diff --git a/.dockerignore b/.dockerignore
index f86479bc7e23f02f6a2fbc981fa2d3ed3b2599aa..0e6eb27466cb61ff5c9c5e396a137fa40bcc1b75 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -1,7 +1,10 @@
env*
+smash/*.txt
+smash/*.sqlite3
**/*.pyc
.vscode/*
Dockerfile
docker-compose.yml
**/__pycache__/*
smash/__pycache__/*
+*.pem
diff --git a/.gitignore b/.gitignore
index c6232b596b3b16d1a71ce5b18d9955ead3f5b132..54229cf8866b6933833500c015ed4342c33d1ad3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -51,3 +51,5 @@ rpm
#OS generated folders
**/.DS_Store
+
+*.pem
\ No newline at end of file
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 2b5b1c58467f3f6778429f98d013fba236f4952d..1020eb338b7b49147818f5682726f24cb26df7df 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -7,6 +7,10 @@ variables:
POSTGRES_DB: smash
POSTGRES_USER: runner
POSTGRES_PASSWORD: password
+ MARIADB_USER: runner
+ MARIADB_PASSWORD: password
+ MARIADB_ROOT_PASSWORD: password
+ MARIADB_DATABASE: dbtest
gemnasium-python-dependency_scanning:
before_script:
@@ -15,7 +19,7 @@ gemnasium-python-dependency_scanning:
.test_template: &test_definition
stage: test
before_script:
- - apt-get update && apt-get install -y --allow-unauthenticated libsasl2-dev libssl-dev locales locales-all libsasl2-dev libldap2-dev libssl-dev
+ - apt-get update && apt-get install -y --allow-unauthenticated libsasl2-dev libssl-dev locales locales-all libsasl2-dev libldap2-dev libssl-dev default-libmysqlclient-dev
- python -V
- pip install --upgrade pip --default-timeout=180 -i https://repomanager.lcsb.uni.lu/repository/pypi-proxy/simple/ --extra-index-url https://pypi.python.org/simple/
@@ -24,7 +28,7 @@ gemnasium-python-dependency_scanning:
- pip install -r requirements-dev.txt --default-timeout=180 -i https://repomanager.lcsb.uni.lu/repository/pypi-proxy/simple/ --extra-index-url https://pypi.python.org/simple/
-test_migrations_created:
+test_migrations_created_postgres:
<<: *test_definition
services:
- postgres:latest
@@ -34,6 +38,16 @@ test_migrations_created:
- python manage.py makemigrations --check --dry-run
- test 1 = $(python manage.py makemigrations --check --dry-run | grep 'No changes detected' |wc -l)
+test_migrations_created_mariadb:
+ <<: *test_definition
+ services:
+ - mariadb:10.6-ubi
+ script:
+ - cp "local_settings_ci_mariadb.py" "smash/smash/local_settings.py"
+ - cd smash
+ - python manage.py makemigrations --check --dry-run
+ - test 1 = $(python manage.py makemigrations --check --dry-run | grep 'No changes detected' |wc -l)
+
test_postgres:
<<: *test_definition
services:
@@ -44,6 +58,18 @@ test_postgres:
- coverage run --source web manage.py test -v3
- coverage report -m --omit="*/test*,*/migrations*,*debug_utils*"
+test_mariadb:
+ <<: *test_definition
+ services:
+ - mariadb:10.6-ubi
+ script:
+ - cp "local_settings_ci_mariadb.py" "smash/smash/local_settings.py"
+ - cd smash
+ - sleep 10
+ - coverage run --source web manage.py test --noinput -v3
+ - coverage report -m --omit="*/test*,*/migrations*,*debug_utils*"
+
+
test_sqlite:
<<: *test_definition
script:
diff --git a/.pylintrc b/.pylintrc
index 003bd7d1290970436db631d79a7c47f30565b601..1072a8ecf34605bcdef4b76121744d762fcac490 100644
--- a/.pylintrc
+++ b/.pylintrc
@@ -7,6 +7,10 @@ disable=
C0114, # missing-module-docstring
C0115, # missing-class-docstring
C0116, # missing-function-docstring
+ R0917, # too-many-positional-arguments
+ R1731, #Â consider-using-max-builtin
+ R1730, # consider-using-min-builtin,
+ E1101, # no-member
# TO BE CHECKED
W0143, # comparison-with-callable
diff --git a/CHANGELOG b/CHANGELOG
index ef620269143aa9bc6ce13c102b6c6e671cdc0cb0..21cb55fdc0dbbe162ea3934b333c328f55d6f72c 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,6 +1,14 @@
+smasch (1.4.5-1) stable; urgency=medium
+ * added support for mariadb
+ * allow overriding the redcap test instance in settings.
