def test_check_fp(self):
obs = check_fp(1, 'uploaded_file.txt')
_, base_fp = get_mountpoint("uploads")[0]
exp = {'status': 'success',
'message': '',
'file': join(base_fp, '1', 'uploaded_file.txt')}
self.assertEqual(obs, exp)
def test_check_fp_bad_fp(self):
obs = check_fp(1, 'badfile')
exp = {
'status': 'error',
'message': 'file does not exist',
'file': 'badfile'
}
self.assertEqual(obs, exp)
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 test_check_fp(self):
obs = check_fp(1, 'uploaded_file.txt')
_, base_fp = get_mountpoint("uploads")[0]
exp = {
'status': 'success',
'message': '',
'file': join(base_fp, '1', 'uploaded_file.txt')
}
self.assertEqual(obs, exp)
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_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
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('update_sample_template')
params = Parameters.load(cmd,
values_dict={
'study': int(study_id),
'template_fp': fp_rsp
})
job = ProcessingJob.create(User(user_id), params)
# 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}))
job.submit()
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 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_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
"""
study_id = int(study_id)
access_error = check_access(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
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
}
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('create_sample_template')
params = Parameters.load(cmd,
values_dict={
'fp': fp_rsp,
'study_id': study_id,
'is_mapping_file': is_mapping_file,
'data_type': data_type
})
job = ProcessingJob.create(User(user_id), params)
r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
dumps({'job_id': job.id}))
# Store the job id attaching it to the sample template id
job.submit()
return {'status': 'success', 'message': '', '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
try:
artifact = Artifact.copy(Artifact(artifact_id), prep)
except Exception as e:
# We should hit this exception rarely (that's why it is an
# exception) since at this point we have done multiple checks.
# However, it can occur in weird cases, so better let the GUI know
# that this failed
return {'status': 'error',
'message': "Error creating artifact: %s" % str(e)}
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."}
try:
artifact = Artifact.create(cleaned_filepaths, artifact_type,
name=name, prep_template=prep)
except Exception as e:
# We should hit this exception rarely (that's why it is an
# exception) since at this point we have done multiple checks.
# However, it can occur in weird cases, so better let the GUI know
# that this failed
return {'status': 'error',
'message': "Error creating artifact: %s" % str(e)}
return {'status': 'success',
'message': '',
'artifact': artifact.id}
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 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_template_id = int(prep_template_id)
prep = PrepTemplate(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
user = User(user_id)
if artifact_id:
# if the artifact id has been provided, import the artifact
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('copy_artifact')
params = Parameters.load(cmd,
values_dict={
'artifact': artifact_id,
'prep_template': prep.id
})
job = ProcessingJob.create(user, params, True)
else:
uploads_path = get_mountpoint('uploads')[0][1]
path_builder = partial(join, uploads_path, str(study_id))
cleaned_filepaths = {}
for ftype, file_list in filepaths.items():
# 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
}
if ftype not in cleaned_filepaths:
cleaned_filepaths[ftype] = []
cleaned_filepaths[ftype].append(full_fp)
# 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."
}
# This try/except will catch the case when the plugins are not
# activated so there is no Validate for the given artifact_type
try:
command = Command.get_validator(artifact_type)
except QiitaDBError as e:
return {'status': 'error', 'message': str(e)}
job = ProcessingJob.create(
user,
Parameters.load(command,
values_dict={
'template': prep_template_id,
'files': dumps(cleaned_filepaths),
'artifact_type': artifact_type,
'name': name,
'analysis': None,
}), True)
# Submit the job
job.submit()
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep.id,
dumps({
'job_id': job.id,
'is_qiita_job': True
}))
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
"""
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_post_req(study_id, user_id, prep_template, data_type,
investigation_type=None,
user_defined_investigation_type=None,
new_investigation_type=None):
"""Adds a prep template to the system
Parameters
----------
study_id : int
Study to attach the prep template to
user_id : str
User adding the prep template
prep_template : str
Filepath to the prep template being added
data_type : str
Data type of the processed samples
investigation_type: str, optional
Existing investigation type to attach to the prep template
user_defined_investigation_type: str, optional
Existing user added investigation type to attach to the prep template
