def get(self):
study_id = self.get_argument('study_id')
study = to_int(study_id)
res = study_get_req(study, self.current_user.id)
study_info = res['study_info']
study_doi = ' '.join(
[doi_linkifier(p) for p in study_info['publications']])
email = '<a href="mailto:{email}">{name} ({affiliation})</a>'
pi = email.format(**study_info['principal_investigator'])
if study_info['lab_person']:
contact = email.format(**study_info['lab_person'])
else:
contact = None
share_access = (self.current_user.id in study_info['shared_with'] or
self.current_user.id == study_info['owner'])
ebi_info = study_info['ebi_submission_status']
if ebi_info == 'submitted':
ebi_info = ''.join([
('<a href="https://www.ebi.ac.uk/ena/data/view/{0}">{0}'
'</a></br>'.format(acc))
for acc in study_info['ebi_study_accession'].split(',')])
self.render('study_ajax/base_info.html',
study_info=study_info, publications=study_doi, pi=pi,
contact=contact, editable=res['editable'],
share_access=share_access, ebi_info=ebi_info)
def post(self, study_id, prep_id):
study = self.safe_get_study(study_id)
if study is None:
return
prep_id = to_int(prep_id)
try:
p = PrepTemplate(prep_id)
except QiitaDBUnknownIDError:
self.fail('Preparation not found', 404)
return
if p.study_id != study.id:
self.fail('Preparation ID not associated with the study', 409)
return
artifact_deets = json_decode(self.request.body)
_, upload = get_mountpoint('uploads')[0]
base = os.path.join(upload, study_id)
filepaths = [(os.path.join(base, fp), fp_type)
for fp, fp_type in artifact_deets['filepaths']]
try:
art = Artifact.create(filepaths,
artifact_deets['artifact_type'],
artifact_deets['artifact_name'],
p)
except QiitaError as e:
self.fail(str(e), 406)
return
self.write({'id': art.id})
self.set_status(201)
self.finish()
def get(self):
prep_id = to_int(self.get_argument('prep_id'))
res = prep_template_summary_get_req(prep_id, self.current_user.id)
self.render('study_ajax/prep_summary_table.html', pid=prep_id,
stats=res['summary'], editable=res['editable'])
def get(self):
study_id = self.get_argument('study_id')
study = to_int(study_id)
res = study_get_req(study, self.current_user.id)
study_info = res['study_info']
pdoi = [doi_linkifier([p]) for p in study_info['publication_doi']]
ppid = [pubmed_linkifier([p]) for p in study_info['publication_pid']]
email = '<a href="mailto:{email}">{name} ({affiliation})</a>'
pi = email.format(**study_info['principal_investigator'])
if study_info['lab_person']:
contact = email.format(**study_info['lab_person'])
else:
contact = None
share_access = (self.current_user.id in study_info['shared_with'] or
self.current_user.id == study_info['owner'])
ebi_info = study_info['ebi_submission_status']
ebi_study_accession = study_info['ebi_study_accession']
if ebi_study_accession:
links = ''.join([EBI_LINKIFIER.format(a)
for a in ebi_study_accession.split(',')])
ebi_info = '%s (%s)' % (links, study_info['ebi_submission_status'])
self.render('study_ajax/base_info.html',
study_info=study_info, publications=', '.join(pdoi + ppid),
pi=pi, contact=contact, editable=res['editable'],
share_access=share_access, ebi_info=ebi_info)
def get(self):
study_id = self.get_argument('study_id')
study = to_int(study_id)
res = study_get_req(study, self.current_user.id)
study_info = res['study_info']
study_doi = ' '.join(
[doi_linkifier(p) for p in study_info['publications']])
email = '<a href="mailto:{email}">{name} ({affiliation})</a>'
pi = email.format(**study_info['principal_investigator'])
if study_info['lab_person']:
contact = email.format(**study_info['lab_person'])
else:
contact = None
share_access = (self.current_user.id in study_info['shared_with']
or self.current_user.id == study_info['owner'])
ebi_info = study_info['ebi_submission_status']
if ebi_info == 'submitted':
