Refactor queries

.gitignore

@@ -1,4 +1,5 @@
 project/local_settings.py
+
 media/*
 staticdev_bk/*
 templates_bk/*
@@ -9,8 +10,19 @@ templates_bk/*
 media
 Icon
 static/CACHE
-static/node_modules
+static/node_modules/
 staticdev/CACHE
 venv
 .coverage
-/static/css/.sass-cache/
+/static/css/.sass-cache/
+.venv
+.vscode
+*.pem
+Dockerfile
+.dockerignore
+.venv/*
+client-cert.pem
+client-key.pem
+server-ca.pem
+project/settings.py
+

apps/a1c_app/urls.py

@@ -14,22 +14,21 @@
 You should have received a copy of the GNU Affero General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>
 """
-from django.conf.urls import url
-
 from a1c_app.views import *
+from django.urls import re_path
 
 urlpatterns = [
-    url(r'^(?P<a1c_id>\d+)/info$', get_a1c_info),
-    url(r'^(?P<value_id>\d+)/value_info$', get_observation_value_info),
-    url(r'^(?P<a1c_id>\d+)/add_note$', add_note),
-    url(r'^(?P<component_id>\d+)/add_value$', add_value),
-    url(r'^(?P<a1c_id>\d+)/patient_refused$', patient_refused),
-    url(r'^note/(?P<note_id>\d+)/edit$', edit_note),
-    url(r'^note/(?P<note_id>\d+)/delete$', delete_note),
-    url(r'^value/(?P<value_id>\d+)/delete$', delete_value),
-    url(r'^value/(?P<value_id>\d+)/edit$', edit_value),
-    url(r'^value/(?P<value_id>\d+)/add_note$', add_value_note),
-    url(r'^value/note/(?P<note_id>\d+)/edit$', edit_value_note),
-    url(r'^value/note/(?P<note_id>\d+)/delete$', delete_value_note),
-    url(r'^(?P<a1c_id>\d+)/track/click/$', track_a1c_click),
+    re_path(r"^(?P<a1c_id>\d+)/info$", get_a1c_info),
+    re_path(r"^(?P<value_id>\d+)/value_info$", get_observation_value_info),
+    re_path(r"^(?P<a1c_id>\d+)/add_note$", add_note),
+    re_path(r"^(?P<component_id>\d+)/add_value$", add_value),
+    re_path(r"^(?P<a1c_id>\d+)/patient_refused$", patient_refused),
+    re_path(r"^note/(?P<note_id>\d+)/edit$", edit_note),
+    re_path(r"^note/(?P<note_id>\d+)/delete$", delete_note),
+    re_path(r"^value/(?P<value_id>\d+)/delete$", delete_value),
+    re_path(r"^value/(?P<value_id>\d+)/edit$", edit_value),
+    re_path(r"^value/(?P<value_id>\d+)/add_note$", add_value_note),
+    re_path(r"^value/note/(?P<note_id>\d+)/edit$", edit_value_note),
+    re_path(r"^value/note/(?P<note_id>\d+)/delete$", delete_value_note),
+    re_path(r"^(?P<a1c_id>\d+)/track/click/$", track_a1c_click),
 ]

apps/colons_app/urls.py

@@ -15,43 +15,34 @@
 along with this program.  If not, see <http://www.gnu.org/licenses/>
 """
 
-from django.conf.urls import url
-
 from colons_app.views import *
+from django.urls import re_path
 
