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']
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 _check_permissions(self, sid):
# Check general access to study
study_info = study_get_req(sid, self.current_user.id)
if study_info['status'] != 'success':
raise HTTPError(405, "%s: %s, %s" % (study_info['message'],
self.current_user.email, sid))
return Study(sid)
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']
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):
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):
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):
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, 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):
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, study_id):
study_id = int(study_id)
# Check access to study
study_info = study_get_req(study_id, self.current_user.id)
if study_info['status'] != 'success':
raise HTTPError(
405,
"%s: %s, %s" % (study_info['message'], self.current_user.email,
str(study_id)))
study = Study(study_id)
basedir = get_db_files_base_dir()
basedir_len = len(basedir) + 1
# loop over artifacts and retrieve those that we have access to
to_download = []
for a in study.artifacts():
if a.artifact_type == 'BIOM':
for i, (fid, path, data_type) in enumerate(a.filepaths):
# ignore if tgz as they could create problems and the
# raw data is in the folder
if data_type == 'tgz':
continue
if data_type == 'directory':
# If we have a directory, we actually need to list
# all the files from the directory so NGINX can
# actually download all of them
for dp, _, fps in walk(path):
for fname in fps:
fullpath = join(dp, fname)
spath = fullpath
if fullpath.startswith(basedir):
spath = fullpath[basedir_len:]
to_download.append((fullpath, spath, spath))
elif path.startswith(basedir):
spath = path[basedir_len:]
to_download.append((path, spath, spath))
else:
# We are not aware of any case that can trigger this
# situation, but we wanted to be overly cautious
# There is no test for this line cause we don't know
# how to trigger it
to_download.append((path, path, path))
for pt in a.prep_templates:
qmf = pt.qiime_map_fp
if qmf is not None:
sqmf = qmf
if qmf.startswith(basedir):
sqmf = qmf[basedir_len:]
to_download.append(
(qmf, sqmf,
'mapping_files/%s_mapping_file.txt' % a.id))
# If we don't have nginx, write a file that indicates this
all_files = '\n'.join([
"- %s /protected/%s %s" % (getsize(fp), sfp, n)
for fp, sfp, n in to_download
])
self.write("%s\n" % all_files)
zip_fn = 'study_%d_%s.zip' % (study_id,
datetime.now().strftime('%m%d%y-%H%M%S'))
self.set_header('Content-Description', 'File Transfer')
self.set_header('Expires', '0')
self.set_header('Cache-Control', 'no-cache')
self.set_header('X-Archive-Files', 'zip')
self.set_header('Content-Disposition',
'attachment; filename=%s' % zip_fn)
self.finish()
