def study_delete_req(study_id, user_id):
"""Delete a given study
Parameters
----------
study_id : int
Study id to delete
user_id : str
User requesting the deletion
Returns
-------
dict
Status of deletion, in the format
{status: status,
message: message}
"""
access_error = check_access(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_study')
params = Parameters.load(cmd, values_dict={'study': study_id})
job = ProcessingJob.create(User(user_id), params, True)
# Store the job id attaching it to the sample template id
r_client.set(STUDY_KEY_FORMAT % study_id,
dumps({'job_id': job.id}))
job.submit()
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
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('delete_artifact')
params = Parameters.load(cmd, values_dict={'artifact': artifact_id})
job = ProcessingJob.create(user, params, True)
r_client.set(redis_key, dumps({'job_id': job.id, 'is_qiita_job': True}))
job.submit()
return {'job': job.id}
def sample_template_handler_post_request(study_id, user, filepath,
data_type=None, direct_upload=False):
"""Creates a new sample template
Parameters
----------
study_id: int
The study to add the sample information
user: qiita_db.user import User
The user performing the request
filepath: str
The path to the sample template file
data_type: str, optional
If filepath is a QIIME mapping file, the data type of the prep
information file
direct_upload: boolean, optional
If filepath is a direct upload; if False we need to process the
filepath as part of the study upload folder
Returns
-------
dict of {'job': str}
job: the id of the job adding the sample information to the study
Raises
------
HTTPError
404 if the filepath doesn't exist
"""
# Check if the current user has access to the study
sample_template_checks(study_id, user)
# Check if the file exists
if not direct_upload:
fp_rsp = check_fp(study_id, filepath)
if fp_rsp['status'] != 'success':
raise HTTPError(404, reason='Filepath not found')
filepath = fp_rsp['file']
is_mapping_file = looks_like_qiime_mapping_file(filepath)
if is_mapping_file and not data_type:
raise HTTPError(400, reason='Please, choose a data type if uploading '
'a QIIME mapping file')
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('create_sample_template')
params = Parameters.load(
cmd, values_dict={'fp': filepath, 'study_id': study_id,
'is_mapping_file': is_mapping_file,
'data_type': data_type})
job = ProcessingJob.create(user, params, True)
r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
dumps({'job_id': job.id}))
job.submit()
return {'job': job.id}
def artifact_summary_post_request(user_id, artifact_id):
"""Launches the HTML summary generation and returns the job information
Parameters
----------
user_id : str
The user making the request
artifact_id : int or str
The artifact id
Returns
-------
dict of objects
A dictionary containing the artifact summary information
{'status': str,
'message': str,
'job': list of [str, str, str]}
"""
artifact_id = int(artifact_id)
artifact = Artifact(artifact_id)
access_error = check_access(artifact.study.id, user_id)
if access_error:
return access_error
# Check if the summary is being generated or has been already generated
command = Command.get_html_generator(artifact.artifact_type)
jobs = artifact.jobs(cmd=command)
jobs = [j for j in jobs if j.status in ['queued', 'running', 'success']]
if jobs:
# The HTML summary is either being generated or already generated.
# Return the information of that job so we only generate the HTML
# once
job = jobs[0]
else:
# Create a new job to generate the HTML summary and return the newly
# created job information
job = ProcessingJob.create(
User(user_id),
Parameters.load(command, values_dict={'input_data': artifact_id}))
job.submit()
return {'status': 'success',
'message': '',
'job': [job.id, job.status, job.step]}
def artifact_summary_post_request(user, artifact_id):
"""Launches the HTML summary generation and returns the job information
Parameters
----------
user : qiita_db.user.User
The user making the request
artifact_id : int or str
The artifact id
Returns
-------
dict of objects
A dictionary containing the job summary information
{'job': [str, str, str]}
"""
artifact_id = int(artifact_id)
artifact = Artifact(artifact_id)
check_artifact_access(user, artifact)
# Check if the summary is being generated or has been already generated
command = Command.get_html_generator(artifact.artifact_type)
jobs = artifact.jobs(cmd=command)
jobs = [j for j in jobs if j.status in ['queued', 'running', 'success']]
if jobs:
# The HTML summary is either being generated or already generated.
# Return the information of that job so we only generate the HTML
# once - Magic number 0 -> we are ensuring that there is only one
# job generating the summary, so we can use the index 0 to access to
# that job
job = jobs[0]
else:
# Create a new job to generate the HTML summary and return the newly
# created job information
job = ProcessingJob.create(user, Parameters.load(
command, values_dict={'input_data': artifact_id}), True)
job.submit()
return {'job': [job.id, job.status, job.step]}
def _submit(ctx, user, parameters):
"""Submit a plugin job to a cluster
Parameters
----------
ctx : qiita_db.ware.Dispatch
A Dispatch object to submit through
user : qiita_db.user.User
The user doing the submission
parameters : qiita_db.software.Parameters
The parameters of the job
Returns
-------
str
The job id
"""
job = ProcessingJob.create(user, parameters)
redis_deets = {'job_id': job.id, 'pubsub': user.id,
'messages': user.id + ':messages'}
ctx.submit_async(_redis_wrap, execute, redis_deets, job.id)
return job.id
def sample_template_handler_delete_request(study_id, user):
"""Deletes the sample template
Parameters
----------
study_id: int
The study to delete the sample information
user: qiita_db.user
The user performing the request
Returns
-------
dict of {'job': str}
job: the id of the job deleting the sample information to the study
Raises
------
HTTPError
404 If the sample template doesn't exist
"""
# Check if the current user has access to the study and if the sample
# template exists
sample_template_checks(study_id, user, check_exists=True)
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('delete_sample_template')
params = Parameters.load(cmd, values_dict={'study': int(study_id)})
job = ProcessingJob.create(user, params, True)
# Store the job if deleteing the sample template
r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
dumps({'job_id': job.id}))
job.submit()
return {'job': job.id}
def sample_template_handler_patch_request(user, req_op, req_path,
req_value=None, req_from=None):
"""Patches the sample template
Parameters
----------
user: qiita_db.user.User
The user performing the request
req_op : str
The operation to perform on the sample template
req_path : str
The path to the attribute to patch
req_value : str, optional
The new value
req_from : str, optional
The original path of the element
Returns
-------
Raises
------
HTTPError
400 If the path parameter doens't follow the expected format
400 If the given operation is not supported
"""
req_path = [v for v in req_path.split('/') if v]
# At this point we know the path should be at least length 2
if len(req_path) < 2:
raise HTTPError(400, reason='Incorrect path parameter')
study_id = int(req_path[0])
# Check if the current user has access to the study and if the sample
# template exists
sample_template_checks(study_id, user, check_exists=True)
if req_op == 'remove':
# Path format
# column: study_id/columns/column_name
# sample: study_id/samples/sample_id
if len(req_path) != 3:
raise HTTPError(400, reason='Incorrect path parameter')
attribute = req_path[1]
attr_id = req_path[2]
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': 'SampleTemplate',
'obj_id': study_id,
'sample_or_col': attribute,
'name': attr_id})
job = ProcessingJob.create(user, params, True)
# 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 {'job': job.id}
elif req_op == 'replace':
# WARNING: Although the patch operation is a replace, is not a full
# true replace. A replace is in theory equivalent to a remove + add.
# In this case, the replace operation doesn't necessarily removes
# anything (e.g. when only new columns/samples are being added to the)
# sample information.
# Path format: study_id/data
# Forcing to specify data for extensibility. In the future we may want
# to use this function to replace other elements of the sample
# information
if len(req_path) != 2:
raise HTTPError(400, reason='Incorrect path parameter')
attribute = req_path[1]
if attribute == 'data':
# Update the sample information
if req_value is None:
raise HTTPError(400, reason="Value is required when updating "
"sample information")
# Check if the file exists
fp_rsp = check_fp(study_id, req_value)
if fp_rsp['status'] != 'success':
raise HTTPError(404, reason='Filepath not found')
filepath = fp_rsp['file']
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('update_sample_template')
params = Parameters.load(
cmd, values_dict={'study': study_id,
'template_fp': filepath})
job = ProcessingJob.create(user, params, True)
# 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 {'job': job.id}
else:
#.........这里部分代码省略.........
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