 urlpatterns = [
-    url(r'^(?P<colon_id>\d+)/info$', get_colon_info),
-    url(r'^(?P<colon_id>\d+)/refuse$', refuse),
-    url(r'^(?P<colon_id>\d+)/not_appropriate$', not_appropriate),
-
-    url(r'^study/(?P<study_id>\d+)/info$', get_study_info),
-    url(r'^(?P<colon_id>\d+)/add_study$', add_study),
-    url(r'^(?P<study_id>\d+)/edit_study$', edit_study),
-    url(r'^(?P<study_id>\d+)/delete_study$', delete_study),
-
-    url(r'^study/(?P<study_id>\d+)/upload_image$', upload_study_image),
-    url(r'^study/(?P<study_id>\d+)/addImage$', add_study_image),
-    url(r'^study/(?P<study_id>\d+)/image/(?P<image_id>\d+)/delete$', delete_study_image),
-
-    url(r'^(?P<colon_id>\d+)/add_factor$', add_factor),
-    url(r'^(?P<colon_id>\d+)/delete_factor$', delete_factor),
-
-
-    url(r'^(?P<colon_id>\d+)/add_note$', add_note),
-    url(r'^note/(?P<note_id>\d+)/edit$', edit_note),
-    url(r'^note/(?P<note_id>\d+)/delete$', delete_note),
-
-    url(r'^(?P<colon_id>\d+)/track/click$', track_colon_click),
-
+    re_path(r"^(?P<colon_id>\d+)/info$", get_colon_info),
+    re_path(r"^(?P<colon_id>\d+)/refuse$", refuse),
+    re_path(r"^(?P<colon_id>\d+)/not_appropriate$", not_appropriate),
+    re_path(r"^study/(?P<study_id>\d+)/info$", get_study_info),
+    re_path(r"^(?P<colon_id>\d+)/add_study$", add_study),
+    re_path(r"^(?P<study_id>\d+)/edit_study$", edit_study),
+    re_path(r"^(?P<study_id>\d+)/delete_study$", delete_study),
+    re_path(r"^study/(?P<study_id>\d+)/upload_image$", upload_study_image),
+    re_path(r"^study/(?P<study_id>\d+)/addImage$", add_study_image),
+    re_path(
+        r"^study/(?P<study_id>\d+)/image/(?P<image_id>\d+)/delete$", delete_study_image
+    ),
+    re_path(r"^(?P<colon_id>\d+)/add_factor$", add_factor),
+    re_path(r"^(?P<colon_id>\d+)/delete_factor$", delete_factor),
+    re_path(r"^(?P<colon_id>\d+)/add_note$", add_note),
+    re_path(r"^note/(?P<note_id>\d+)/edit$", edit_note),
+    re_path(r"^note/(?P<note_id>\d+)/delete$", delete_note),
+    re_path(r"^(?P<colon_id>\d+)/track/click$", track_colon_click),
     # new restURL
-    url(r'^(?P<colon_id>\d+)$', get_colon_info),
-    url(r'^(?P<colon_id>\d+)/studies$', get_colon_cancer_studies),
-    url(r'^(?P<colon_id>\d+)/studies/(?P<study_id>\d+)$', colon_cancer_study),
-
-    url(r'^(?P<colon_id>\d+)/risk-factors$', get_risk_factors),
-    url(r'^(?P<colon_id>\d+)/risk-factors/(?P<risk_factor_id>\d+)$', risk_factor),
-
-    url(r'^(?P<colon_id>\d+)/notes$', get_notes),
-    url(r'^(?P<colon_id>\d+)/notes/(?P<note_id>\d+)$', note),
-
+    re_path(r"^(?P<colon_id>\d+)$", get_colon_info),
+    re_path(r"^(?P<colon_id>\d+)/studies$", get_colon_cancer_studies),
+    re_path(r"^(?P<colon_id>\d+)/studies/(?P<study_id>\d+)$", colon_cancer_study),
+    re_path(r"^(?P<colon_id>\d+)/risk-factors$", get_risk_factors),
+    re_path(r"^(?P<colon_id>\d+)/risk-factors/(?P<risk_factor_id>\d+)$", risk_factor),
+    re_path(r"^(?P<colon_id>\d+)/notes$", get_notes),
+    re_path(r"^(?P<colon_id>\d+)/notes/(?P<note_id>\d+)$", note),
 ]

apps/data_app/operations.py

@@ -14,11 +14,8 @@
 You should have received a copy of the GNU Affero General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>
 """
-from itertools import izip
-
-from django.db import connection
-
 from common.views import timeit
+from django.db import connection
 from emr.models import ObservationValue
 