ebi_info = ''.join([
('<a href="https://www.ebi.ac.uk/ena/data/view/{0}">{0}'
'</a></br>'.format(acc))
for acc in study_info['ebi_study_accession'].split(',')
])
self.render('study_ajax/base_info.html',
study_info=study_info,
publications=study_doi,
pi=pi,
contact=contact,
editable=res['editable'],
share_access=share_access,
ebi_info=ebi_info)
def get(self):
study_id = self.get_argument('study_id')
study = to_int(study_id)
res = study_get_req(study, self.current_user.id)
study_info = res['study_info']
pdoi = [doi_linkifier([p]) for p in study_info['publication_doi']]
ppid = [pubmed_linkifier([p]) for p in study_info['publication_pid']]
email = '<a href="mailto:{email}">{name} ({affiliation})</a>'
pi = email.format(**study_info['principal_investigator'])
if study_info['lab_person']:
contact = email.format(**study_info['lab_person'])
else:
contact = None
share_access = (self.current_user.id in study_info['shared_with']
or self.current_user.id == study_info['owner'])
ebi_info = study_info['ebi_submission_status']
ebi_study_accession = study_info['ebi_study_accession']
if ebi_study_accession:
links = ''.join([
EBI_LINKIFIER.format(a) for a in ebi_study_accession.split(',')
])
ebi_info = '%s (%s)' % (links, study_info['ebi_submission_status'])
self.render('study_ajax/base_info.html',
study_info=study_info,
publications=', '.join(pdoi + ppid),
pi=pi,
contact=contact,
editable=res['editable'],
share_access=share_access,
ebi_info=ebi_info)
def get(self, study_id):
study = to_int(study_id)
study_info = study_get_req(study, self.current_user.id)
if study_info['status'] != 'success':
raise HTTPError(404, study_info['message'])
self.render("study_base.html", **study_info)
def get(self):
study_id = to_int(self.get_argument('study_id'))
result = new_prep_template_get_req(study_id)
self.render('study_ajax/add_prep_template.html',
prep_files=result['prep_files'],
data_types=result['data_types'],
ontology=result['ontology'],
study_id=study_id)
def get(self):
"""Send formatted summary page of prep template"""
prep_id = to_int(self.get_argument('prep_id'))
res = prep_template_ajax_get_req(self.current_user.id, prep_id)
res['prep_id'] = prep_id
self.render('study_ajax/prep_summary.html', **res)
def get(self, study_id):
study = to_int(study_id)
study_info = study_get_req(study, self.current_user.id)
if study_info['status'] != 'success':
raise HTTPError(404, study_info['message'])
self.render("study_base.html", **study_info)
def get(self):
study_id = to_int(self.get_argument('study_id'))
result = new_prep_template_get_req(study_id)
self.render('study_ajax/add_prep_template.html',
prep_files=result['prep_files'],
data_types=result['data_types'],
ontology=result['ontology'],
study_id=study_id)
def get(self):
study_id = to_int(self.get_argument('study_id'))
atype = self.get_argument('artifact_type')
pt_id = self.get_argument('prep_template_id')
res = study_files_get_req(self.current_user.id, study_id, pt_id, atype)
self.render('study_ajax/artifact_file_selector.html', **res)
def get(self):
prep_id = to_int(self.get_argument('prep_id'))
res = prep_template_summary_get_req(prep_id, self.current_user.id)
self.render('study_ajax/prep_summary_table.html', pid=prep_id,
stats=res['summary'], editable=res['editable'],
num_samples=res['num_samples'])
def get(self):
study_id = to_int(self.get_argument('study_id'))
atype = self.get_argument('artifact_type')
pt_id = self.get_argument('prep_template_id')
res = study_files_get_req(self.current_user.id, study_id, pt_id, atype)
self.render('study_ajax/artifact_file_selector.html', **res)
def get(self):
"""Send formatted summary page of prep template"""
prep_id = to_int(self.get_argument('prep_id'))
res = prep_template_ajax_get_req(self.current_user.id, prep_id)
res['prep_id'] = prep_id
