def fetch_phenotips_pdf_page(request, eid):
"""
A proxy for phenotips view and edit patient pages
Notes:
- Exempting csrf here since phenotips doesn't have this support
- Each call to this endpoint is atomic, no session information is kept
between calls. Each call to this is from within a new Frame, hence no
notion of session is kept. Each is a new login into PhenoTips.
"""
try:
current_user = request.user
project_id = request.GET['project']
uname, pwd = get_uname_pwd_for_project(project_id, read_only=True)
patient_id = get_phenotips_internal_id(eid, project_id)
auth_level = get_auth_level(project_id, request.user)
if auth_level == 'unauthorized':
raise PermissionDenied
url = settings.PHENOPTIPS_BASE_URL + '/bin/export/data/' + patient_id + '?format=pdf&pdfcover=0&pdftoc=0&pdftemplate=PhenoTips.PatientSheetCode'
response, curr_session = do_authenticated_call_to_phenotips(
url, uname, pwd)
http_response = HttpResponse(response.content)
for header in response.headers.keys():
if header != 'connection' and header != 'Transfer-Encoding': # these hop-by-hop headers are not allowed by Django
http_response[header] = response.headers[header]
return http_response
except Exception as e:
print e
raise Http404
def fetch_phenotips_pdf_page(request, eid):
"""
A proxy for phenotips view and edit patient pages
Notes:
- Exempting csrf here since phenotips doesn't have this support
- Each call to this endpoint is atomic, no session information is kept
between calls. Each call to this is from within a new Frame, hence no
notion of session is kept. Each is a new login into PhenoTips.
"""
try:
current_user = request.user
project_id = request.GET['project']
uname, pwd = get_uname_pwd_for_project(project_id, read_only=True)
patient_id = get_phenotips_internal_id(eid, project_id)
auth_level = get_auth_level(project_id, request.user)
if auth_level == 'unauthorized':
raise PermissionDenied
url = settings.PHENOPTIPS_BASE_URL + '/bin/export/data/' + patient_id + '?format=pdf&pdfcover=0&pdftoc=0&pdftemplate=PhenoTips.PatientSheetCode'
response, curr_session = do_authenticated_call_to_phenotips(url, uname, pwd)
http_response = HttpResponse(response.content)
for header in response.headers.keys():
if header != 'connection' and header != 'Transfer-Encoding': # these hop-by-hop headers are not allowed by Django
http_response[header] = response.headers[header]
return http_response
except Exception as e:
print e
raise Http404
def fetch_phenotips_edit_page(request, eid):
"""
A proxy for phenotips view and edit patient pages
Note: exempting csrf here since phenotips doesn't have this support
"""
try:
current_user = request.user
# if projectID key is found in in GET, it is the first connection call from browser
if request.GET.has_key('project'):
# adding project id and patient_id to session for later use in proxying
project_id = request.GET['project']
request.session['current_project_id'] = project_id
patient_id = get_phenotips_internal_id(eid, project_id)
request.session['current_patient_id'] = patient_id
auth_level = get_auth_level(project_id, request.user)
if auth_level == 'unauthorized':
raise PermissionDenied
if auth_level == 'admin':
phenotips_uname, phenotips_pwd = get_uname_pwd_for_project(
project_id, read_only=False)
else:
phenotips_uname, phenotips_pwd = get_uname_pwd_for_project(
project_id, read_only=True)
url = settings.PHENOPTIPS_BASE_URL + '/bin/' + patient_id
if auth_level == 'admin':
url = settings.PHENOPTIPS_BASE_URL + '/bin/edit/data/' + patient_id
response, curr_session = do_authenticated_call_to_phenotips(
url, phenotips_uname, phenotips_pwd)
# save this session with PhenoTips in current seqr session to be used within it to prevent
# re-authenticating
request.session['current_phenotips_session'] = pickle.dumps(
curr_session)
http_response = HttpResponse(response.content)
for header in response.headers.keys():
http_response[header] = response.headers[header]
return http_response
# this is a subsequent call made during the opening of the frame by phenotips
# and will use session info for required variables
else:
project_id = request.session['current_project_id']
patient_id = request.session['current_patient_id']
auth_level = get_auth_level(request.session['current_project_id'],
request.user)
if auth_level == 'unauthorized':
raise PermissionDenied
if auth_level == 'admin':
phenotips_uname, phenotips_pwd = get_uname_pwd_for_project(
project_id, read_only=False)
else:
phenotips_uname, phenotips_pwd = get_uname_pwd_for_project(
project_id, read_only=True)
url = settings.PHENOPTIPS_BASE_URL + '/bin/' + patient_id
if auth_level == 'admin':
url = settings.PHENOPTIPS_BASE_URL + '/bin/edit/data/' + patient_id
if not request.GET.has_key('project'):
url += '?'
