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 = 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 _build_single_study_info(study, info, study_proc, proc_samples):
"""Clean up and add to the study info for HTML purposes
Parameters
----------
study : Study object
The study to build information for
info : dict
Information from Study.get_info
study_proc : dict of dict of lists
Dictionary keyed on study_id that lists all processed data associated
with that study. This list of processed data ids is keyed by data type
proc_samples : dict of lists
Dictionary keyed on proc_data_id that lists all samples associated with
that processed data.
Returns
-------
dict
info-information + extra information for the study,
slightly HTML formatted
"""
PI = StudyPerson(info['principal_investigator_id'])
status = study.status
if info['publication_doi'] is not None:
pmids = get_pubmed_ids_from_dois(info['publication_doi']).values()
info['pmid'] = ", ".join([pubmed_linkifier([p]) for p in pmids])
info['publication_doi'] = ", ".join(
[doi_linkifier([p]) for p in info['publication_doi']])
else:
info['publication_doi'] = ""
info['pmid'] = ""
if info["number_samples_collected"] is None:
info["number_samples_collected"] = 0
info["shared"] = _get_shared_links_for_study(study)
# raw data is any artifact that is not Demultiplexed or BIOM
info["num_raw_data"] = len([
a for a in study.artifacts()
if a.artifact_type not in ['Demultiplexed', 'BIOM']
])
info["status"] = status
info["study_id"] = study.id
info["pi"] = study_person_linkifier((PI.email, PI.name))
del info["principal_investigator_id"]
del info["email"]
# Build the proc data info list for the child row in datatable
info["proc_data_info"] = []
for data_type, proc_datas in viewitems(study_proc[study.id]):
info["proc_data_info"].extend([
_build_single_proc_data_info(pd_id, data_type, proc_samples[pd_id])
for pd_id in proc_datas
])
return info
def _build_single_study_info(study, info, study_proc, proc_samples):
"""Clean up and add to the study info for HTML purposes
Parameters
----------
study : Study object
The study to build information for
info : dict
Information from Study.get_info
study_proc : dict of dict of lists
Dictionary keyed on study_id that lists all processed data associated
with that study. This list of processed data ids is keyed by data type
proc_samples : dict of lists
Dictionary keyed on proc_data_id that lists all samples associated with
that processed data.
Returns
-------
dict
info-information + extra information for the study,
slightly HTML formatted
"""
PI = StudyPerson(info['principal_investigator_id'])
status = study.status
if info['publication_doi'] is not None:
pmids = get_pubmed_ids_from_dois(info['publication_doi']).values()
info['pmid'] = ", ".join([pubmed_linkifier([p]) for p in pmids])
info['publication_doi'] = ", ".join([doi_linkifier([p])
for p in info['publication_doi']])
else:
info['publication_doi'] = ""
info['pmid'] = ""
if info["number_samples_collected"] is None:
info["number_samples_collected"] = 0
info["shared"] = _get_shared_links_for_study(study)
# raw data is any artifact that is not Demultiplexed or BIOM
info["num_raw_data"] = len([a for a in study.artifacts()
if a.artifact_type not in ['Demultiplexed',
'BIOM']])
info["status"] = status
info["study_id"] = study.id
info["pi"] = study_person_linkifier((PI.email, PI.name))
del info["principal_investigator_id"]
del info["email"]
# Build the proc data info list for the child row in datatable
info["proc_data_info"] = []
for data_type, proc_datas in viewitems(study_proc[study.id]):
info["proc_data_info"].extend([
_build_single_proc_data_info(pd_id, data_type, proc_samples[pd_id])
for pd_id in proc_datas])
return 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, ignore):
user = self.get_argument('user')
visibility = self.get_argument('visibility')
echo = int(self.get_argument('sEcho'))
if user != self.current_user.id:
raise HTTPError(403, reason='Unauthorized search!')
if visibility not in ['user', 'public']:
raise HTTPError(400, reason='Not a valid visibility')
info = generate_study_list(self.current_user, visibility)
# linkifying data
len_info = len(info)
for i in range(len_info):
info[i]['shared'] = ", ".join([
study_person_linkifier(element)
for element in info[i]['shared']
])
ppid = [pubmed_linkifier([p]) for p in info[i]['publication_pid']]
pdoi = [doi_linkifier([p]) for p in info[i]['publication_doi']]
del info[i]['publication_pid']
del info[i]['publication_doi']
info[i]['pubs'] = ', '.join(ppid + pdoi)
info[i]['pi'] = study_person_linkifier(info[i]['pi'])
info[i]['ebi_info'] = info[i]['ebi_submission_status']
ebi_study_accession = info[i]['ebi_study_accession']
if ebi_study_accession:
info[i]['ebi_info'] = '%s (%s)' % (''.join([
EBI_LINKIFIER.format(a)
for a in ebi_study_accession.split(',')
]), info[i]['ebi_submission_status'])
# build the table json
results = {
"sEcho": echo,
"iTotalRecords": len_info,
"iTotalDisplayRecords": len_info,
"aaData": info
}
# return the json in compact form to save transmit size
self.write(dumps(results, separators=(',', ':')))
def get(self, ignore):
user = self.get_argument('user')
visibility = self.get_argument('visibility')
echo = int(self.get_argument('sEcho'))
if user != self.current_user.id:
raise HTTPError(403, reason='Unauthorized search!')
