Merge pull request #724 from rcpch:logging

Implements more detailed logging

.gitignore

@@ -56,7 +56,7 @@ coverage.xml
 *.pot
 
 # Django stuff:
-*.log
+*.log*
 local_settings.py
 db.sqlite3
 db.sqlite3-journal
@@ -145,4 +145,4 @@ data.csv
 
 # exclude github actions local testing secret file
 .secrets
-*.csv
+*.csv

documentation/docs/development/user-groups.md

@@ -103,7 +103,7 @@ A security requirement was the ability to track user activity. This is done in a
 ```python
 @receiver(user_logged_in)
 def log_user_login(sender, request, user, **kwargs):
-    print(f'{user} ({user.email}) logged in from {get_client_ip(request)}.')
+    logger.info(f'{user} ({user.email}) logged in from {get_client_ip(request)}.')
     VisitActivity.objects.create(
         activity=1,
         ip_address=get_client_ip(request),

epilepsy12/common_view_functions/aggregate_by.py

@@ -1,5 +1,6 @@
 from typing import Literal, Union
 from datetime import date
+import logging
 
 # Django imports
 from django.apps import apps
@@ -16,11 +17,12 @@
 # E12 imports
 from epilepsy12.constants import ETHNICITIES, SEX_TYPE, EnumAbstractionLevel
 
+# Logging setup
+logger = logging.getLogger(__name__)
+
 """
 Reporting
 """
-
-
 def cases_aggregated_by_sex(selected_organisation):
     # aggregate queries on trust level cases
 
@@ -369,7 +371,7 @@ def update_kpi_aggregation_model(
                     "open_access": open_access,
                 },
             )
-            print(f"created {new_obj}")
+            logger.debug(f"created {new_obj}")
 
         else:
             new_obj, created = NationalKPIAggregation.objects.update_or_create(
@@ -383,9 +385,9 @@ def update_kpi_aggregation_model(
             )
 
             if created:
-                print(f"created {new_obj}")
+                logger.debug(f"created {new_obj}")
             else:
-                print(f"updated {new_obj}")
+                logger.debug(f"updated {new_obj}")
 
         return None
 
@@ -412,10 +414,10 @@ def update_kpi_aggregation_model(
             value_count["open_access"] = open_access
             try:
                 new_obj = AbstractionKPIAggregationModel.objects.create(**value_count)
-                print(f"created {new_obj}")
+                logger.debug(f"created {new_obj}")
             except Exception as error:
-                print(
-                    f"PUBLIC VIEW: Can't save new KPIAggregations for {abstraction_level} for {abstraction_relation_instance}: {error}"
+                logger.exception(
+                    f"Can't save new KPIAggregations for {abstraction_level} for {abstraction_relation_instance}: {error}"
                 )
                 return
 
@@ -436,15 +438,15 @@ def update_kpi_aggregation_model(
                     open_access=open_access,
                 )
             except Exception as error:
-                print(
+                logger.exception(
                     f"CLOSED VIEW: Can't update/save KPIAggregations for {abstraction_level} for {abstraction_relation_instance}: {error}"
                 )
                 return
 
             if created:
-                print(f"created {new_obj}")
+                logger.debug(f"created {new_obj}")
             else:
-                print(f"updated {new_obj}")
+                logger.debug(f"updated {new_obj}")
 
 
 def aggregate_kpis_update_models_all_abstractions_for_organisation(
@@ -688,38 +690,38 @@ def _seed_all_aggregation_models() -> None:
     ]
 
     if len(all_entities) + 1 != len(all_agg_models):
-        print(
+        logger.error(
             f"Incorrect lengths for entities. KPIAggregations not seeded. {len(all_entities)+1=}{len(all_agg_models)=}"
         )
         return
 
     for entities, AggregationModel in zip(all_entities, all_agg_models):
-        print(f"Creating aggregations for {AggregationModel}")
+        logger.info(f"Creating aggregations for {AggregationModel}")
         for entity in entities:
             if AggregationModel.objects.filter(
                 abstraction_relation=entity,
                 cohort=current_cohort,
             ).exists():
-                print(f"AggregationModel for {entity} already exists. Skipping...")
+                logger.info(f"AggregationModel for {entity} already exists. Skipping...")
                 continue
 
             new_agg_model = AggregationModel.objects.create(
                 abstraction_relation=entity,
                 cohort=current_cohort,
