def test_check_artifact_access(self):
# "Study" artifact
a = Artifact(1)
# The user has access
u = User('*****@*****.**')
check_artifact_access(u, a)
# Admin has access to everything
admin = User('*****@*****.**')
check_artifact_access(admin, a)
# Demo user doesn't have access
demo_u = User('*****@*****.**')
with self.assertRaises(HTTPError):
check_artifact_access(demo_u, a)
# "Analysis" artifact
a = Artifact(8)
a.visibility = 'private'
check_artifact_access(u, a)
check_artifact_access(admin, a)
with self.assertRaises(HTTPError):
check_artifact_access(demo_u, a)
check_artifact_access(User('*****@*****.**'), a)
a.visibility = 'public'
check_artifact_access(demo_u, a)
def test_check_artifact_access(self):
# "Study" artifact
a = Artifact(1)
# The user has access
u = User('*****@*****.**')
check_artifact_access(u, a)
# Admin has access to everything
admin = User('*****@*****.**')
check_artifact_access(admin, a)
# Demo user doesn't have access
demo_u = User('*****@*****.**')
with self.assertRaises(HTTPError):
check_artifact_access(demo_u, a)
# "Analysis" artifact
a = Artifact(8)
a.visibility = 'private'
check_artifact_access(u, a)
check_artifact_access(admin, a)
with self.assertRaises(HTTPError):
check_artifact_access(demo_u, a)
check_artifact_access(User('*****@*****.**'), a)
a.visibility = 'public'
check_artifact_access(demo_u, a)
def artifact_status_put_req(artifact_id, user_id, visibility):
"""Set the status of the artifact given
Parameters
----------
artifact_id : int
Artifact being acted on
user_id : str
The user requesting the action
visibility : {'sandbox', 'awaiting_approval', 'private', 'public'}
What to change the visibility to
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
"""
if visibility not in get_visibilities():
return {'status': 'error',
'message': 'Unknown visibility value: %s' % visibility}
pd = Artifact(int(artifact_id))
sid = pd.study.id
access_error = check_access(sid, user_id)
if access_error:
return access_error
user = User(str(user_id))
status = 'success'
msg = 'Artifact visibility changed to %s' % visibility
# Set the approval to private if needs approval and admin
if visibility == 'private':
if not qiita_config.require_approval:
pd.visibility = 'private'
# Set the approval to private if approval not required
elif user.level == 'admin':
pd.visibility = 'private'
# Trying to set approval without admin privileges
else:
status = 'error'
msg = 'User does not have permissions to approve change'
else:
pd.visibility = visibility
LogEntry.create('Warning', '%s changed artifact %s (study %d) to %s' % (
user_id, artifact_id, sid, visibility))
return {'status': status,
'message': msg}
def approve_study(self, study, user, callback):
"""Approves the current study if and only if the current user is admin
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
"""
if _approve(user.level):
pd_id = int(self.get_argument('pd_id'))
pd = Artifact(pd_id)
pd.visibility = 'private'
_propagate_visibility(pd)
msg = "Processed data approved"
msg_level = "success"
else:
msg = ("The current user does not have permission to approve "
"the processed data")
msg_level = "danger"
callback((msg, msg_level, "processed_data_tab", pd_id, None))
def approve_study(self, study, user, callback):
"""Approves the current study if and only if the current user is admin
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
"""
if _approve(user.level):
pd_id = int(self.get_argument('pd_id'))
pd = Artifact(pd_id)
pd.visibility = 'private'
_propagate_visibility(pd)
msg = "Processed data approved"
msg_level = "success"
else:
msg = ("The current user does not have permission to approve "
"the processed data")
msg_level = "danger"
callback((msg, msg_level, "processed_data_tab", pd_id, None))
def artifact_status_put_req(artifact_id, user_id, visibility):
"""Set the status of the artifact given
Parameters
----------
artifact_id : int
Artifact being acted on
user_id : str
The user requesting the action
visibility : {'sandbox', 'awaiting_approval', 'private', 'public'}
What to change the visibility to
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
"""
if visibility not in get_visibilities():
return {'status': 'error',
'message': 'Unknown visiblity value: %s' % visibility}
pd = Artifact(int(artifact_id))
access_error = check_access(pd.study.id, user_id)
if access_error:
return access_error
user = User(str(user_id))
status = 'success'
msg = 'Artifact visibility changed to %s' % visibility
# Set the approval to private if needs approval and admin
if visibility == 'private':
if not qiita_config.require_approval:
pd.visibility = 'private'
# Set the approval to private if approval not required
elif user.level == 'admin':
pd.visibility = 'private'
# Trying to set approval without admin privileges
else:
status = 'error'
msg = 'User does not have permissions to approve change'
else:
pd.visibility = visibility
return {'status': status,
'message': msg}
def test_propagate_visibility(self):
a = Artifact(4)
a.visibility = 'public'
_propagate_visibility(a)
self.assertEqual(Artifact(1).visibility, 'public')
self.assertEqual(Artifact(2).visibility, 'public')
self.assertEqual(Artifact(4).visibility, 'public')
a.visibility = 'private'
_propagate_visibility(a)
self.assertEqual(Artifact(1).visibility, 'private')
self.assertEqual(Artifact(2).visibility, 'private')
self.assertEqual(Artifact(4).visibility, 'private')
a = Artifact(2)
a.visibility = 'public'
_propagate_visibility(a)
self.assertEqual(Artifact(1).visibility, 'private')
self.assertEqual(Artifact(2).visibility, 'private')
self.assertEqual(Artifact(4).visibility, 'private')
