def proxy_post(request):
"""
To act as a proxy for POST requests from Phenotips
note: exempting csrf here since phenotips doesn't have this support
"""
try:
# print type(pickle.loads(request.session['current_phenotips_session']))
# re-construct proxy-ed URL again
url, parameters = __aggregate_url_parameters(request)
project_name = request.session['current_project_id']
uname, pwd = get_uname_pwd_for_project(project_name)
curr_session = pickle.loads(
request.session['current_phenotips_session'])
response = curr_session.post(url, data=dict(request.POST))
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]
# persist outside of PhenoTips db as well
if len(request.POST) != 0:
patient_id = request.session['current_patient_id']
__process_sync_request_helper(
patient_id, request.user, project_name, parameters,
pickle.loads(request.session['current_phenotips_session']))
return http_response
except Exception as e:
print 'proxy post error:', e
logger.error('phenotips.views:' + str(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_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 proxy_post(request):
"""
To act as a proxy for POST requests from Phenotips
note: exempting csrf here since phenotips doesn't have this support
"""
try:
# print type(pickle.loads(request.session['current_phenotips_session']))
# re-construct proxy-ed URL again
url, parameters = __aggregate_url_parameters(request)
project_name = request.session['current_project_id']
uname, pwd = get_uname_pwd_for_project(project_name)
curr_session = pickle.loads(request.session['current_phenotips_session'])
response = curr_session.post(url, data=dict(request.POST))
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]
# persist outside of PhenoTips db as well
if len(request.POST) != 0:
patient_id = request.session['current_patient_id']
__process_sync_request_helper(patient_id,
request.user.username,
project_name,
parameters,
pickle.loads(request.session['current_phenotips_session'])
)
return http_response
except Exception as e:
print 'proxy post error:', e
logger.error('phenotips.views:' + str(e))
raise Http404
def delete_these_phenotips_patient_ids(project_id, patient_ids):
"""
Deletes the input list of patient IDs
Inputs:
1.A list of patient ids (ex: [P0000138, P0000134,..]
Outputs:
A list of True/False of all patients were deleted
"""
uname, pwd = get_uname_pwd_for_project(project_id, read_only=False)
base_uri = settings.PHENOPTIPS_HOST_NAME + '/rest/patients/'
for p in patient_ids:
delete_phenotips_patient_id(project_id, p)
def generate_guid(apps, schema_editor):
# figure out which indiv. ids are unique
indiv_id_counts = collections.Counter([
indiv.indiv_id
for indiv in Individual.objects.raw('select * from base_individual')
])
non_unique_ids = set(
[indiv_id for indiv_id, count in indiv_id_counts.items() if count > 1])
for indiv in Individual.objects.raw('select * from base_individual'):
# by default, for previously-existing Individual records, set guid = just the indiv_id
indiv.guid = indiv.indiv_id
# for non-unique ids, only one of these records can be attached to a phenotips record, so check if this is it. If not, switch this to the new-style date-based guid.
if indiv.indiv_id in non_unique_ids:
print(
"non-unique id: %s. Checking if this patient is in phenotips for this project."
% indiv.indiv_id)
ok_to_use_new_guid = False
if settings.PROJECTS_WITHOUT_PHENOTIPS and indiv.project.project_id in settings.PROJECTS_WITHOUT_PHENOTIPS:
# phenotips is disabled for this project, so nothing will break if switching to the new-style guid.
ok_to_use_new_guid = True
else:
try:
admin_uname, admin_pwd = get_uname_pwd_for_project(
indiv.project.project_id)
patient_id = convert_external_id_to_internal_id(
indiv.indiv_id, admin_uname, admin_pwd)
ok_to_use_new_guid = False # patient is in phenotips, so can't use new id
print("Reusuing original id: " + str(indiv.indiv_id))
except django.db.utils.IntegrityError:
# this means the individual is not in phenotips, so switching to the new guid won't break things
# create the new guid with timestamp
ok_to_use_new_guid = True
except requests.exceptions.ConnectionError:
raw_input(
"ERROR: Could not connect to PhenoTips. Continue? ")
ok_to_use_new_guid = True
except Exception as e:
raw_input("ERROR on project: %s. %s. Continue? " %
(indiv.indiv_id, e))
ok_to_use_new_guid = True
if ok_to_use_new_guid:
indiv.guid = datetime.now().strftime("%Y%m%d_%H%M%S_%f" +
"_%s" % indiv.indiv_id)
indiv.save()
print("Set guid = " + indiv.guid)
def proxy_post(request):
"""
To act as a proxy for POST requests from Phenotips
note: exempting csrf here since phenotips doesn't have this support
"""
try:
# print type(pickle.loads(request.session['current_phenotips_session']))
# re-construct proxy-ed URL again
url, parameters = __aggregate_url_parameters(request)
project_name = request.session['current_project_id']
uname, pwd = get_uname_pwd_for_project(project_name)
curr_session = pickle.loads(request.session['current_phenotips_session'])
logger.info("===> POSTING to url: " + url)
logger.info("===> DATA: " + str(dict(request.POST)))
logger.info("===> SESSION - headers: " + str(curr_session.headers))
logger.info("===> SESSION - cookies: " + str(curr_session.cookies))
logger.info("===> SESSION - auth: " + str(curr_session.auth))
import requests
#response = requests.post(url, headers=curr_session.headers, cookies=curr_session.cookies, auth=curr_session.auth)
response = curr_session.post(url, data=dict(request.POST))
from requests_toolbelt.utils import dump
data = dump.dump_all(response)
logger.info("===> dump - original:\n" + data.decode('utf-8'))
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]
# persist outside of PhenoTips db as well
if len(request.POST) != 0:
patient_id = request.session['current_patient_id']
__process_sync_request_helper(patient_id,
request.user,
project_name,
parameters,
pickle.loads(request.session['current_phenotips_session'])
)
logger.info("===> original api - HTTP RESPONSE DICT: ")
for k,v in http_response.__dict__.items():
logger.info("===> %s: %s" % (k,v))
return http_response
except Exception as e:
print 'proxy post error:', e
logger.error('phenotips.views:' + str(e))
raise Http404
def get_phenotypes_entered_for_individual(indiv_id,project_id):
'''
Get phenotype data enterred for this individual.
Inputs:
indiv_id: an individual ID (ex: PIE-OGI855-001726)
'''
try:
uname,pwd = get_uname_pwd_for_project(project_id,read_only=True)
url = os.path.join(settings.PHENOPTIPS_HOST_NAME,'rest/patients/eid/' + indiv_id)
response = requests.get(url, auth=HTTPBasicAuth(uname,pwd))
return response.json()
except Exception as e:
print 'patient phenotype export error:',e
raise
def get_phenotypes_entered_for_individual(project_id, external_id):
"""
Get phenotype data enterred for this individual.
