raise ValueError("Collision among the %s field." % key)
return result[0]
if __name__ == '__main__':
xnat_url = 'http://masi.vuse.vanderbilt.edu/xnat'
api_key = rc_keys['vuiis-projectapp']
""" Initialize redcap project with url and key"""
rc_project = redcap.Project('https://redcap.vanderbilt.edu/api/', api_key)
fields_of_interest = ['request_number', 'principal_investigator',
'project_title', 'project_description', 'email']
project_data = rc_project.export_records(fields=fields_of_interest)
""" Initialize the XNAT interface """
admin_xnat = xutil.xnat()
""" Grab all existing project IDs """
existing_projects = admin_xnat.select.projects().get('id')
""" Grab all projects (with proper request codes) in redcap """
all_project_ids = [p['request_number'] for p in project_data if len(p['request_number']) > 0]
""" Find the project ids not currently in xnat """
projects_to_insert = list(set(all_project_ids) - set(existing_projects))
pis = []
print("%s: %d project(s) to be imported..." % (time.strftime('%Y-%m-%d %H:%M'), len(projects_to_insert)))
for project_id in projects_to_insert:
body += "End disk usage \n\n"
""" DCM Relay Error files """
body += "Begin Error files...\n"
for err in glob(os.path.expanduser('~/dcmrelay/*.err')):
text_lines = []
text_lines.append("Begin %s..." % err)
out, _ = tail(err, n=20)
text_lines.append(out)
text_lines.append("End %s.\n\n" % err)
body += '\n'.join(text_lines)
body += "End Error files.\n"
""" Xnat statistics """
body += "XNAT system statistics...\n"
x = xnat()
body += "# users: %d\n" % len(x.manage.users())
all_projs = x.select.projects().get()
body += "# projects: %d\n" % len(all_projs)
# There's probably a better way to do this, but for now...
all_sessions = []
for p in all_projs:
proj = x.select.project(p)
all_sessions.extend(proj.experiments().get())
body += "# sessions: %d\n" % len(all_sessions)
# We could go deeper into database if we wanted...
body += "Finish at %s" % time.strftime('%H:%M:%S')
to = ['*****@*****.**', '*****@*****.**']
sub = "XNAT Health Check %s" % time.strftime('%a %d %b %Y %H:%M')
mail(to=to, subject=sub, body=body)
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from xnat import util
if __name__ == '__main__':
x = util.xnat()
all_projs = x.select.projects().get()
print('\n'.join(all_projs))