def test_propagate_visibility(self):
a = Artifact(4)
a.visibility = 'public'
_propagate_visibility(a)
self.assertEqual(Artifact(1).visibility, 'public')
self.assertEqual(Artifact(2).visibility, 'public')
self.assertEqual(Artifact(4).visibility, 'public')
a.visibility = 'private'
_propagate_visibility(a)
self.assertEqual(Artifact(1).visibility, 'private')
self.assertEqual(Artifact(2).visibility, 'private')
self.assertEqual(Artifact(4).visibility, 'private')
a = Artifact(2)
a.visibility = 'public'
_propagate_visibility(a)
self.assertEqual(Artifact(1).visibility, 'private')
self.assertEqual(Artifact(2).visibility, 'private')
self.assertEqual(Artifact(4).visibility, 'private')
def make_public(self, study, user, callback):
"""Makes the current study public
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
"""
pd_id = int(self.get_argument('pd_id'))
pd = Artifact(pd_id)
pd.visibility = 'public'
_propagate_visibility(pd)
msg = "Processed data set to public"
msg_level = "success"
callback((msg, msg_level, "processed_data_tab", pd_id, None))
def make_sandbox(self, study, user, callback):
"""Reverts the current study to the 'sandbox' status
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
"""
pd_id = int(self.get_argument('pd_id'))
pd = Artifact(pd_id)
pd.visibility = 'sandbox'
_propagate_visibility(pd)
msg = "Processed data reverted to sandbox"
msg_level = "success"
callback((msg, msg_level, "processed_data_tab", pd_id, None))
def request_approval(self, study, user, callback):
"""Changes the status of the current study to "awaiting_approval"
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
"""
pd_id = int(self.get_argument('pd_id'))
pd = Artifact(pd_id)
pd.visibility = 'awaiting_approval'
_propagate_visibility(pd)
msg = "Processed data sent to admin for approval"
msg_level = "success"
callback((msg, msg_level, "processed_data_tab", pd_id, None))
def make_sandbox(self, study, user, callback):
"""Reverts the current study to the 'sandbox' status
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
"""
pd_id = int(self.get_argument('pd_id'))
pd = Artifact(pd_id)
pd.visibility = 'sandbox'
_propagate_visibility(pd)
msg = "Processed data reverted to sandbox"
msg_level = "success"
callback((msg, msg_level, "processed_data_tab", pd_id, None))
def request_approval(self, study, user, callback):
"""Changes the status of the current study to "awaiting_approval"
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
"""
pd_id = int(self.get_argument('pd_id'))
pd = Artifact(pd_id)
pd.visibility = 'awaiting_approval'
_propagate_visibility(pd)
msg = "Processed data sent to admin for approval"
msg_level = "success"
callback((msg, msg_level, "processed_data_tab", pd_id, None))
def make_public(self, study, user, callback):
"""Makes the current study public
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
"""
pd_id = int(self.get_argument('pd_id'))
pd = Artifact(pd_id)
pd.visibility = 'public'
_propagate_visibility(pd)
msg = "Processed data set to public"
msg_level = "success"
callback((msg, msg_level, "processed_data_tab", pd_id, None))
def test_artifact_summary_get_request(self):
# Artifact w/o summary
obs = artifact_summary_get_request('*****@*****.**', 1)
exp_p_jobs = [[
'063e553b-327c-4818-ab4a-adfe58e49860', 'Split libraries FASTQ',
'queued', None, None
],
[
'bcc7ebcd-39c1-43e4-af2d-822e3589f14d',
'Split libraries', 'running', 'demultiplexing', None
]]
exp_files = [
(1L, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)'),
(2L, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)')
]
exp = {
'status':
'success',
'message':
'',
'name':
'Raw data 1',
'summary':
None,
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': [],
'visibility':
'private',
'buttons':
'<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public</button>'
' <button onclick="if (confirm(\'Are you sure you '
'want to revert to sandbox artifact id: 1?\')) '
'{ set_artifact_visibility(\'sandbox\', 1) }" '
'class="btn btn-primary btn-sm">Revert to '
'sandbox</button>',
'files':
exp_files,
'editable':
True,
'prep_id':
1,
'study_id':
1
}
self.assertEqual(obs, exp)
# Artifact with summary being generated
job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command(7), values_dict={'input_data': 1}))
job._set_status('queued')
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {
'status':
'success',
'message':
'',
'name':
'Raw data 1',
'summary':
None,
'job': [job.id, 'queued', None],
'processing_jobs':
exp_p_jobs,
'errored_jobs': [],
'visibility':
'private',
'buttons':
'<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public</button>'
' <button onclick="if (confirm(\'Are you sure you '
'want to revert to sandbox artifact id: 1?\')) { '
'set_artifact_visibility(\'sandbox\', 1) }" '
'class="btn btn-primary btn-sm">Revert to '
'sandbox</button>',
'files':
exp_files,
'editable':
True,
'prep_id':
1,
'study_id':
1
}
self.assertEqual(obs, exp)
# Artifact with summary
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.html_summary_fp = fp
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
exp_files.append(
(a.html_summary_fp[0],
'%s (html summary)' % basename(a.html_summary_fp[1])))
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {
'status':
'success',
'message':
'',
'name':
'Raw data 1',
'summary':
'<b>HTML TEST - not important</b>\n',
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': [],
'visibility':
'private',
'buttons':
'<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public</button>'
' <button onclick="if (confirm(\'Are you sure you '
'want to revert to sandbox artifact id: 1?\')) { '
