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(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_shared_for_study(self, study, callback):
shared_links = get_shared_links(study)
users = [u.email for u in study.shared_with]
callback((users, shared_links))
def _get_shared_for_study(self, analysis, callback):
shared_links = get_shared_links(analysis)
users = [u.email for u in analysis.shared_with]
callback((users, shared_links))
def _get_shared_for_study(self, study, callback):
shared_links = get_shared_links(study)
users = [u.email for u in study.shared_with]
callback((users, shared_links))
def _get_shared_for_study(self, analysis, callback):
shared_links = get_shared_links(analysis)
users = [u.email for u in analysis.shared_with]
callback((users, shared_links))