def analyisis_job_handler_get_request(analysis_id, user):
"""Returns the job information of the analysis
Parameters
----------
analysis_id: int
The analysis id
user : qiita_db.user.User
The user performing the request
Returns
-------
dict with the jobs information
"""
analysis = Analysis(analysis_id)
# Check if the user actually has access to the analysis
check_analysis_access(user, analysis)
return {
j.id: {
'status': j.status,
'step': j.step,
'error': j.log.msg if j.log else ""
}
for j in analysis.jobs
}
def analyisis_graph_handler_get_request(analysis_id, user):
"""Returns the graph information of the analysis
Parameters
----------
analysis_id : int
The analysis id
user : qiita_db.user.User
The user performing the request
Returns
-------
dict with the graph information
"""
analysis = Analysis(analysis_id)
# Check if the user actually has access to the analysis
check_analysis_access(user, analysis)
# A user has full access to the analysis if it is one of its private
# analyses, the analysis has been shared with the user or the user is a
# superuser or admin
full_access = (analysis in (user.private_analyses | user.shared_analyses)
or user.level in {'superuser', 'admin'})
nodes = set()
edges = set()
# Loop through all the initial artifacts of the analysis
for a in analysis.artifacts:
g = a.descendants_with_jobs
# Loop through all the nodes in artifact descendants graph
for n in g.nodes():
# Get if the object is an artifact or a job
obj_type = n[0]
# Get the actual object
obj = n[1]
if obj_type == 'job':
name = obj.command.name
elif not full_access and not obj.visibility == 'public':
# The object is an artifact, it is not public and the user
# doesn't have full access, so we don't include it in the
# graph
continue
else:
name = '%s - %s' % (obj.name, obj.artifact_type)
nodes.add((obj_type, obj.id, name))
edges.update({(s[1].id, t[1].id) for s, t in g.edges()})
# Nodes and Edges are sets, but the set object can't be serialized using
# JSON. Transforming them to lists so when this is returned to the GUI
# over HTTP can be JSONized.
return {'edges': list(edges), 'nodes': list(nodes)}
def analyisis_graph_handler_get_request(analysis_id, user):
"""Returns the graph information of the analysis
Parameters
----------
analysis_id : int
The analysis id
user : qiita_db.user.User
The user performing the request
Returns
-------
dict with the graph information
Raises
------
ValueError
If there is more than one workflow in a single analysis
"""
analysis = Analysis(analysis_id)
# Check if the user actually has access to the analysis
check_analysis_access(user, analysis)
# A user has full access to the analysis if it is one of its private
# analyses, the analysis has been shared with the user or the user is a
# superuser or admin
full_access = (analysis in (user.private_analyses | user.shared_analyses)
or user.level in {'superuser', 'admin'})
nodes = []
edges = []
wf_id = None
# Loop through all the initial artifacts of the analysis
for a in analysis.artifacts:
if a.processing_parameters is None:
g = a.descendants_with_jobs
nodes, edges, a_wf_id = get_network_nodes_edges(g,
full_access,
nodes=nodes,
edges=edges)
if wf_id is None:
wf_id = a_wf_id
elif a_wf_id is not None and wf_id != a_wf_id:
# This should never happen, but worth having a useful message
raise ValueError('More than one workflow in a single analysis')
return {'edges': edges, 'nodes': nodes, 'workflow': wf_id}
def post(self):
analysis_id = int(self.get_argument('analysis_id'))
user = self.current_user
check_analysis_access(user, Analysis(analysis_id))
qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
cmd = qiita_plugin.get_command('delete_analysis')
params = Parameters.load(cmd, values_dict={'analysis_id': analysis_id})
job = ProcessingJob.create(user, params, True)
# Store the job id attaching it to the sample template id
r_client.set('analysis_delete_%d' % analysis_id,
dumps({'job_id': job.id}))
job.submit()
self.redirect("%s/analysis/list/" % (qiita_config.portal_dir))
def analysis_description_handler_get_request(analysis_id, user):
"""Returns the analysis information
Parameters
----------
analysis_id : int
The analysis id
user : qiita_db.user.User
The user performing the request
"""
analysis = Analysis(analysis_id)
check_analysis_access(user, analysis)
job_info = r_client.get("analysis_%s" % analysis.id)
alert_type = 'info'
alert_msg = ''
if job_info:
job_info = loads(job_info)
job_id = job_info['job_id']
if job_id:
r_payload = r_client.get(job_id)
if r_payload:
redis_info = loads(r_client.get(job_id))
if redis_info['status_msg'] == 'running':
alert_msg = ('An artifact is being deleted from this '
'analysis')
elif redis_info['return'] is not None:
alert_type = redis_info['return']['status']
alert_msg = redis_info['return']['message'].replace(
'\n', '</br>')
artifacts = {}
for aid, samples in analysis.samples.items():
artifact = Artifact(aid)
study = artifact.study
artifacts[aid] = (study.id, study.title, artifact.merging_scheme,
samples)
return {
'analysis_name': analysis.name,
'analysis_id': analysis.id,
'analysis_is_public': analysis.is_public,
'analysis_description': analysis.description,
'analysis_mapping_id': analysis.mapping_file,
'alert_type': alert_type,
'artifacts': artifacts,
'alert_msg': alert_msg
}
def analyisis_graph_handler_get_request(analysis_id, user):
"""Returns the graph information of the analysis
Parameters