'set_artifact_visibility(\'sandbox\', 1) }" '
'class="btn btn-primary btn-sm">Revert to '
'sandbox</button>',
'files':
exp_files,
'editable':
True,
'prep_id':
1,
'study_id':
1
}
self.assertEqual(obs, exp)
# No access
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {
'status': 'error',
'message': 'User does not have access to study'
}
self.assertEqual(obs, exp)
# A non-owner/share user can't see the files
a.visibility = 'public'
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {
'status': 'success',
'message': '',
'name': 'Raw data 1',
'summary': '<b>HTML TEST - not important</b>\n',
'job': None,
'processing_jobs': exp_p_jobs,
'errored_jobs': [],
'visibility': 'public',
'buttons': '',
'files': [],
'editable': False,
'prep_id': 1,
'study_id': 1
}
self.assertEqual(obs, exp)
def test_artifact_summary_get_request(self):
user = User('*****@*****.**')
# Artifact w/o summary
obs = artifact_summary_get_request(user, 1)
exp_p_jobs = [[
'063e553b-327c-4818-ab4a-adfe58e49860', 'Split libraries FASTQ',
'queued', None, None
],
[
'bcc7ebcd-39c1-43e4-af2d-822e3589f14d',
'Split libraries', 'running', 'demultiplexing', None
]]
exp_files = [
(1L, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)'),
(2L, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)')
]
exp = {
'name':
'Raw data 1',
'artifact_id':
1,
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_parameters': {},
'files':
exp_files,
'summary':
None,
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# Artifact with summary being generated
job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command(7), values_dict={'input_data': 1}))
job._set_status('queued')
obs = artifact_summary_get_request(user, 1)
exp = {
'name':
'Raw data 1',
'artifact_id':
1,
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_parameters': {},
'files':
exp_files,
'summary':
None,
'job': [job.id, 'queued', None],
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# Artifact with summary
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.set_html_summary(fp)
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
exp_files.append(
(a.html_summary_fp[0],
'%s (html summary)' % basename(a.html_summary_fp[1])))
exp_summary_path = relpath(a.html_summary_fp[1],
qiita_config.base_data_dir)
obs = artifact_summary_get_request(user, 1)
exp = {
'name':
'Raw data 1',
'artifact_id':
1,
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_parameters': {},
'files':
exp_files,
'summary':
exp_summary_path,
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# No access
demo_u = User('*****@*****.**')
with self.assertRaises(QiitaHTTPError):
obs = artifact_summary_get_request(demo_u, 1)
# A non-owner/share user can't see the files
a.visibility = 'public'
obs = artifact_summary_get_request(demo_u, 1)
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'visibility': 'public',
'editable': False,
'buttons': '',
'processing_parameters': {},
'files': [],
'summary': exp_summary_path,
'job': None,
'processing_jobs': exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# returnig to private
a.visibility = 'private'
# admin gets buttons
obs = artifact_summary_get_request(User('*****@*****.**'), 2)
exp_p_jobs = [[
'd19f76ee-274e-4c1b-b3a2-a12d73507c55',
'Pick closed-reference OTUs', 'error', 'generating demux file',
'Error message'
]]
exp_files = [(3L, '1_seqs.fna (preprocessed fasta)'),
(4L, '1_seqs.qual (preprocessed fastq)'),
(5L, '1_seqs.demux (preprocessed demux)')]
exp = {
'name':
'Demultiplexed 1',
'artifact_id':
2,
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 2?\')) { '
'set_artifact_visibility(\'public\', 2) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'2?\')) { set_artifact_visibility(\'sandbox\', 2) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button> <a class="btn btn-primary '
'btn-sm" href="/ebi_submission/2"><span '
'class="glyphicon glyphicon-export"></span> '
'Submit to EBI</a> <a class="btn btn-primary '
'btn-sm" href="/vamps/2"><span class="glyphicon '
'glyphicon-export"></span> Submit to VAMPS</a>'),
'processing_parameters': {
'max_barcode_errors': 1.5,
'sequence_max_n': 0,
'max_bad_run_length': 3,
'phred_offset': u'auto',
'rev_comp': False,
'phred_quality_threshold': 3,
'input_data': 1,
'rev_comp_barcode': False,
'rev_comp_mapping_barcodes': False,
'min_per_read_length_fraction': 0.75,
'barcode_type': u'golay_12'
},
'files':
exp_files,
'summary':
None,
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': []
}
self.assertEqual(obs, exp)
# analysis artifact
obs = artifact_summary_get_request(user, 8)
exp = {
'name': 'noname',
'artifact_id': 8,
'visibility': 'sandbox',
'editable': True,
'buttons': '',
'processing_parameters': {},
'files': [(27, 'biom_table.biom (biom)')],
'summary': None,
'job': None,
'processing_jobs': [],
'errored_jobs': []
}
self.assertEqual(obs, exp)
def artifact_patch_request(user,
artifact_id,
req_op,
req_path,
req_value=None,
req_from=None):
"""Modifies an attribute of the artifact
Parameters
----------
user : qiita_db.user.User
The user performing the patch operation
artifact_id : int
Id of the artifact in which the patch operation is being performed
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
Raises
------
QiitaHTTPError
If `req_op` != 'replace'
If the path parameter is incorrect
If missing req_value
If the attribute to replace is not known
"""
if req_op == 'replace':
req_path = [v for v in req_path.split('/') if v]
if len(req_path) != 1:
raise QiitaHTTPError(404, 'Incorrect path parameter')
attribute = req_path[0]
# Check if the user actually has access to the artifact
artifact = Artifact(artifact_id)