             )
 
-            print(f"Created {new_agg_model}")
+            logger.info(f"Created {new_agg_model}")
 
     # National handled separately as it has no abstraction relation field
     if NationalKPIAggregation.objects.filter(
         cohort=current_cohort,
     ).exists():
-        print(f"NationalKPIAggregation for {entity} already exists. Skipping...")
+        logger.info(f"NationalKPIAggregation for {entity} already exists. Skipping...")
     else:
         new_agg_model = NationalKPIAggregation.objects.create(
             cohort=current_cohort,
         )
-        print(f"Created {new_agg_model} (Cohort {current_cohort})")
+        logger.info(f"Created {new_agg_model} (Cohort {current_cohort})")
 
 
 def ___delete_and_recreate_all_kpi_aggregation_models():

epilepsy12/decorator.py

@@ -1,3 +1,6 @@
+# python imports
+import logging
+
 from django.core.exceptions import PermissionDenied
 from django.contrib.auth.decorators import login_required
 from .models import (
@@ -18,6 +21,8 @@
     Epilepsy12User,
 )
 
+# Logging setup
+logger = logging.getLogger(__name__)
 
 model_primary_keys = [
     {"id": "case_id", "model": "Case"},
@@ -404,7 +409,7 @@ def wrapper(request, *args, **kwargs):
             user = request.user
 
             if not user.is_verified():
-                print(f"{user=} is unverified. Tried accessing {view}")
+                logger.info(f"{user=} is unverified. Tried accessing {view}")
                 raise PermissionDenied()
 
             return view(request, *args, **kwargs)

epilepsy12/forms_folder/epilepsy12_user_form.py

@@ -1,4 +1,6 @@
 from typing import Any
+import logging
+
 from django import forms
 from django.conf import settings
 from django.core import validators
@@ -15,6 +17,8 @@
 )
 from ..models import Epilepsy12User, Organisation, VisitActivity
 
+# Logging setup
+logger = logging.getLogger(__name__)
 
 class Epilepsy12UserUpdatePasswordForm(SetPasswordForm):
     # form show when setting or resetting password
@@ -46,7 +50,7 @@ def save(self, *args, commit=True, **kwargs):
         user = super().save(*args, commit=False, **kwargs)
         user.password_last_set = timezone.now()
         if commit:
-            print(f"Updating password_last_set to {timezone.now()}")
+            logger.debug(f"Updating password_last_set to {timezone.now()}")
             user.save()
         return user
 

epilepsy12/general_functions/fetch_snomed.py

@@ -1,4 +1,5 @@
 # standard imports
+import logging
 import requests
 
 # third party imports
@@ -7,6 +8,9 @@
 # RCPCH imports
 from ..constants import BENZODIAZEPINE_TYPES, ANTIEPILEPSY_MEDICINE_TYPES
 
+# Logging setup
+logger = logging.getLogger(__name__)
+
 
 def fetch_ecl(ecl):
     """
@@ -16,7 +20,7 @@ def fetch_ecl(ecl):
     response = requests.get(search_url)
 
     if response.status_code == 404:
-        print("Could not get SNOMED data from server...")
+        logger.warning("Could not get SNOMED data from server...")
         return None
 
     serialised = response.json()
@@ -33,7 +37,7 @@ def fetch_concept(concept_id):
     response = requests.get(search_url)
 
     if response.status_code == 404:
-        print("Could not get SNOMED data from server...")
+        logger.warning("Could not get SNOMED data from server...")
         return None
 
     serialised = response.json()
@@ -49,7 +53,7 @@ def fetch_paediatric_neurodisability_outpatient_diagnosis_simple_reference_set()
     response = requests.get(search_url)
 
     if response.status_code == 404:
-        print("Could not get SNOMED data from server...")
+        logger.warning("Could not get SNOMED data from server...")
         return None
 
     # filters out Autism-related entries

epilepsy12/general_functions/ods_update.py

@@ -1,4 +1,5 @@
 # python imports
+import logging
 import requests
 from requests.exceptions import HTTPError
 
@@ -7,6 +8,8 @@
 from django.utils import timezone, dateformat
 from django.apps import apps
 
+# Logging setup
+logger = logging.getLogger(__name__)
 
 def fetch_updated_organisations(time_frame: int = 30):
     """
@@ -37,7 +40,7 @@ def fetch_updated_organisations(time_frame: int = 30):
         )
         response.raise_for_status()
     except HTTPError as e:
-        print(e.response.text)
+        logger.exception(e.response.text)
 
     return response.json()["Organisations"]
 
@@ -51,7 +54,7 @@ def get_organisation(org_link):
