def _build_study_info(studytype, user=None):
"""builds list of namedtuples for study listings"""
if studytype == "private":
studylist = user.user_studies
elif studytype == "shared":
studylist = user.shared_studies
elif studytype == "public":
studylist = Study.get_by_status('public')
else:
raise IncompetentQiitaDeveloperError("Must use private, shared, "
"or public!")
StudyTuple = namedtuple(
'StudyInfo', 'id title meta_complete '
'num_samples_collected shared num_raw_data pi '
'pmids owner status')
infolist = []
for s_id in studylist:
study = Study(s_id)
status = study.status
# Just passing the email address as the name here, since
# name is not a required field in qiita.qiita_user
owner = study_person_linkifier((study.owner, study.owner))
info = study.info
PI = StudyPerson(info['principal_investigator_id'])
PI = study_person_linkifier((PI.email, PI.name))
pmids = ", ".join([pubmed_linkifier([pmid]) for pmid in study.pmids])
shared = _get_shared_links_for_study(study)
infolist.append(
StudyTuple(study.id, study.title, info["metadata_complete"],
info["number_samples_collected"], shared,
len(study.raw_data()), PI, pmids, owner, status))
return infolist
def _build_study_info(studytype, user=None):
"""builds list of namedtuples for study listings"""
if studytype == "private":
studylist = user.user_studies
elif studytype == "shared":
studylist = user.shared_studies
elif studytype == "public":
studylist = Study.get_by_status('public')
else:
raise IncompetentQiitaDeveloperError("Must use private, shared, "
"or public!")
StudyTuple = namedtuple('StudyInfo', 'id title meta_complete '
'num_samples_collected shared num_raw_data pi '
'pmids owner status')
infolist = []
for s_id in studylist:
study = Study(s_id)
status = study.status
# Just passing the email address as the name here, since
# name is not a required field in qiita.qiita_user
owner = study_person_linkifier((study.owner, study.owner))
info = study.info
PI = StudyPerson(info['principal_investigator_id'])
PI = study_person_linkifier((PI.email, PI.name))
pmids = ", ".join([pubmed_linkifier([pmid])
for pmid in study.pmids])
shared = _get_shared_links_for_study(study)
infolist.append(StudyTuple(study.id, study.title,
info["metadata_complete"],
info["number_samples_collected"],
shared, len(study.raw_data()),
PI, pmids, owner, status))
return infolist
def _get_shared_links_for_study(study):
shared = []
for person in study.shared_with:
name = person.info['name']
email = person.email
# Name is optional, so default to email if non existant
if name:
shared.append(study_person_linkifier((email, name)))
else:
shared.append(study_person_linkifier((email, email)))
return ", ".join(shared)
def _get_shared_links_for_study(study):
shared = []
for person in study.shared_with:
name = person.info['name']
email = person.email
# Name is optional, so default to email if non existant
if name:
shared.append(study_person_linkifier(
(email, name)))
else:
shared.append(study_person_linkifier(
(email, email)))
return ", ".join(shared)
def _get_shared_links_for_study(study):
shared = []
for person in study.shared_with:
person = User(person)
shared.append(study_person_linkifier(
(person.email, person.info['name'])))
return ", ".join(shared)
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 _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, 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=(',', ':')))
LogEntry.create('Runtime', str(e),
info={'User': self.current_user.id,
'query': query})
return
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)
def _build_study_info(user, results=None):
"""builds list of dicts for studies table, with all html formatted"""
# get list of studies for table
study_list = user.user_studies.union(
Study.get_by_status('public')).union(user.shared_studies)
if results is not None:
study_list = study_list.intersection(results)
if not study_list:
# No studies left so no need to continue
return []
# get info for the studies
cols = ['study_id', 'email', 'principal_investigator_id',
'pmid', 'study_title', 'metadata_complete',
'number_samples_collected', 'study_abstract']
study_info = Study.get_info(study_list, cols)
infolist = []
for row, info in enumerate(study_info):
study = Study(info['study_id'])
status = study.status
# Just passing the email address as the name here, since
# name is not a required field in qiita.qiita_user
PI = StudyPerson(info['principal_investigator_id'])
PI = study_person_linkifier((PI.email, PI.name))
if info['pmid'] is not None:
pmids = ", ".join([pubmed_linkifier([p])
for p in info['pmid']])
else:
pmids = ""
if info["number_samples_collected"] is None:
info["number_samples_collected"] = "0"
shared = _get_shared_links_for_study(study)
meta_complete_glyph = "ok" if info["metadata_complete"] else "remove"
# build the HTML elements needed for table cell
title = ("<a href='#' data-toggle='modal' "
"data-target='#study-abstract-modal' "
"onclick='fillAbstract(\"studies-table\", {0})'>"
"<span class='glyphicon glyphicon-file' "
"aria-hidden='true'></span></a> | "
"<a href='/study/description/{1}' "
"id='study{0}-title'>{2}</a>").format(
str(row), str(study.id), info["study_title"])
meta_complete = "<span class='glyphicon glyphicon-%s'></span>" % \
meta_complete_glyph
if status == 'public':
shared = "Not Available"
else:
shared = ("<span id='shared_html_{0}'>{1}</span><br/>"
"<a class='btn btn-primary btn-xs' data-toggle='modal' "
"data-target='#share-study-modal-view' "
"onclick='modify_sharing({0});'>Modify</a>".format(
study.id, shared))
infolist.append({
"checkbox": "<input type='checkbox' value='%d' />" % study.id,
"id": study.id,
"title": title,
"meta_complete": meta_complete,
"num_samples": info["number_samples_collected"],
"shared": shared,
"num_raw_data": len(study.raw_data()),
"pi": PI,
"pmid": pmids,
"status": status,
"abstract": info["study_abstract"]
})
return infolist