if visibility not in ['user', 'public']:
raise HTTPError(400, reason='Not a valid visibility')
info = generate_study_list(self.current_user, visibility)
# linkifying data
len_info = len(info)
for i in range(len_info):
info[i]['shared'] = ", ".join([study_person_linkifier(element)
for element in info[i]['shared']])
ppid = [pubmed_linkifier([p]) for p in info[i]['publication_pid']]
pdoi = [doi_linkifier([p]) for p in info[i]['publication_doi']]
del info[i]['publication_pid']
del info[i]['publication_doi']
info[i]['pubs'] = ', '.join(ppid + pdoi)
info[i]['pi'] = study_person_linkifier(info[i]['pi'])
info[i]['ebi_info'] = info[i]['ebi_submission_status']
ebi_study_accession = info[i]['ebi_study_accession']
if ebi_study_accession:
info[i]['ebi_info'] = '%s (%s)' % (
''.join([EBI_LINKIFIER.format(a)
for a in ebi_study_accession.split(',')]),
info[i]['ebi_submission_status'])
# build the table json
results = {
"sEcho": echo,
"iTotalRecords": len_info,
"iTotalDisplayRecords": len_info,
"aaData": info
}
# return the json in compact form to save transmit size
self.write(dumps(results, separators=(',', ':')))
def get(self, ignore):
user = self.get_argument('user')
query = self.get_argument('query')
search_type = self.get_argument('search_type')
echo = int(self.get_argument('sEcho'))
if user != self.current_user.id:
raise HTTPError(403, 'Unauthorized search!')
if search_type not in ['user', 'public']:
raise HTTPError(400, 'Not a valid search type')
if query:
# Search for samples matching the query
search = QiitaStudySearch()
try:
search(query, self.current_user)
study_proc, proc_samples, _ = search.filter_by_processed_data()
except ParseException:
self.clear()
self.set_status(400)
self.write('Malformed search query. Please read "search help" '
'and try again.')
return
except QiitaDBIncompatibleDatatypeError as e:
self.clear()
self.set_status(400)
searchmsg = ''.join(e)
self.write(searchmsg)
return
except Exception as e:
# catch any other error as generic server error
self.clear()
self.set_status(500)
self.write("Server error during search. Please try again "
"later")
LogEntry.create('Runtime', str(e),
info={'User': self.current_user.id,
'query': query})
return
else:
study_proc = proc_samples = None
info = _build_study_info(self.current_user, search_type, study_proc,
proc_samples)
# linkifying data
len_info = len(info)
for i in range(len_info):
info[i]['shared'] = ", ".join([study_person_linkifier(element)
for element in info[i]['shared']])
ppid = [pubmed_linkifier([p]) for p in info[i]['publication_pid']]
pdoi = [doi_linkifier([p]) for p in info[i]['publication_doi']]
del info[i]['publication_pid']
del info[i]['publication_doi']
info[i]['pubs'] = ', '.join(ppid + pdoi)
info[i]['pi'] = study_person_linkifier(info[i]['pi'])
info[i]['ebi_info'] = info[i]['ebi_submission_status']
ebi_study_accession = info[i]['ebi_study_accession']
if ebi_study_accession:
info[i]['ebi_info'] = '%s (%s)' % (
''.join([EBI_LINKIFIER.format(a)
for a in ebi_study_accession.split(',')]),
info[i]['ebi_submission_status'])
# build the table json
results = {
"sEcho": echo,
"iTotalRecords": len_info,
"iTotalDisplayRecords": len_info,
"aaData": info
}
# return the json in compact form to save transmit size
self.write(dumps(results, separators=(',', ':')))
def get(self, ignore):
user = self.get_argument('user')
query = self.get_argument('query')
search_type = self.get_argument('search_type')
echo = int(self.get_argument('sEcho'))
if user != self.current_user.id:
raise HTTPError(403, 'Unauthorized search!')
if search_type not in ['user', 'public']:
raise HTTPError(400, 'Not a valid search type')
if query:
# Search for samples matching the query
search = QiitaStudySearch()
try:
search(query, self.current_user)
study_proc, proc_samples, _ = search.filter_by_processed_data()
except ParseException:
self.clear()
self.set_status(400)
self.write('Malformed search query. Please read "search help" '
'and try again.')