check_artifact_access(user, artifact)
if not req_value:
raise QiitaHTTPError(404, 'Missing value to replace')
if attribute == 'name':
artifact.name = req_value
return
elif attribute == 'visibility':
if req_value not in get_visibilities():
raise QiitaHTTPError(
400, 'Unknown visibility value: %s' % req_value)
# Set the approval to private if needs approval and admin
if req_value == 'private':
if not qiita_config.require_approval:
artifact.visibility = 'private'
# Set the approval to private if approval not required
elif user.level == 'admin':
artifact.visibility = 'private'
# Trying to set approval without admin privileges
else:
raise QiitaHTTPError(
403, 'User does not have permissions '
'to approve change')
else:
artifact.visibility = req_value
else:
# We don't understand the attribute so return an error
raise QiitaHTTPError(
404, 'Attribute "%s" not found. Please, '
'check the path parameter' % attribute)
else:
raise QiitaHTTPError(
400, 'Operation "%s" not supported. Current '
'supported operations: replace' % req_op)
def test_artifact_summary_get_request(self):
# Artifact w/o summary
obs = artifact_summary_get_request('*****@*****.**', 1)
exp_p_jobs = [[
'063e553b-327c-4818-ab4a-adfe58e49860', 'Split libraries FASTQ',
'queued', None, None
],
[
'bcc7ebcd-39c1-43e4-af2d-822e3589f14d',
'Split libraries', 'running', 'demultiplexing', None
]]
exp_files = [
(1L, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)'),
(2L, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)')
]
exp = {
'status':
'success',
'message':
'',
'name':
'Raw data 1',
'summary':
None,
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': [],
'visibility':
'private',
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'files':
exp_files,
'editable':
True,
'prep_id':
1,
'study_id':
1
}
self.assertEqual(obs, exp)
# Artifact with summary being generated
job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command(7), values_dict={'input_data': 1}))
job._set_status('queued')
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {
'status':
'success',
'message':
'',
'name':
'Raw data 1',
'summary':
None,
'job': [job.id, 'queued', None],
'processing_jobs':
exp_p_jobs,
'errored_jobs': [],
'visibility':
'private',
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'files':
exp_files,
'editable':
True,
'prep_id':
1,
'study_id':
1
}
self.assertEqual(obs, exp)
# Artifact with summary
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.html_summary_fp = fp
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
exp_files.append(
(a.html_summary_fp[0],
'%s (html summary)' % basename(a.html_summary_fp[1])))
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {
'status':
'success',
'message':
'',
'name':
'Raw data 1',
'summary':
'<b>HTML TEST - not important</b>\n',
'job':
None,
'processing_jobs':
exp_p_jobs,
'errored_jobs': [],
'visibility':
'private',
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'files':
exp_files,
'editable':
True,
'prep_id':
1,
'study_id':
1
}
self.assertEqual(obs, exp)
# No access
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {
'status': 'error',
'message': 'User does not have access to study'
}
self.assertEqual(obs, exp)
# A non-owner/share user can't see the files
a.visibility = 'public'
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {
'status': 'success',
'message': '',
'name': 'Raw data 1',
'summary': '<b>HTML TEST - not important</b>\n',
'job': None,
'processing_jobs': exp_p_jobs,
'errored_jobs': [],
'visibility': 'public',
'buttons': '',
'files': [],
'editable': False,
'prep_id': 1,
'study_id': 1
}
self.assertEqual(obs, exp)
# returnig to private
a.visibility = 'sandbox'
# admin gets buttons
obs = artifact_summary_get_request('*****@*****.**', 2)
exp_p_jobs = [[
'd19f76ee-274e-4c1b-b3a2-a12d73507c55',
'Pick closed-reference OTUs', 'error', 'generating demux file',
'Error message'
]]
exp_files = [(3L, '1_seqs.fna (preprocessed fasta)'),
(4L, '1_seqs.qual (preprocessed fastq)'),
(5L, '1_seqs.demux (preprocessed demux)')]
exp = {
'status':
'success',
'files':
exp_files,
'errored_jobs': [],
'editable':
True,
'visibility':
'private',
'job':
None,
'message':
'',
'name':
'Demultiplexed 1',
'processing_jobs':
exp_p_jobs,
'summary':
None,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 2?\')) { '
'set_artifact_visibility(\'public\', 2) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'2?\')) { set_artifact_visibility(\'sandbox\', 2) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button> <a class="btn btn-primary '
'btn-sm" href="/vamps/2"><span class="glyphicon '
'glyphicon-export"></span> Submit to VAMPS</a>'),
'study_id':
1,
'prep_id':
1
}
self.assertEqual(obs, exp)
def test_artifact_summary_get_request(self):
# Artifact w/o summary
obs = artifact_summary_get_request('*****@*****.**', 1)
exp_p_jobs = [
['063e553b-327c-4818-ab4a-adfe58e49860', 'Split libraries FASTQ',
'queued', None, None],
['bcc7ebcd-39c1-43e4-af2d-822e3589f14d', 'Split libraries',
'running', 'demultiplexing', None]]
exp_files = [
(1L, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)'),
(2L, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)')]
exp = {'status': 'success',
'message': '',
'name': 'Raw data 1',
'processing_parameters': {},
'summary': None,
'job': None,
'processing_jobs': exp_p_jobs,
'errored_jobs': [],
'visibility': 'private',
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'files': exp_files,
'editable': True,
'prep_id': 1,
'study_id': 1}
self.assertEqual(obs, exp)
# Artifact with summary being generated
job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command(7), values_dict={'input_data': 1})