# Escape the message just in case javascript breaking characters in it
res['alert_message'] = url_escape(res['alert_message'])
self.render('study_ajax/prep_summary.html', **res)
def get(self):
"""Send formatted summary page of prep template"""
prep_id = to_int(self.get_argument('prep_id'))
res = prep_template_ajax_get_req(self.current_user.id, prep_id)
res['prep_id'] = prep_id
# Escape the message just in case javascript breaking characters in it
res['alert_message'] = url_escape(res['alert_message'])
self.render('study_ajax/prep_summary.html', **res)
def safe_get_study(self, study_id):
study_id = to_int(study_id)
s = None
try:
s = Study(study_id)
except QiitaDBUnknownIDError:
self.fail('Study not found', 404)
finally:
return s
def get(self):
study_id = to_int(self.get_argument('study_id'))
# Retrieve the prep template information for the menu
prep_info = study_prep_get_req(study_id, self.current_user.id)
# Make sure study exists
if prep_info['status'] != 'success':
raise HTTPError(404, prep_info['message'])
prep_info = prep_info['info']
self.render('study_ajax/data_type_menu.html', prep_info=prep_info,
study_id=study_id)
def get(self):
study_id = to_int(self.get_argument('study_id'))
# Retrieve the prep template information for the menu
prep_info = study_prep_get_req(study_id, self.current_user.id)
# Make sure study exists
if prep_info['status'] != 'success':
raise HTTPError(404, prep_info['message'])
prep_info = prep_info['info']
self.render('study_ajax/data_type_menu.html',
prep_info=prep_info,
study_id=study_id)
def get(self, study_id):
study = to_int(study_id)
level = self.get_argument('level', '')
message = self.get_argument('message', '')
study_info = study_get_req(study, self.current_user.id)
if study_info['status'] != 'success':
raise HTTPError(404, study_info['message'])
if message != '' and level != '':
study_info['level'] = level
study_info['message'] = message
self.render("study_base.html", **study_info)
def get(self):
artifact_id = to_int(self.get_argument('artifact_id'))
info = artifact_get_req(self.current_user.id, artifact_id)
status = info['visibility']
buttons = []
btn_base = ('<button onclick="set_admin_visibility(\'%s\', {0})" '
'class="btn btn-primary">%s</button>').format(artifact_id)
if qiita_config.require_approval:
if status == 'sandbox':
# The request approval button only appears if the processed
# data issandboxed and the qiita_config specifies that the
# approval should be requested
buttons.append(btn_base %
('awaiting_approval', 'Request approval'))
elif self.current_user.level == 'admin' and \
status == 'awaiting_approval':
# The approve processed data button only appears if the user is
# an admin, the processed data is waiting to be approved and
# the qiita config requires processed data approval
buttons.append(btn_base % ('private', 'Approve artifact'))
if status == 'private':
# The make public button only appears if the status is private
buttons.append(btn_base % ('public', 'Make public'))
# The revert to sandbox button only appears if the processed data is
# not sandboxed or public
if status not in {'sandbox', 'public'}:
buttons.append(btn_base % ('sandbox', 'Revert to sandbox'))
# Add EBI and VAMPS submission buttons if allowed
if not info['ebi_run_accessions'] and info['can_submit_ebi']:
buttons.append('<a class="btn btn-primary glyphicon '
'glyphicon-export" href="/ebi_submission/{{ppd_id}}'
'" style="word-spacing: -10px;"> Submit to EBI</a>')
if not info['is_submitted_vamps'] and \
info['can_submit_vamps']:
buttons.append('<a class="btn btn-primary glyphicon '
'glyphicon-export" href="/vamps/{{ppd_id}}" '
'style="word-spacing: -10px;"> Submit to VAMPS</a>')
# Add delete button if in sandbox status
if status == 'sandbox':
buttons = [
'<button class="btn btn-danger" '