         response = requests.get(url=org_link, timeout=10)
         response.raise_for_status()
     except HTTPError as e:
-        print(e.response.text)
+        logger.exception(e.response.text)
 
     return response.json()["Organisation"]
 
@@ -108,37 +111,37 @@ def update_organisation_model_with_ORD_changes():
         ods_code = extract_ods_code(org_link=org_link["OrgLink"])
         organisation = match_organisation(ods_code=ods_code)
         if organisation:
-            print(
+            logger.info(
                 f"{index}. {ods_code} has a match with {organisation} in the E12 database"
             )
             ord_organisation_update = get_organisation(org_link["OrgLink"])
-            print(ord_organisation_update["Name"])
-            print(ord_organisation_update["GeoLoc"]["Location"]["AddrLn1"])
-            print(ord_organisation_update["GeoLoc"]["Location"]["AddrLn2"])
-            print(ord_organisation_update["GeoLoc"]["Location"]["Town"])
-            print(ord_organisation_update["GeoLoc"]["Location"]["PostCode"])
-            print(ord_organisation_update["GeoLoc"]["Location"]["Country"])
-            print(ord_organisation_update["Contacts"]["Contact"]["value"])
+            logger.info(ord_organisation_update["Name"])
+            logger.info(ord_organisation_update["GeoLoc"]["Location"]["AddrLn1"])
+            logger.info(ord_organisation_update["GeoLoc"]["Location"]["AddrLn2"])
+            logger.info(ord_organisation_update["GeoLoc"]["Location"]["Town"])
+            logger.info(ord_organisation_update["GeoLoc"]["Location"]["PostCode"])
+            logger.info(ord_organisation_update["GeoLoc"]["Location"]["Country"])
+            logger.info(ord_organisation_update["Contacts"]["Contact"]["value"])
         else:
             trust = match_trust(ods_code=ods_code)
             if trust:
-                print(
+                logger.info(
                     f"{index}. {ods_code} has a match with {trust} in the E12 database"
                 )
                 ord_trust_update = get_organisation(org_link["OrgLink"])
-                print(ord_trust_update["Name"])
-                print(ord_trust_update["GeoLoc"]["Location"]["AddrLn1"])
+                logger.info(ord_trust_update["Name"])
+                logger.info(ord_trust_update["GeoLoc"]["Location"]["AddrLn1"])
                 try:
                     line_two = ord_trust_update["GeoLoc"]["Location"]["AddrLn2"]
-                    print(line_two)
+                    logger.info(line_two)
                 except Exception:
                     pass
 
-                print(ord_trust_update["GeoLoc"]["Location"]["Town"])
-                print(ord_trust_update["GeoLoc"]["Location"]["PostCode"])
-                print(ord_trust_update["GeoLoc"]["Location"]["Country"])
+                logger.info(ord_trust_update["GeoLoc"]["Location"]["Town"])
+                logger.info(ord_trust_update["GeoLoc"]["Location"]["PostCode"])
+                logger.info(ord_trust_update["GeoLoc"]["Location"]["Country"])
                 for i in ord_trust_update["Contacts"]["Contact"]:
                     if i["type"] == "http":
-                        print(f'website: {i["value"]}')
+                        logger.info(f'website: {i["value"]}')
                     else:
-                        print(f'telephone: {i["value"]}')
+                        logger.info(f'telephone: {i["value"]}')

epilepsy12/general_functions/postcode.py

@@ -1,7 +1,11 @@
 import requests
+import logging
+
 from django.conf import settings
 from ..constants import UNKNOWN_POSTCODES_NO_SPACES
 
+# Logging setup
+logger = logging.getLogger(__name__)
 
 def is_valid_postcode(postcode: str) -> bool:
     """
@@ -23,7 +27,7 @@ def is_valid_postcode(postcode: str) -> bool:
         return True
 
     # Only other possibility should be 404, but handle any other status code
-    print(
+    logger.error(
         f"Postcode validation failure. Could not validate postcode at {url}. {response.status_code=}"
     )
     return False
@@ -36,7 +40,7 @@ def return_random_postcode(country_boundary_identifier: str):
     response = requests.get(url=url)
 
     if response.status_code == 404:
-        print("Postcode generation failure. Could not get random postcode.")
+        logger.error("Postcode generation failure. Could not get random postcode.")
         return None
 
     return response.json()["data"]["relationships"]["example_postcodes"]["data"][0][