)
job._set_status('queued')
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {'status': 'success',
'message': '',
'name': 'Raw data 1',
'processing_parameters': {},
'summary': None,
'job': [job.id, 'queued', None],
'processing_jobs': exp_p_jobs,
'errored_jobs': [],
'visibility': 'private',
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'files': exp_files,
'editable': True,
'prep_id': 1,
'study_id': 1}
self.assertEqual(obs, exp)
# Artifact with summary
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.html_summary_fp = fp
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
exp_files.append(
(a.html_summary_fp[0],
'%s (html summary)' % basename(a.html_summary_fp[1])))
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {'status': 'success',
'message': '',
'name': 'Raw data 1',
'processing_parameters': {},
'summary': '<b>HTML TEST - not important</b>\n',
'job': None,
'processing_jobs': exp_p_jobs,
'errored_jobs': [],
'visibility': 'private',
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'files': exp_files,
'editable': True,
'prep_id': 1,
'study_id': 1}
self.assertEqual(obs, exp)
# No access
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)
# A non-owner/share user can't see the files
a.visibility = 'public'
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {'status': 'success',
'message': '',
'name': 'Raw data 1',
'processing_parameters': {},
'summary': '<b>HTML TEST - not important</b>\n',
'job': None,
'processing_jobs': exp_p_jobs,
'errored_jobs': [],
'visibility': 'public',
'buttons': '',
'files': [],
'editable': False,
'prep_id': 1,
'study_id': 1}
self.assertEqual(obs, exp)
# returnig to private
a.visibility = 'sandbox'
# admin gets buttons
obs = artifact_summary_get_request('*****@*****.**', 2)
exp_p_jobs = [
['d19f76ee-274e-4c1b-b3a2-a12d73507c55',
'Pick closed-reference OTUs', 'error', 'generating demux file',
'Error message']]
exp_files = [
(3L, '1_seqs.fna (preprocessed fasta)'),
(4L, '1_seqs.qual (preprocessed fastq)'),
(5L, '1_seqs.demux (preprocessed demux)')]
exp = {'status': 'success',
'files': exp_files,
'errored_jobs': [],
'editable': True,
'visibility': 'private',
'job': None,
'message': '',
'name': 'Demultiplexed 1',
'processing_jobs': exp_p_jobs,
'processing_parameters': {
'max_barcode_errors': 1.5, 'sequence_max_n': 0,
'max_bad_run_length': 3, 'phred_offset': u'auto',
'rev_comp': False, 'phred_quality_threshold': 3,
'input_data': 1, 'rev_comp_barcode': False,
'rev_comp_mapping_barcodes': False,
'min_per_read_length_fraction': 0.75,
'barcode_type': u'golay_12'},
'summary': None,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 2?\')) { '
'set_artifact_visibility(\'public\', 2) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'2?\')) { set_artifact_visibility(\'sandbox\', 2) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button> <a class="btn btn-primary '
'btn-sm" href="/vamps/2"><span class="glyphicon '
'glyphicon-export"></span> Submit to VAMPS</a>'),
'study_id': 1,
'prep_id': 1}
self.assertEqual(obs, exp)
def test_artifact_summary_get_request(self):
user = User('*****@*****.**')
main_buttons = (
'<button onclick="if (confirm('
"\'Are you sure you want to make "
"public artifact id: 1?')) { set_artifact_visibility('public', 1) "
'}" class="btn btn-primary btn-sm">Make public</button> <button '
'onclick="if (confirm('
"'Are you sure you want to revert to "
"sandbox artifact id: 1?')) { set_artifact_visibility('sandbox', 1"
') }" class="btn btn-primary btn-sm">Revert to sandbox</button> ')
private_download_button = (
'<button class="btn btn-primary btn-sm" type="button" '
'aria-expanded="false" aria-controls="privateDownloadLink" '
'onclick="generate_private_download_link(%s)">Generate Download '
'Link</button><div class="collapse" id="privateDownloadLink"><div '
'class="card card-body" id="privateDownloadText">Generating '
'Download Link...</div></div>')
# Artifact w/o summary
obs = artifact_summary_get_request(user, 1)
exp_files = [
(1, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)',
'2125826711', '58 Bytes'),
(2, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)',
'2125826711', '58 Bytes')
]
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': main_buttons + private_download_button % 1,
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': None,
'job': None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# Artifact with summary being generated
job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command(7), values_dict={'input_data': 1}))
job._set_status('queued')
obs = artifact_summary_get_request(user, 1)
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': main_buttons + private_download_button % 1,
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': None,
'job': [job.id, 'queued', None],
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# Artifact with summary
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.set_html_summary(fp)
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
exp_files.append((a.html_summary_fp[0],
'%s (html summary)' % basename(a.html_summary_fp[1]),
'1642196267', '33 Bytes'))
exp_summary_path = relpath(a.html_summary_fp[1],
qiita_config.base_data_dir)
obs = artifact_summary_get_request(user, 1)
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': main_buttons + private_download_button % 1,
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# No access
demo_u = User('*****@*****.**')
with self.assertRaises(QiitaHTTPError):
obs = artifact_summary_get_request(demo_u, 1)