 
@@ -56,7 +53,7 @@ def query_to_dicts(query_string, *query_args):
         row = cursor.fetchone()
         if row is None:
             break
-        row_dict = dict(izip(col_names, row))
+        row_dict = dict(zip(col_names, row))
         yield row_dict
     return
 

apps/data_app/urls.py

@@ -14,27 +14,33 @@
 You should have received a copy of the GNU Affero General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>
 """
-from django.conf.urls import url
-
 from data_app.views import *
+from django.urls import re_path
 
 urlpatterns = [
-    url(r'^track/click$', track_observation_click),
-    url(r'^(?P<observation_id>\d+)/info$', get_observation_info),
-    url(r'^(?P<patient_id>\d+)/(?P<value_id>\d+)/individual_data_info$', get_individual_data_info),
-    url(r'^(?P<patient_id>\d+)/get_datas$', get_datas),
-    url(r'^(?P<patient_id>\d+)/add_new_data_type$', add_new_data_type),
-    url(r'^(?P<patient_id>\d+)/(?P<observation_id>\d+)/save_data_type$', save_data_type),
-    url(r'^(?P<patient_id>\d+)/(?P<observation_id>\d+)/delete_data$', delete_data),
-    url(r'^updateOrder$', update_order),
-    url(r'^(?P<observation_id>\d+)/get_pins$', get_pins),
-    url(r'^(?P<patient_id>\d+)/pin_to_problem$', obseration_pin_to_problem),
-    url(r'^(?P<patient_id>\d+)/(?P<component_id>\d+)/add_new_data$', add_new_data),
-    url(r'^(?P<patient_id>\d+)/(?P<value_id>\d+)/delete_individual_data$', delete_individual_data),
-    url(r'^(?P<patient_id>\d+)/(?P<value_id>\d+)/save_data$', save_data),
-    url(r'^update_graph$', update_graph),
-
+    re_path(r"^track/click$", track_observation_click),
+    re_path(r"^(?P<observation_id>\d+)/info$", get_observation_info),
+    re_path(
+        r"^(?P<patient_id>\d+)/(?P<value_id>\d+)/individual_data_info$",
+        get_individual_data_info,
+    ),
+    re_path(r"^(?P<patient_id>\d+)/get_datas$", get_datas),
+    re_path(r"^(?P<patient_id>\d+)/add_new_data_type$", add_new_data_type),
+    re_path(
+        r"^(?P<patient_id>\d+)/(?P<observation_id>\d+)/save_data_type$", save_data_type
+    ),
+    re_path(r"^(?P<patient_id>\d+)/(?P<observation_id>\d+)/delete_data$", delete_data),
+    re_path(r"^updateOrder$", update_order),
+    re_path(r"^(?P<observation_id>\d+)/get_pins$", get_pins),
+    re_path(r"^(?P<patient_id>\d+)/pin_to_problem$", obseration_pin_to_problem),
+    re_path(r"^(?P<patient_id>\d+)/(?P<component_id>\d+)/add_new_data$", add_new_data),
+    re_path(
+        r"^(?P<patient_id>\d+)/(?P<value_id>\d+)/delete_individual_data$",
+        delete_individual_data,
+    ),
+    re_path(r"^(?P<patient_id>\d+)/(?P<value_id>\d+)/save_data$", save_data),
+    re_path(r"^update_graph$", update_graph),
     # Allow to edit multiple observation component value
-    url(r'^(?P<patient_id>\d+)/delete$', delete_component_values),
-    url(r'(?P<observation_id>\d+)/values$', get_observation_values),
+    re_path(r"^(?P<patient_id>\d+)/delete$", delete_component_values),
+    re_path(r"(?P<observation_id>\d+)/values$", get_observation_values),
 ]