new_investigation_type: str, optional
Investigation type to add to the system
Returns
-------
dict of str
{'status': status,
'message': message,
'file': prep_template,
'id': id}
"""
access_error = check_access(study_id, user_id)
if access_error:
return access_error
fp_rpt = check_fp(study_id, prep_template)
if fp_rpt['status'] != 'success':
# Unknown filepath, so return the error message
return fp_rpt
fp_rpt = fp_rpt['file']
# Add new investigation type if needed
investigation_type = _process_investigation_type(
investigation_type, user_defined_investigation_type,
new_investigation_type)
msg = ''
status = 'success'
prep = None
try:
with warnings.catch_warnings(record=True) as warns:
# deleting previous uploads and inserting new one
prep = PrepTemplate.create(
load_template_to_dataframe(fp_rpt), Study(study_id), data_type,
investigation_type=investigation_type)
remove(fp_rpt)
# join all the warning messages into one. Note that this info
# will be ignored if an exception is raised
if warns:
msg = '\n'.join(set(str(w.message) for w in warns))
status = 'warning'
except Exception as e:
# Some error occurred while processing the prep template
# Show the error to the user so he can fix the template
status = 'error'
msg = str(e)
info = {'status': status,
'message': msg,
'file': prep_template,
'id': prep.id if prep is not None else None}
return info
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_post_req(study_id, user_id, prep_template, data_type,
investigation_type=None,
user_defined_investigation_type=None,
new_investigation_type=None, name=None):
"""Adds a prep template to the system
Parameters
----------
study_id : int
Study to attach the prep template to
user_id : str
User adding the prep template
prep_template : str
Filepath to the prep template being added
data_type : str
Data type of the processed samples
investigation_type: str, optional
Existing investigation type to attach to the prep template
user_defined_investigation_type: str, optional
Existing user added investigation type to attach to the prep template
new_investigation_type: str, optional
Investigation type to add to the system
name : str, optional
The name of the new prep template
Returns
-------
dict of str
{'status': status,
'message': message,
'file': prep_template,
'id': id}
"""
access_error = check_access(study_id, user_id)
if access_error:
return access_error
fp_rpt = check_fp(study_id, prep_template)
if fp_rpt['status'] != 'success':
# Unknown filepath, so return the error message
return fp_rpt
fp_rpt = fp_rpt['file']
# Add new investigation type if needed
investigation_type = _process_investigation_type(
investigation_type, user_defined_investigation_type,
new_investigation_type)
msg = ''
status = 'success'
prep = None
if name:
name = name if name.strip() else None
try:
with warnings.catch_warnings(record=True) as warns:
# deleting previous uploads and inserting new one
prep = PrepTemplate.create(
load_template_to_dataframe(fp_rpt), Study(study_id), data_type,
investigation_type=investigation_type, name=name)
remove(fp_rpt)
# join all the warning messages into one. Note that this info
# will be ignored if an exception is raised
if warns:
msg = '\n'.join(set(str(w.message) for w in warns))
status = 'warning'
except Exception as e:
# Some error occurred while processing the prep template
# Show the error to the user so he can fix the template
status = 'error'
msg = str(e)
info = {'status': status,
'message': msg,
'file': prep_template,
'id': prep.id if prep is not None else None}
return info
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 test_check_fp_bad_fp(self):
obs = check_fp(1, 'badfile')
exp = {'status': 'error',
'message': 'file does not exist',
'file': 'badfile'}
self.assertEqual(obs, exp)
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_template_id = int(prep_template_id)
prep = PrepTemplate(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
user = User(user_id)
if artifact_id:
# if the artifact id has been provided, import the artifact
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('copy_artifact')
params = Parameters.load(cmd, values_dict={'artifact': artifact_id,
'prep_template': prep.id})
job = ProcessingJob.create(user, params, True)
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}
if ftype not in cleaned_filepaths:
cleaned_filepaths[ftype] = []
cleaned_filepaths[ftype].append(full_fp)
# 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."}
# This try/except will catch the case when the plugins are not
# activated so there is no Validate for the given artifact_type
try:
command = Command.get_validator(artifact_type)
except QiitaDBError as e:
return {'status': 'error', 'message': str(e)}
job = ProcessingJob.create(
user,
Parameters.load(command, values_dict={
'template': prep_template_id,
'files': dumps(cleaned_filepaths),
'artifact_type': artifact_type,
'name': name,
'analysis': None,
}), True)
# Submit the job
job.submit()
r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep.id,
dumps({'job_id': job.id, 'is_qiita_job': True}))
return {'status': 'success', 'message': ''}