# A non-owner/share user can't see the files
a.visibility = 'public'
obs = artifact_summary_get_request(demo_u, 1)
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'public',
'editable': False,
'buttons': '',
'processing_info': {},
'files': [],
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# testing sandbox
a.visibility = 'sandbox'
obs = artifact_summary_get_request(user, 1)
exp = {
'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'sandbox',
'editable': True,
'buttons': private_download_button % 1,
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# returnig to private
a.visibility = 'private'
# admin gets buttons
obs = artifact_summary_get_request(User('*****@*****.**'), 2)
exp_files = [(3, '1_seqs.fna (preprocessed fasta)', '', '0 Bytes'),
(4, '1_seqs.qual (preprocessed fastq)', '', '0 Bytes'),
(5, '1_seqs.demux (preprocessed demux)', '', '0 Bytes')]
exp = {
'name':
'Demultiplexed 1',
'artifact_id':
2,
'artifact_type':
'Demultiplexed',
'artifact_timestamp':
'2012-10-01 10:10',
'visibility':
'private',
'editable':
True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 2?\')) { '
'set_artifact_visibility(\'public\', 2) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'2?\')) { set_artifact_visibility(\'sandbox\', 2) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button> <a class="btn btn-primary '
'btn-sm" href="/ebi_submission/2"><span '
'class="glyphicon glyphicon-export"></span> '
'Submit to EBI</a> <a class="btn btn-primary '
'btn-sm" href="/vamps/2"><span class="glyphicon '
'glyphicon-export"></span> Submit to VAMPS</a> ' +
private_download_button % 2),
'processing_info': {
'command_active': True,
'software_deprecated': False,
'command': 'Split libraries FASTQ',
'processing_parameters': {
'max_barcode_errors': '1.5',
'sequence_max_n': '0',
'max_bad_run_length': '3',
'phred_offset': 'auto',
'rev_comp': 'False',
'phred_quality_threshold': '3',
'input_data': '1',
'rev_comp_barcode': 'False',
'rev_comp_mapping_barcodes': 'False',
'min_per_read_length_fraction': '0.75',
'barcode_type': 'golay_12'
},
'software_version': '1.9.1',
'software': 'QIIME'
},
'files':
exp_files,
'is_from_analysis':
False,
'summary':
None,
'job':
None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
# analysis artifact
obs = artifact_summary_get_request(user, 8)
exp = {
'name': 'noname',
'artifact_id': 8,
'artifact_type': 'BIOM',
# this value changes on build so copy from obs
'artifact_timestamp': obs['artifact_timestamp'],
'visibility': 'sandbox',
'editable': True,
'buttons': private_download_button % 8,
'processing_info': {},
'files': [(22, 'biom_table.biom (biom)', '1756512010', '1.1 MB')],
'is_from_analysis': True,
'summary': None,
'job': None,
'errored_summary_jobs': []
}
self.assertEqual(obs, exp)
def artifact_patch_request(user,
artifact_id,
req_op,
req_path,
req_value=None,
req_from=None):
"""Modifies an attribute of the artifact
Parameters
----------
user : qiita_db.user.User
The user performing the patch operation
artifact_id : int
Id of the artifact in which the patch operation is being performed
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
Raises
------
QiitaHTTPError
If `req_op` != 'replace'
If the path parameter is incorrect
If missing req_value
If the attribute to replace is not known
"""
if req_op == 'replace':
req_path = [v for v in req_path.split('/') if v]
if len(req_path) != 1:
raise QiitaHTTPError(404, 'Incorrect path parameter')
attribute = req_path[0]
# Check if the user actually has access to the artifact
artifact = Artifact(artifact_id)
check_artifact_access(user, artifact)
if not req_value:
raise QiitaHTTPError(404, 'Missing value to replace')
if attribute == 'name':
artifact.name = req_value
return
elif attribute == 'visibility':
if req_value not in get_visibilities():
raise QiitaHTTPError(
400, 'Unknown visibility value: %s' % req_value)
if (req_value == 'private' and qiita_config.require_approval
and not user.level == 'admin'):
raise QiitaHTTPError(
403, 'User does not have permissions '
'to approve change')
try:
artifact.visibility = req_value
except Exception as e:
raise QiitaHTTPError(403, str(e).replace('\n', '<br/>'))
sid = artifact.study.id
if artifact.visibility == 'awaiting_approval':
email_to = '*****@*****.**'
subject = ('QIITA: Artifact %s awaiting_approval. Study %d, '
'Prep %d' %
(artifact_id, sid, artifact.prep_templates[0].id))
message = ('%s requested approval. <a '
'href="https://qiita.ucsd.edu/study/description/'
'%d">Study %d</a>.' % (user.email, sid, sid))
try:
send_email(email_to, subject, message)
except Exception:
msg = ("Couldn't send email to admins, please email us "
"directly to <a href='mailto:{0}'>{0}</a>.".format(
email_to))
raise QiitaHTTPError(400, msg)
else:
msg = '%s changed artifact %s (study %d) to %s' % (
user.email, artifact_id, sid, req_value)
LogEntry.create('Warning', msg)
else:
# We don't understand the attribute so return an error
raise QiitaHTTPError(
404, 'Attribute "%s" not found. Please, '
'check the path parameter' % attribute)
else:
raise QiitaHTTPError(
400, 'Operation "%s" not supported. Current '
'supported operations: replace' % req_op)
def test_artifact_summary_get_request(self):
user = User('*****@*****.**')
# Artifact w/o summary
obs = artifact_summary_get_request(user, 1)
exp_files = [
(1L, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)'),
(2L, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)')]
exp = {'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': None,
'job': None,
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
# Artifact with summary being generated
job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command(7), values_dict={'input_data': 1})