return
except QiitaDBIncompatibleDatatypeError as e:
self.clear()
self.set_status(400)
searchmsg = ''.join(e)
self.write(searchmsg)
return
except Exception as e:
# catch any other error as generic server error
self.clear()
self.set_status(500)
self.write("Server error during search. Please try again "
"later")
LogEntry.create('Runtime',
str(e),
info={
'User': self.current_user.id,
'query': query
})
return
else:
study_proc = proc_samples = None
info = _build_study_info(self.current_user, search_type, study_proc,
proc_samples)
# linkifying data
len_info = len(info)
for i in range(len_info):
info[i]['shared'] = ", ".join([
study_person_linkifier(element)
for element in info[i]['shared']
])
ppid = [pubmed_linkifier([p]) for p in info[i]['publication_pid']]
pdoi = [doi_linkifier([p]) for p in info[i]['publication_doi']]
del info[i]['publication_pid']
del info[i]['publication_doi']
info[i]['pubs'] = ', '.join(ppid + pdoi)
info[i]['pi'] = study_person_linkifier(info[i]['pi'])
info[i]['ebi_info'] = info[i]['ebi_submission_status']
ebi_study_accession = info[i]['ebi_study_accession']
if ebi_study_accession:
info[i]['ebi_info'] = '%s (%s)' % (''.join([
EBI_LINKIFIER.format(a)
for a in ebi_study_accession.split(',')
]), info[i]['ebi_submission_status'])
# build the table json
results = {
"sEcho": echo,
"iTotalRecords": len_info,
"iTotalDisplayRecords": len_info,
"aaData": info
}
# return the json in compact form to save transmit size
self.write(dumps(results, separators=(',', ':')))
else:
study_proc = proc_samples = None
<<<<<<< HEAD
info = _build_study_info(self.current_user, study_proc=study_proc,
proc_samples=proc_samples)
=======
info = _build_study_info(self.current_user, search_type, study_proc,
proc_samples)
# linkifying data
len_info = len(info)
for i in range(len_info):
info[i]['shared'] = ", ".join([study_person_linkifier(element)
for element in info[i]['shared']])
ppid = [pubmed_linkifier([p]) for p in info[i]['publication_pid']]
pdoi = [doi_linkifier([p]) for p in info[i]['publication_doi']]
del info[i]['publication_pid']
del info[i]['publication_doi']
info[i]['pubs'] = ', '.join(ppid + pdoi)
info[i]['pi'] = study_person_linkifier(info[i]['pi'])
info[i]['ebi_info'] = info[i]['ebi_submission_status']
ebi_study_accession = info[i]['ebi_study_accession']
if ebi_study_accession:
info[i]['ebi_info'] = '%s (%s)' % (
''.join([EBI_LINKIFIER.format(a)
for a in ebi_study_accession.split(',')]),
info[i]['ebi_submission_status'])
>>>>>>> 405cbef0c9f71c620da95a0c1ba6c7d3d588b3ed
def get(self):
study_id = self.get_argument("study_id", None)
artifact_id = self.get_argument("artifact_id", None)
if study_id is None and artifact_id is None:
raise HTTPError(
422, reason='You need to specify study_id or artifact_id')
self.finish()
elif study_id is not None:
try:
study = Study(int(study_id))
except QiitaDBUnknownIDError:
raise HTTPError(422,
reason="Study %s doesn't exist" % study_id)
self.finish()
artifact_ids = [
a.id for a in study.artifacts() if a.visibility == 'public'
]
else:
try:
artifact = Artifact(int(artifact_id))
except QiitaDBUnknownIDError:
raise HTTPError(422,
reason="Artifact %s doesn't exist" %
artifact_id)
self.finish()
if artifact.visibility != 'public':
raise HTTPError(422,
reason="Artifact %s is not public" %
artifact_id)
self.finish()
study = artifact.study
if study is None:
raise HTTPError(422,
reason="Artifact %s doesn't belong to "
"a study" % artifact_id)
self.finish()
artifact_ids = [artifact.id]
if study.status != 'public':
raise HTTPError(422, reason='Not a public study')
self.finish()
study_info = study.info
study_info['study_id'] = study.id
study_info['study_title'] = study.title
study_info['shared_with'] = [s.id for s in study.shared_with]
study_info['status'] = study.status
study_info['ebi_study_accession'] = study.ebi_study_accession
study_info['ebi_submission_status'] = study.ebi_submission_status
# Clean up StudyPerson objects to string for display
email = '<a href="mailto:{email}">{name} ({affiliation})</a>'
pi = study.info['principal_investigator']
study_info['principal_investigator'] = email.format(
**{
'name': pi.name,
'email': pi.email,
'affiliation': pi.affiliation
})
study_info['owner'] = study.owner.id
# Add needed info that is not part of the initial info pull
study_info['publications'] = []
for pub, is_doi in study.publications:
if is_doi:
study_info['publications'].append(pubmed_linkifier([pub]))
else:
study_info['publications'].append(doi_linkifier([pub]))
study_info['publications'] = ', '.join(study_info['publications'])
if study_info['ebi_study_accession']:
links = ''.join([
EBI_LINKIFIER.format(a)
for a in study_info['ebi_study_accession'].split(',')
])
study_info['ebi_study_accession'] = '%s (%s)' % (
links, study_info['ebi_submission_status'])
self.render("public.html",
study_info=study_info,
artifacts_info=get_artifacts_information(
artifact_ids, False))