----------
analysis_id : int
The analysis id
user : qiita_db.user.User
The user performing the request
Returns
-------
dict with the graph information
Raises
------
ValueError
If there is more than one workflow in a single analysis
"""
analysis = Analysis(analysis_id)
# Check if the user actually has access to the analysis
check_analysis_access(user, analysis)
# A user has full access to the analysis if it is one of its private
# analyses, the analysis has been shared with the user or the user is a
# superuser or admin
full_access = (analysis in (user.private_analyses | user.shared_analyses)
or user.level in {'superuser', 'admin'})
nodes = []
edges = []
wf_id = None
# Loop through all the initial artifacts of the analysis
for a in analysis.artifacts:
if a.processing_parameters is None:
g = a.descendants_with_jobs
nodes, edges, a_wf_id = get_network_nodes_edges(
g, full_access, nodes=nodes, edges=edges)
if wf_id is None:
wf_id = a_wf_id
elif a_wf_id is not None and wf_id != a_wf_id:
# This should never happen, but worth having a useful message
raise ValueError('More than one workflow in a single analysis')
return {'edges': edges, 'nodes': nodes, 'workflow': wf_id}
def analysis_description_handler_get_request(analysis_id, user):
"""Returns the analysis information
Parameters
----------
analysis_id : int
The analysis id
user : qiita_db.user.User
The user performing the request
"""
analysis = Analysis(analysis_id)
check_analysis_access(user, analysis)
job_info = r_client.get("analysis_%s" % analysis.id)
alert_type = 'info'
alert_msg = ''
if job_info:
job_info = loads(job_info)
job_id = job_info['job_id']
if job_id:
r_payload = r_client.get(job_id)
if r_payload:
redis_info = loads(r_client.get(job_id))
if redis_info['status_msg'] == 'running':
alert_msg = ('An artifact is being deleted from this '
'analysis')
elif redis_info['return'] is not None:
alert_type = redis_info['return']['status']
alert_msg = redis_info['return']['message'].replace(
'\n', '</br>')
artifacts = {}
for aid, samples in analysis.samples.items():
artifact = Artifact(aid)
study = artifact.study
artifacts[aid] = (
study.id, study.title, artifact.merging_scheme, samples)
return {'analysis_name': analysis.name,
'analysis_id': analysis.id,
'analysis_is_public': analysis.is_public,
'analysis_description': analysis.description,
'analysis_mapping_id': analysis.mapping_file,
'alert_type': alert_type,
'artifacts': artifacts,
'alert_msg': alert_msg}
def post(self, analysis_id):
analysis = Analysis(analysis_id)
check_analysis_access(self.current_user, analysis)
message = ''
try:
Analysis(analysis_id).make_public()
except Exception as e:
message = str(e)
res = analysis_description_handler_get_request(
analysis_id, self.current_user)
if message:
# this will display the error message in the main banner
res['level'] = 'danger'
res['message'] = message
self.render("analysis_description.html", **res)
def analyisis_job_handler_get_request(analysis_id, user):
"""Returns the job information of the analysis
Parameters
----------
analysis_id: int
The analysis id
user : qiita_db.user.User
The user performing the request
Returns
-------
dict with the jobs information
"""
analysis = Analysis(analysis_id)
# Check if the user actually has access to the analysis
check_analysis_access(user, analysis)
return {
j.id: {'status': j.status, 'step': j.step,
'error': j.log.msg if j.log else ""}
for j in analysis.jobs}
def analysis_description_handler_get_request(analysis_id, user):
"""Returns the analysis information
Parameters
----------
analysis_id : int
The analysis id
user : qiita_db.user.User
The user performing the request
"""
analysis = Analysis(analysis_id)
check_analysis_access(user, analysis)
job_info = r_client.get("analysis_%s" % analysis.id)
alert_type = 'info'
alert_msg = ''
if job_info:
job_info = loads(job_info)
job_id = job_info['job_id']
if job_id:
r_payload = r_client.get(job_id)
if r_payload:
redis_info = loads(r_client.get(job_id))
if redis_info['status_msg'] == 'running':
alert_msg = ('An artifact is being deleted from this '
'analysis')
elif redis_info['return'] is not None:
alert_type = redis_info['return']['status']
alert_msg = redis_info['return']['message'].replace(
'\n', '</br>')
return {
'analysis_name': analysis.name,
'analysis_id': analysis.id,
'analysis_description': analysis.description,
'alert_type': alert_type,
'alert_msg': alert_msg
}
def post(self):
analysis_id = int(self.get_argument('analysis_id'))
analysis = Analysis(analysis_id)
analysis_name = analysis.name.decode('utf-8')
check_analysis_access(self.current_user, analysis)
try:
Analysis.delete(analysis_id)
msg = ("Analysis <b><i>%s</i></b> has been deleted." %
(analysis_name))
level = "success"
except Exception as e:
e = str(e)
msg = ("Couldn't remove <b><i>%s</i></b> analysis: %s" %
(analysis_name, e))
level = "danger"
LogEntry.create(
'Runtime',
"Couldn't remove analysis ID %d: %s" % (analysis_id, e))
self.redirect(u"%s/analysis/list/?level=%s&message=%s" %
(qiita_config.portal_dir, level, msg))
def test_check_analysis_access(self):
# Has access, so it allows execution
u = User('*****@*****.**')
a = Analysis(1)
check_analysis_access(u, a)
# Admin has access to everything
u = User('*****@*****.**')
check_analysis_access(u, a)
# Raises an error because it doesn't have access
u = User('*****@*****.**')
with self.assertRaises(HTTPError):
check_analysis_access(u, a)