'onclick="delete_artifact(%d)">Delete Artifact</button>' %
(artifact_id)
]
self.write(' '.join(buttons))
def get(self, study_id):
study = to_int(study_id)
level = self.get_argument('level', '')
message = self.get_argument('message', '')
study_info = study_get_req(study, self.current_user.id)
if study_info['status'] != 'success':
raise HTTPError(404, study_info['message'])
if message != '' and level != '':
study_info['level'] = level
study_info['message'] = message
self.render("study_base.html", **study_info)
def get(self):
artifact_id = to_int(self.get_argument('artifact_id'))
info = artifact_get_req(self.current_user.id, artifact_id)
status = info['visibility']
buttons = []
btn_base = ('<button onclick="set_admin_visibility(\'%s\', {0})" '
'class="btn btn-primary">%s</button>').format(artifact_id)
if qiita_config.require_approval:
if status == 'sandbox':
# The request approval button only appears if the processed
# data issandboxed and the qiita_config specifies that the
# approval should be requested
buttons.append(
btn_base % ('awaiting_approval', 'Request approval'))
elif self.current_user.level == 'admin' and \
status == 'awaiting_approval':
# The approve processed data button only appears if the user is
# an admin, the processed data is waiting to be approved and
# the qiita config requires processed data approval
buttons.append(btn_base % ('private', 'Approve artifact'))
if status == 'private':
# The make public button only appears if the status is private
buttons.append(btn_base % ('public', 'Make public'))
# The revert to sandbox button only appears if the processed data is
# not sandboxed or public
if status not in {'sandbox', 'public'}:
buttons.append(btn_base % ('sandbox', 'Revert to sandbox'))
# Add EBI and VAMPS submission buttons if allowed
if not info['ebi_run_accessions'] and info['can_submit_ebi']:
buttons.append('<a class="btn btn-primary glyphicon '
'glyphicon-export" href="/ebi_submission/{{ppd_id}}'
'" style="word-spacing: -10px;"> Submit to EBI</a>')
if not info['is_submitted_vamps'] and \
info['can_submit_vamps']:
buttons.append('<a class="btn btn-primary glyphicon '
'glyphicon-export" href="/vamps/{{ppd_id}}" '
'style="word-spacing: -10px;"> Submit to VAMPS</a>')
# Add delete button if in sandbox status
if status == 'sandbox':
buttons = ['<button class="btn btn-danger" '
'onclick="delete_artifact(%d)">Delete Artifact</button>'
% (artifact_id)]
self.write(' '.join(buttons))
def patch(self, study_id):
"""Patches a prep template in the system
Follows the JSON PATCH specification:
https://tools.ietf.org/html/rfc6902
"""
study_id = to_int(study_id)
req_op = self.get_argument('op')
req_path = self.get_argument('path')
req_value = self.request.arguments.get('value[]', [])
req_form = self.get_argument('form', None)
response = study_tags_patch_request(
self.current_user.id, study_id, req_op, req_path,
req_value, req_form)
self.write(response)
def patch(self, study_id):
"""Patches a prep template in the system
Follows the JSON PATCH specification:
https://tools.ietf.org/html/rfc6902
"""
study_id = to_int(study_id)
req_op = self.get_argument('op')
req_path = self.get_argument('path')
req_value = self.request.arguments.get('value[]', [])
req_form = self.get_argument('form', None)
response = study_tags_patch_request(self.current_user.id, study_id,
req_op, req_path, req_value,
req_form)
self.write(response)
def patch(self, study_id):
"""Patches a study in the system
Follows the JSON PATCH specification:
https://tools.ietf.org/html/rfc6902
"""
study_id = to_int(study_id)
data = json_decode(self.request.body)
req_op = data.get('op')
req_path = data.get('path')
req_value = data.get('value')
req_from = data.get('from', None)
response = study_patch_request(self.current_user.id, study_id,
req_op, req_path, req_value, req_from)