apps/data_app/views.py

@@ -16,21 +16,37 @@
 """
 from math import pow
 
+from common.views import *
+from data_app.operations import (
+    get_observation_most_common_value,
+    get_observation_value_pair,
+)
 from django.contrib.auth.decorators import login_required
 from django.contrib.auth.models import User
 from django.db.models import *
-from rest_framework.decorators import api_view
-
-from common.views import *
-from data_app.operations import get_observation_most_common_value, get_observation_value_pair
-from emr.models import OBSERVATION_TYPES
-from emr.models import Observation, ObservationComponent, ObservationOrder, \
-    PhysicianTeam, ObservationPinToProblem, Problem, ObservationUnit, ObservationValue, \
-    Inr, UserProfile
+from emr.models import (
+    OBSERVATION_TYPES,
+    Inr,
+    Observation,
+    ObservationComponent,
+    ObservationOrder,
+    ObservationPinToProblem,
+    ObservationUnit,
+    ObservationValue,
+    PhysicianTeam,
+    Problem,
+    UserProfile,
+)
 from emr.operations import op_add_event
 from inr_app.serializers import InrSerializer
+from rest_framework.decorators import api_view
 from users_app.views import permissions_accessed
-from .serializers import ObservationSerializer, ObservationPinToProblemSerializer, ObservationValueSerializer
+
+from .serializers import (
+    ObservationPinToProblemSerializer,
+    ObservationSerializer,
+    ObservationValueSerializer,
+)
 
 
 @login_required

apps/document_app/urls.py

@@ -14,24 +14,23 @@
 You should have received a copy of the GNU Affero General Public License
 along with this program.  If not, see <http://www.gnu.org/licenses/>
 """
-from django.conf.urls import url
-
+from django.urls import re_path
 from document_app.views import *
 
 urlpatterns = [
-    url(r'^$', get_document_list),
-    url(r'^upload_document$', upload_document),
-    url(r'^info/(?P<document_id>\d+)$', document_info),
-    url(r'^pin/patient$', pin_patient_2_document),
-    url(r'^pin/label$', pin_label_2_document),
-    url(r'^remove/label$', remove_document_label),
-    url(r'^pin/todo$', pin_todo_2_document),
-    url(r'^unpin/todo$', unpin_document_todo),
-    url(r'^pin/problem$', pin_problem_2_document),
-    url(r'^unpin/problem$', unpin_document_problem),
-    url(r'^search_patient$', search_patient),
-    url(r'^(?P<patient_id>\d+)/get_pinned_document$', get_patient_document),
-    url(r'^delete/(?P<document_id>\d+)$', delete_document),
-    url(r'^remove/(?P<document_id>\d+)$', remove_document),
-    url(r'^(?P<document_id>\d+)/name$', update_name)
+    re_path(r"^$", get_document_list),
+    re_path(r"^upload_document$", upload_document),
+    re_path(r"^info/(?P<document_id>\d+)$", document_info),
+    re_path(r"^pin/patient$", pin_patient_2_document),
+    re_path(r"^pin/label$", pin_label_2_document),
+    re_path(r"^remove/label$", remove_document_label),
+    re_path(r"^pin/todo$", pin_todo_2_document),
+    re_path(r"^unpin/todo$", unpin_document_todo),
+    re_path(r"^pin/problem$", pin_problem_2_document),
+    re_path(r"^unpin/problem$", unpin_document_problem),
+    re_path(r"^search_patient$", search_patient),
+    re_path(r"^(?P<patient_id>\d+)/get_pinned_document$", get_patient_document),
+    re_path(r"^delete/(?P<document_id>\d+)$", delete_document),
+    re_path(r"^remove/(?P<document_id>\d+)$", remove_document),
+    re_path(r"^(?P<document_id>\d+)/name$", update_name),
 ]

apps/emr/middleware.py

@@ -15,13 +15,15 @@
 along with this program.  If not, see <http://www.gnu.org/licenses/>
 """
 
+from django.utils.deprecation import MiddlewareMixin
+
 from .models import AccessLog
 
 
-class AccessLogMiddleware(object):
+class AccessLogMiddleware(MiddlewareMixin):
 
     def process_request(self, request):
-        if request.user.is_authenticated() and not request.path.startswith('/list_of') and not request.path.endswith(
+        if request.user.is_authenticated and not request.path.startswith('/list_of') and not request.path.endswith(
                 '/encounter/status'):
             access_log = AccessLog(user=request.user, summary=request.path)
             access_log.save()