counter = 0
for param, val in request.GET.iteritems():
url += param + '=' + val
if counter < len(request.GET) - 1:
url += '&'
counter += 1
# pedigree editor is special
if 'sheet' in request.GET.keys():
url += '#'
# get back a session and a result
curr_session = pickle.loads(
request.session['current_phenotips_session'])
response, _ = do_authenticated_call_to_phenotips(
url, phenotips_uname, phenotips_pwd, curr_session)
http_response = HttpResponse(response.content)
for header in response.headers.keys():
http_response[header] = response.headers[header]
return http_response
except Exception as e:
print e
raise Http404
def fetch_phenotips_edit_page(request, eid):
"""
A proxy for phenotips view and edit patient pages
Note: exempting csrf here since phenotips doesn't have this support
"""
try:
current_user = request.user
# if projectID key is found in in GET, it is the first connection call from browser
if request.GET.has_key('project'):
# adding project id and patient_id to session for later use in proxying
project_id = request.GET['project']
request.session['current_project_id'] = project_id
patient_id = get_phenotips_internal_id(eid, project_id)
request.session['current_patient_id'] = patient_id
auth_level = get_auth_level(project_id, request.user)
if auth_level == 'unauthorized':
raise PermissionDenied
if auth_level == 'admin':
phenotips_uname, phenotips_pwd = get_uname_pwd_for_project(project_id, read_only=False)
else:
phenotips_uname, phenotips_pwd = get_uname_pwd_for_project(project_id, read_only=True)
url = settings.PHENOPTIPS_BASE_URL + '/bin/' + patient_id
if auth_level == 'admin':
url = settings.PHENOPTIPS_BASE_URL + '/bin/edit/data/' + patient_id
response, curr_session = do_authenticated_call_to_phenotips(url, phenotips_uname, phenotips_pwd)
# save this session with PhenoTips in current seqr session to be used within it to prevent
# re-authenticating
request.session['current_phenotips_session'] = pickle.dumps(curr_session)
http_response = HttpResponse(response.content)
for header in response.headers.keys():
http_response[header] = response.headers[header]
return http_response
# this is a subsequent call made during the opening of the frame by phenotips
# and will use session info for required variables
else:
project_id = request.session['current_project_id']
patient_id = request.session['current_patient_id']
auth_level = get_auth_level(request.session['current_project_id'], request.user)
if auth_level == 'unauthorized':
raise PermissionDenied
if auth_level == 'admin':
phenotips_uname, phenotips_pwd = get_uname_pwd_for_project(project_id, read_only=False)
else:
phenotips_uname, phenotips_pwd = get_uname_pwd_for_project(project_id, read_only=True)
url = settings.PHENOPTIPS_BASE_URL + '/bin/' + patient_id
if auth_level == 'admin':
url = settings.PHENOPTIPS_BASE_URL + '/bin/edit/data/' + patient_id
if not request.GET.has_key('project'):
url += '?'
counter = 0
for param, val in request.GET.iteritems():
url += param + '=' + val
if counter < len(request.GET) - 1:
url += '&'
counter += 1
# pedigree editor is special
if 'sheet' in request.GET.keys():
url += '#'
# get back a session and a result
curr_session = pickle.loads(request.session['current_phenotips_session'])
response, _ = do_authenticated_call_to_phenotips(url, phenotips_uname, phenotips_pwd, curr_session)
http_response = HttpResponse(response.content)
for header in response.headers.keys():
http_response[header] = response.headers[header]
return http_response
except Exception as e:
print e
raise Http404