)
job._set_status('queued')
obs = artifact_summary_get_request(user, 1)
exp = {'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': None,
'job': [job.id, 'queued', None],
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
# Artifact with summary
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.set_html_summary(fp)
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
exp_files.append(
(a.html_summary_fp[0],
'%s (html summary)' % basename(a.html_summary_fp[1])))
exp_summary_path = relpath(
a.html_summary_fp[1], qiita_config.base_data_dir)
obs = artifact_summary_get_request(user, 1)
exp = {'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'private',
'editable': True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'1?\')) { set_artifact_visibility(\'sandbox\', 1) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button>'),
'processing_info': {},
'files': exp_files,
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
# No access
demo_u = User('*****@*****.**')
with self.assertRaises(QiitaHTTPError):
obs = artifact_summary_get_request(demo_u, 1)
# A non-owner/share user can't see the files
a.visibility = 'public'
obs = artifact_summary_get_request(demo_u, 1)
exp = {'name': 'Raw data 1',
'artifact_id': 1,
'artifact_type': 'FASTQ',
'artifact_timestamp': '2012-10-01 09:10',
'visibility': 'public',
'editable': False,
'buttons': '',
'processing_info': {},
'files': [],
'is_from_analysis': False,
'summary': exp_summary_path,
'job': None,
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
# returnig to private
a.visibility = 'private'
# admin gets buttons
obs = artifact_summary_get_request(User('*****@*****.**'), 2)
exp_files = [
(3L, '1_seqs.fna (preprocessed fasta)'),
(4L, '1_seqs.qual (preprocessed fastq)'),
(5L, '1_seqs.demux (preprocessed demux)')]
exp = {'name': 'Demultiplexed 1',
'artifact_id': 2,
'artifact_type': 'Demultiplexed',
'artifact_timestamp': '2012-10-01 10:10',
'visibility': 'private',
'editable': True,
'buttons': ('<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 2?\')) { '
'set_artifact_visibility(\'public\', 2) }" '
'class="btn btn-primary btn-sm">Make public'
'</button> <button onclick="if (confirm(\'Are you '
'sure you want to revert to sandbox artifact id: '
'2?\')) { set_artifact_visibility(\'sandbox\', 2) '
'}" class="btn btn-primary btn-sm">Revert to '
'sandbox</button> <a class="btn btn-primary '
'btn-sm" href="/ebi_submission/2"><span '
'class="glyphicon glyphicon-export"></span> '
'Submit to EBI</a> <a class="btn btn-primary '
'btn-sm" href="/vamps/2"><span class="glyphicon '
'glyphicon-export"></span> Submit to VAMPS</a>'),
'processing_info': {
'command': 'Split libraries FASTQ',
'software': 'QIIME',
'software_version': '1.9.1',
'processing_parameters': {
'max_barcode_errors': '1.5', 'sequence_max_n': '0',
'max_bad_run_length': '3', 'phred_offset': u'auto',
'rev_comp': 'False', 'phred_quality_threshold': '3',
'input_data': '1', 'rev_comp_barcode': 'False',
'rev_comp_mapping_barcodes': 'False',
'min_per_read_length_fraction': '0.75',
'barcode_type': u'golay_12'}},
'files': exp_files,
'is_from_analysis': False,
'summary': None,
'job': None,
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
# analysis artifact
obs = artifact_summary_get_request(user, 8)
exp = {'name': 'noname',
'artifact_id': 8,
'artifact_type': 'BIOM',
# this value changes on build so copy from obs
'artifact_timestamp': obs['artifact_timestamp'],
'visibility': 'sandbox',
'editable': True,
'buttons': '',
'processing_info': {},
'files': [(27, 'biom_table.biom (biom)')],
'is_from_analysis': True,
'summary': None,
'job': None,
'errored_summary_jobs': []}
self.assertEqual(obs, exp)
def artifact_patch_request(user, artifact_id, req_op, req_path, req_value=None,
req_from=None):
"""Modifies an attribute of the artifact
Parameters
----------
user : qiita_db.user.User
The user performing the patch operation
artifact_id : int
Id of the artifact in which the patch operation is being performed
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
Raises
------
QiitaHTTPError
If `req_op` != 'replace'
If the path parameter is incorrect
If missing req_value
If the attribute to replace is not known
"""
if req_op == 'replace':
req_path = [v for v in req_path.split('/') if v]
if len(req_path) != 1:
raise QiitaHTTPError(404, 'Incorrect path parameter')
attribute = req_path[0]
# Check if the user actually has access to the artifact
artifact = Artifact(artifact_id)
check_artifact_access(user, artifact)
if not req_value:
raise QiitaHTTPError(404, 'Missing value to replace')
if attribute == 'name':
artifact.name = req_value
return
elif attribute == 'visibility':
if req_value not in get_visibilities():
raise QiitaHTTPError(400, 'Unknown visibility value: %s'
% req_value)
if (req_value == 'private' and qiita_config.require_approval
and not user.level == 'admin'):
raise QiitaHTTPError(403, 'User does not have permissions '
'to approve change')
try:
artifact.visibility = req_value
except Exception as e:
raise QiitaHTTPError(403, str(e).replace('\n', '<br/>'))
if artifact.visibility == 'awaiting_approval':
email_to = '*****@*****.**'
sid = artifact.study.id
subject = ('QIITA: Artifact %s awaiting_approval. Study %d, '
'Prep %d' % (artifact_id, sid,
artifact.prep_templates[0].id))
message = ('%s requested approval. <a '
'href="https://qiita.ucsd.edu/study/description/'
'%d">Study %d</a>.' % (user.email, sid, sid))
try:
send_email(email_to, subject, message)
except Exception:
msg = ("Couldn't send email to admins, please email us "