Inputs:
external_id: an individual ID (ex: PIE-OGI855-001726)
"""
try:
uname, pwd = get_uname_pwd_for_project(project_id, read_only=True)
url = os.path.join(settings.PHENOPTIPS_HOST_NAME,
'rest/patients/eid/' + external_id)
response = requests.get(url, auth=HTTPBasicAuth(uname, pwd))
return response.json()
except Exception as e:
print 'patient phenotype export error:', e
raise
def proxy_post(request):
"""
To act as a proxy for POST requests from Phenotips
note: exempting csrf here since phenotips doesn't have this support
"""
try:
# print type(pickle.loads(request.session['current_phenotips_session']))
# re-construct proxy-ed URL again
url, parameters = __aggregate_url_parameters(request)
project_name = request.session['current_project_id']
uname, pwd = get_uname_pwd_for_project(project_name)
curr_session = pickle.loads(
request.session['current_phenotips_session'])
logger.info("===> POSTING to url: " + url)
logger.info("===> DATA: " + str(dict(request.POST)))
logger.info("===> SESSION - headers: " + str(curr_session.headers))
logger.info("===> SESSION - cookies: " + str(curr_session.cookies))
logger.info("===> SESSION - auth: " + str(curr_session.auth))
import requests
#response = requests.post(url, headers=curr_session.headers, cookies=curr_session.cookies, auth=curr_session.auth)
response = curr_session.post(url, data=dict(request.POST))
from requests_toolbelt.utils import dump
data = dump.dump_all(response)
logger.info("===> dump - original:\n" + data.decode('utf-8'))
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]
# persist outside of PhenoTips db as well
if len(request.POST) != 0:
patient_id = request.session['current_patient_id']
__process_sync_request_helper(
patient_id, request.user, project_name, parameters,
pickle.loads(request.session['current_phenotips_session']))
logger.info("===> original api - HTTP RESPONSE DICT: ")
for k, v in http_response.__dict__.items():
logger.info("===> %s: %s" % (k, v))
return http_response
except Exception as e:
print 'proxy post error:', e
logger.error('phenotips.views:' + str(e))
raise Http404
def get_phenotypes_entered_for_individual(project_id, external_id):
"""
Get phenotype data enterred for this individual.
Inputs:
external_id: an individual ID (ex: PIE-OGI855-001726)
"""
try:
uname, pwd = get_uname_pwd_for_project(project_id, read_only=True)
url = os.path.join(settings.PHENOPTIPS_BASE_URL, 'rest/patients/eid/' + external_id)
response = requests.get(url, auth=HTTPBasicAuth(uname, pwd))
if 404 != response.status_code:
return response.json()
return {}
except Exception as e:
print 'patient phenotype export error:', e
raise
def fetch_project_phenotips_patient_ids(project_id):
'''
Find all patients IDs (external) belonging to this project
Inputs:
1. A project ID
Outputs:
1. A list of IDs (ex: P0000138) of patients belonging to this
'''
uname,pwd = get_uname_pwd_for_project(project_id,read_only=False)
url = settings.PHENOPTIPS_HOST_NAME + '/rest/patients?number=100000'
headers = {'Accept': 'application/json'}
r = requests.get(url, headers=headers, auth=(uname,pwd))
patient_data = r.json()
patient_ids=[]
for patient_summary in patient_data['patientSummaries']:
patient_ids.append(patient_summary['id'])
return patient_ids
def fetch_project_phenotips_patient_ids(project_id):
"""
Find all patients IDs (external) belonging to this project
Inputs:
1. A project ID
Outputs:
1. A list of IDs (ex: P0000138) of patients belonging to this
"""
uname, pwd = get_uname_pwd_for_project(project_id, read_only=False)
url = settings.PHENOPTIPS_BASE_URL + '/rest/patients?number=100000'
headers = {'Accept': 'application/json'}
r = requests.get(url, headers=headers, auth=(uname, pwd))
patient_data = r.json()
patient_ids = []
for patient_summary in patient_data['patientSummaries']:
patient_ids.append(patient_summary['id'])
return patient_ids
def delete_phenotips_patient_id(project_id, patient_id):
"""
Deletes a single PhenoTips patient ID
Inputs:
1. A single patient id (ex:P0000134)
Outputs:
True if success, raises exception otherwise
"""
uname, pwd = get_uname_pwd_for_project(project_id, read_only=False)
base_uri = settings.PHENOPTIPS_HOST_NAME + '/rest/patients/'
url = os.path.join(base_uri, patient_id)
print url
r = requests.delete(url, auth=(uname, pwd))
if r.status_code == 204:
print 'deleted phenotips patient', patient_id, '....'