self.write(response)
def patch(self, study_id):
"""Patches a study in the system
Follows the JSON PATCH specification:
https://tools.ietf.org/html/rfc6902
"""
study_id = to_int(study_id)
data = json_decode(self.request.body)
req_op = data.get('op')
req_path = data.get('path')
req_value = data.get('value')
req_from = data.get('from', None)
response = study_patch_request(self.current_user.id, study_id, req_op,
req_path, req_value, req_from)
self.write(response)
def get(self):
study_id = self.get_argument('study_id')
study = to_int(study_id)
res = study_get_req(study, self.current_user.id)
study_info = res['study_info']
study_doi = ' '.join(
[doi_linkifier(p) for p in study_info['publications']])
email = '<a href="mailto:{email}">{name} ({affiliation})</a>'
pi = email.format(**study_info['principal_investigator'])
if study_info['lab_person']:
contact = email.format(**study_info['lab_person'])
else:
contact = None
self.render('study_ajax/base_info.html',
study_info=study_info, publications=study_doi, pi=pi,
contact=contact, editable=res['editable'])
def get(self):
artifact_id = to_int(self.get_argument('artifact_id'))
name = artifact_get_req(self.current_user.id, artifact_id)['name']
self.write(name)
def get(self, artifact_id):
# Check if the user has access to the artifact
artifact_id = to_int(artifact_id)
res = process_artifact_handler_get_req(artifact_id)
self.render('artifact_ajax/processing_artifact.html', **res)
def get(self, study_id):
study_id = to_int(study_id)
response = study_get_tags_request(self.current_user.id, study_id)
self.write(response)
def get(self):
artifact_id = to_int(self.get_argument('artifact_id'))
name = artifact_get_req(self.current_user.id, artifact_id)['name']
self.write(name)
def get(self):
prep = to_int(self.get_argument('prep_id'))
self.write(prep_template_graph_get_req(prep, self.current_user.id))
def post(self):
artifact_id = to_int(self.get_argument('artifact_id'))
self.write(artifact_delete_req(artifact_id, self.current_user.id))
def get(self):
artifact_id = to_int(self.get_argument('artifact_id'))
res = process_artifact_handler_get_req(artifact_id)
res['artifact_id'] = artifact_id
self.render('study_ajax/processing_artifact.html', **res)
def post(self):
artifact_id = to_int(self.get_argument('artifact_id'))
self.write(artifact_delete_req(artifact_id, self.current_user.id))
def get(self):
prep = to_int(self.get_argument('prep_id'))
self.write(prep_template_graph_get_req(prep, self.current_user.id))
def get(self):
user_id = self.current_user.id
study_id = to_int(self.get_argument('study_id'))
result = analyses_associated_with_study(study_id, user_id)
self.render('study_ajax/study_analyses.html',
analyses=result['values'])
def get(self):
artifact_id = to_int(self.get_argument('artifact_id'))
res = process_artifact_handler_get_req(artifact_id)
res['artifact_id'] = artifact_id
self.render('study_ajax/processing_artifact.html', **res)
def get(self, analysis_id):
analysis_id = to_int(analysis_id)
response = analyisis_job_handler_get_request(
analysis_id, self.current_user)
self.write(response)
def get(self):
direction = self.get_argument('direction')
artifact = to_int(self.get_argument('artifact_id'))
self.write(artifact_graph_get_req(artifact, direction,
self.current_user.id))
def get(self):
direction = self.get_argument('direction')
artifact = to_int(self.get_argument('artifact_id'))
self.write(
artifact_graph_get_req(artifact, direction, self.current_user.id))
def get(self, analysis_id):
analysis_id = to_int(analysis_id)
response = analyisis_job_handler_get_request(
analysis_id, self.current_user)
self.write(response)
def get(self, study_id):
study_id = to_int(study_id)
response = study_get_tags_request(self.current_user.id, study_id)
self.write(response)