"directly to <a href='mailto:{0}'>{0}</a>.".format(
email_to))
raise QiitaHTTPError(400, msg)
else:
# We don't understand the attribute so return an error
raise QiitaHTTPError(404, 'Attribute "%s" not found. Please, '
'check the path parameter' % attribute)
else:
raise QiitaHTTPError(400, 'Operation "%s" not supported. Current '
'supported operations: replace' % req_op)
def test_artifact_summary_get_request(self):
# Artifact w/o summary
obs = artifact_summary_get_request('*****@*****.**', 1)
exp_p_jobs = [
['063e553b-327c-4818-ab4a-adfe58e49860', 'Split libraries FASTQ',
'queued', None, None],
['bcc7ebcd-39c1-43e4-af2d-822e3589f14d', 'Split libraries',
'running', 'demultiplexing', None]]
exp_files = [
(1L, '1_s_G1_L001_sequences.fastq.gz (raw forward seqs)'),
(2L, '1_s_G1_L001_sequences_barcodes.fastq.gz (raw barcodes)')]
exp = {'status': 'success',
'message': '',
'name': 'Raw data 1',
'summary': None,
'job': None,
'processing_jobs': exp_p_jobs,
'errored_jobs': [],
'visibility': 'private',
'buttons': '<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public</button>'
' <button onclick="if (confirm(\'Are you sure you '
'want to revert to sandbox artifact id: 1?\')) '
'{ set_artifact_visibility(\'sandbox\', 1) }" '
'class="btn btn-primary btn-sm">Revert to '
'sandbox</button>',
'files': exp_files,
'editable': True}
self.assertEqual(obs, exp)
# Artifact with summary being generated
job = ProcessingJob.create(
User('*****@*****.**'),
Parameters.load(Command(7), values_dict={'input_data': 1})
)
job._set_status('queued')
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {'status': 'success',
'message': '',
'name': 'Raw data 1',
'summary': None,
'job': [job.id, 'queued', None],
'processing_jobs': exp_p_jobs,
'errored_jobs': [],
'visibility': 'private',
'buttons': '<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public</button>'
' <button onclick="if (confirm(\'Are you sure you '
'want to revert to sandbox artifact id: 1?\')) { '
'set_artifact_visibility(\'sandbox\', 1) }" '
'class="btn btn-primary btn-sm">Revert to '
'sandbox</button>',
'files': exp_files,
'editable': True}
self.assertEqual(obs, exp)
# Artifact with summary
fd, fp = mkstemp(suffix=".html")
close(fd)
with open(fp, 'w') as f:
f.write('<b>HTML TEST - not important</b>\n')
a = Artifact(1)
a.html_summary_fp = fp
self._files_to_remove.extend([fp, a.html_summary_fp[1]])
exp_files.append(
(a.html_summary_fp[0],
'%s (html summary)' % basename(a.html_summary_fp[1])))
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {'status': 'success',
'message': '',
'name': 'Raw data 1',
'summary': '<b>HTML TEST - not important</b>\n',
'job': None,
'processing_jobs': exp_p_jobs,
'errored_jobs': [],
'visibility': 'private',
'buttons': '<button onclick="if (confirm(\'Are you sure you '
'want to make public artifact id: 1?\')) { '
'set_artifact_visibility(\'public\', 1) }" '
'class="btn btn-primary btn-sm">Make public</button>'
' <button onclick="if (confirm(\'Are you sure you '
'want to revert to sandbox artifact id: 1?\')) { '
'set_artifact_visibility(\'sandbox\', 1) }" '
'class="btn btn-primary btn-sm">Revert to '
'sandbox</button>',
'files': exp_files,
'editable': True}
self.assertEqual(obs, exp)
# No access
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {'status': 'error',
'message': 'User does not have access to study'}
self.assertEqual(obs, exp)
# A non-owner/share user can't see the files
a.visibility = 'public'
obs = artifact_summary_get_request('*****@*****.**', 1)
exp = {'status': 'success',
'message': '',
'name': 'Raw data 1',
'summary': '<b>HTML TEST - not important</b>\n',
'job': None,
'processing_jobs': exp_p_jobs,
'errored_jobs': [],
'visibility': 'public',
'buttons': '',
'files': [],
'editable': False}
self.assertEqual(obs, exp)
def artifact_patch_request(user, artifact_id, req_op, req_path, req_value=None,
req_from=None):
"""Modifies an attribute of the artifact
Parameters
----------
user : qiita_db.user.User
The user performing the patch operation
artifact_id : int
Id of the artifact in which the patch operation is being performed
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
Raises
------
QiitaHTTPError
If `req_op` != 'replace'
If the path parameter is incorrect
If missing req_value
If the attribute to replace is not known
"""
if req_op == 'replace':
req_path = [v for v in req_path.split('/') if v]
if len(req_path) != 1:
raise QiitaHTTPError(404, 'Incorrect path parameter')
attribute = req_path[0]
# Check if the user actually has access to the artifact
artifact = Artifact(artifact_id)
check_artifact_access(user, artifact)
if not req_value:
raise QiitaHTTPError(404, 'Missing value to replace')
if attribute == 'name':
artifact.name = req_value
return
elif attribute == 'visibility':
if req_value not in get_visibilities():
raise QiitaHTTPError(400, 'Unknown visibility value: %s'
% req_value)
# Set the approval to private if needs approval and admin
if req_value == 'private':
if not qiita_config.require_approval:
artifact.visibility = 'private'
# Set the approval to private if approval not required
elif user.level == 'admin':
artifact.visibility = 'private'
# Trying to set approval without admin privileges
else:
raise QiitaHTTPError(403, 'User does not have permissions '
'to approve change')
else:
artifact.visibility = req_value
else:
# We don't understand the attribute so return an error
raise QiitaHTTPError(404, 'Attribute "%s" not found. Please, '
'check the path parameter' % attribute)
else:
raise QiitaHTTPError(400, 'Operation "%s" not supported. Current '
'supported operations: replace' % req_op)