return True
def proxy_get(request):
"""
To act as a proxy for get requests for Phenotips
Note: exempting csrf here since phenotips doesn't have this support
"""
project_name = request.session['current_project_id']
project_phenotips_uname, project_phenotips_pwd = get_uname_pwd_for_project(project_name)
try:
curr_session = pickle.loads(request.session['current_phenotips_session'])
url, parameters = __aggregate_url_parameters(request)
response = curr_session.get(url, data=request.GET)
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 'proxy get error:', e
logger.error('phenotips.views:' + str(e))
raise Http404
def proxy_get(request):
"""
To act as a proxy for get requests for Phenotips
Note: exempting csrf here since phenotips doesn't have this support
"""
project_name = request.session['current_project_id']
project_phenotips_uname, project_phenotips_pwd = get_uname_pwd_for_project(project_name)
try:
curr_session = pickle.loads(request.session['current_phenotips_session'])
url, parameters = __aggregate_url_parameters(request)
response = curr_session.get(url, data=request.GET)
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 'proxy get error:', e
logger.error('phenotips.views:' + str(e))
raise Http404
def get_phenotypes_entered_for_individual(project_id, external_id):
"""
Get phenotype data enterred for this individual.
Inputs:
external_id: an individual ID (ex: PIE-OGI855-001726)
"""
try:
uname, pwd = get_uname_pwd_for_project(project_id, read_only=True)
url = os.path.join(settings.PHENOPTIPS_HOST_NAME, 'rest/patients/eid/' + external_id)
#temp debug
print ">>> phenotips API call:",url
response = requests.get(url, auth=HTTPBasicAuth(uname, pwd))
#temp error message to track tricky bug
print ">>> phenotips API call response_state:",response.status_code,response.text
if 404 != response.status_code:
return response.json()
return {}
except Exception as e:
print 'patient phenotype export error:', e
raise
def generate_guid(apps, schema_editor):
# figure out which indiv. ids are unique
indiv_id_counts = collections.Counter([indiv.indiv_id for indiv in Individual.objects.all()])
non_unique_ids = set([indiv_id for indiv_id, count in indiv_id_counts.items() if count > 1])
for indiv in Individual.objects.all():
# by default, for previously-existing Individual records, set guid = just the indiv_id
indiv.guid = indiv.indiv_id
# for non-unique ids, only one of these records can be attached to a phenotips record, so check if this is it. If not, switch this to the new-style date-based guid.
if indiv.indiv_id in non_unique_ids:
print("non-unique id: %s. Checking if this patient is in phenotips for this project." % indiv.indiv_id )
ok_to_use_new_guid = False
if settings.PROJECTS_WITHOUT_PHENOTIPS and indiv.project.project_id in settings.PROJECTS_WITHOUT_PHENOTIPS:
# phenotips is disabled for this project, so nothing will break if switching to the new-style guid.
ok_to_use_new_guid = True
else:
try:
admin_uname, admin_pwd = get_uname_pwd_for_project(indiv.project.project_id)
patient_id = convert_external_id_to_internal_id(indiv.indiv_id, admin_uname, admin_pwd)
ok_to_use_new_guid = False # patient is in phenotips, so can't use new id
print("Reusuing original id: " + str(indiv.indiv_id))
except django.db.utils.IntegrityError:
# this means the individual is not in phenotips, so switching to the new guid won't break things
# create the new guid with timestamp
ok_to_use_new_guid = True
except requests.exceptions.ConnectionError:
raw_input("ERROR: Could not connect to PhenoTips. Continue? ")
ok_to_use_new_guid = True
except Exception as e:
raw_input("ERROR on project: %s. %s. Continue? " % (indiv.indiv_id, e))
ok_to_use_new_guid = True
if ok_to_use_new_guid:
indiv.guid = datetime.now().strftime("%Y%m%d_%H%M%S_%f" + "_%s" % indiv.indiv_id)
indiv.save()
print("Set guid = " + indiv.guid)
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
