builder(fp)
exists = check_fp(study_id, full_fp)
if exists['status'] != 'success':
return {
'status': 'error',
'message': 'File does not exist: %s' % fp
}
cleaned_filepaths.append((full_fp, ftype))
# This should never happen, but it doesn't hurt to actually have
# a explicit check, in case there is something odd with the JS
if not cleaned_filepaths:
return {
'status': 'error',
'message': "Can't create artifact, no files provided."
}
job_id = safe_submit(user_id,
create_raw_data,
artifact_type,
prep,
cleaned_filepaths,
name=name)
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep.id, dumps({'job_id': job_id}))
return {'status': 'success', 'message': ''}
def artifact_post_req(user_id, filepaths, artifact_type, name,
prep_template_id, artifact_id=None):
"""Creates the initial artifact for the prep template
Parameters
----------
user_id : str
User adding the atrifact
filepaths : dict of str
Comma-separated list of files to attach to the artifact,
keyed by file type
artifact_type : str
The type of the artifact
name : str
Name to give the artifact
prep_template_id : int or str castable to int
Prep template to attach the artifact to
artifact_id : int or str castable to int, optional
The id of the imported artifact
Returns
-------
dict of objects
A dictionary containing the new artifact ID
{'status': status,
'message': message,
'artifact': id}
"""
prep = PrepTemplate(int(prep_template_id))
study_id = prep.study_id
# First check if the user has access to the study
access_error = check_access(study_id, user_id)
if access_error:
return access_error
if artifact_id:
# if the artifact id has been provided, import the artifact
job_id = safe_submit(user_id, copy_raw_data, prep, artifact_id)
else:
uploads_path = get_mountpoint('uploads')[0][1]
path_builder = partial(join, uploads_path, str(study_id))
cleaned_filepaths = []
for ftype, file_list in viewitems(filepaths):
# JavaScript sends us this list as a comma-separated list
for fp in file_list.split(','):
# JavaScript will send this value as an empty string if the
# list of files was empty. In such case, the split will
# generate a single element containing the empty string. Check
# for that case here and, if fp is not the empty string,
# proceed to check if the file exists
if fp:
# Check if filepath being passed exists for study
full_fp = path_builder(fp)
exists = check_fp(study_id, full_fp)
if exists['status'] != 'success':
return {'status': 'error',
'message': 'File does not exist: %s' % fp}
cleaned_filepaths.append((full_fp, ftype))
# This should never happen, but it doesn't hurt to actually have
# a explicit check, in case there is something odd with the JS
if not cleaned_filepaths:
return {'status': 'error',
'message': "Can't create artifact, no files provided."}
job_id = safe_submit(user_id, create_raw_data, artifact_type, prep,
cleaned_filepaths, name=name)
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep.id, dumps({'job_id': job_id}))
return {'status': 'success',
'message': ''}
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}
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}