+
+ -- Carlos Vega <carlos.vega@lih.lu> Wed, 31 Jul 2024 10:11:00 +0200
+
smasch (1.4.4-1) stable; urgency=high
* fix bug in api/availabilities endpoint
+ -- Carlos Vega <carlos.vega@lih.lu> Thu, 13 Jun 2024 9:56:00 +0200
+
smasch (1.4.3-1) stable; urgency=medium
* make export faster
* make API endpoint /api/subjects/GENERIC faster
diff --git a/Dockerfile b/Dockerfile
index d6e9c0a795c0b5da71e17ba7cad33e6a6546e1aa..95606d491429f50b7b26c01d9229aa1cbda5071d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -10,7 +10,7 @@ RUN node --version \
FROM python:3.11-bookworm
RUN apt-get update \
- && apt-get install -y --allow-unauthenticated libsasl2-dev python-dev-is-python3 libldap2-dev libssl-dev locales locales-all
+ && apt-get install -y --allow-unauthenticated libsasl2-dev python-dev-is-python3 libldap2-dev libssl-dev locales locales-all default-libmysqlclient-dev
RUN mkdir /code
ADD . /code/
diff --git a/local_settings_ci.py b/local_settings_ci.py
index 54c32696d747b51f9a9e353644f67ecdc131fd2b..7d323b3a14620baa358b103602a34bf579cd1dcd 100644
--- a/local_settings_ci.py
+++ b/local_settings_ci.py
@@ -1,5 +1,5 @@
# SECURITY WARNING: keep the secret key used in production secret!
-SECRET_KEY = 'Paste long random string here' # Insert long random string
+SECRET_KEY = "Paste long random string here" # Insert long random string
# SECURITY WARNING: don't run with debug turned on in production!
DEBUG = True
@@ -10,28 +10,31 @@ SERVE_STATIC = True
# https://docs.djangoproject.com/en/1.10/ref/settings/#databases
DATABASES = {
- 'default': {
- 'ENGINE': 'django.db.backends.postgresql_psycopg2',
- 'NAME': 'smash', # Insert your database's name
- 'USER': 'runner', # Insert your database's user
- 'PASSWORD': 'password', # Insert your user's password
- 'HOST': 'postgres',
- 'PORT': '',
- 'TEST': {
- 'NAME': 'dbtest',
+ "default": {
+ "ENGINE": "django.db.backends.postgresql_psycopg2",
+ "NAME": "smash", # Insert your database's name
+ "USER": "runner", # Insert your database's user
+ "PASSWORD": "password", # Insert your user's password
+ "HOST": "postgres",
+ "PORT": "",
+ "TEST": {
+ "NAME": "dbtest",
}, # '' === default one # Empty string is OK
-
# If to use sqlite
# 'ENGINE': 'django.db.backends.sqlite3',
# 'NAME': os.path.join(BASE_DIR, 'db.sqlite3'),
}
}
-STATIC_ROOT = '/tmp/static' # Warning! `/tmp` directory can be flushed in any moment; use a persistent one; e.g. ~/tmp/static
-MEDIA_ROOT = '/tmp/media' # Warning! `/tmp` directory can be flushed in any moment; use a persistent one, e.g. ~/tmp/media
-UPLOAD_ROOT = '~/tmp/upload'
-ETL_ROOT = '/tmp/etl'
+STATIC_ROOT = (
+ "/tmp/static" # Warning! `/tmp` directory can be flushed in any moment; use a persistent one; e.g. ~/tmp/static
+)
+MEDIA_ROOT = (
+ "/tmp/media" # Warning! `/tmp` directory can be flushed in any moment; use a persistent one, e.g. ~/tmp/media
+)
+UPLOAD_ROOT = "/tmp/upload"
+ETL_ROOT = "/tmp/etl"
-STATICFILES_STORAGE = 'django.contrib.staticfiles.storage.StaticFilesStorage'
+STATICFILES_STORAGE = "django.contrib.staticfiles.storage.StaticFilesStorage"
ALLOWED_HOSTS = ["127.0.0.1", "localhost"]
diff --git a/local_settings_ci_mariadb.py b/local_settings_ci_mariadb.py
new file mode 100644
index 0000000000000000000000000000000000000000..1c4ecc5e8df6a7860dc125c5245050e8fa3b3c47
--- /dev/null
+++ b/local_settings_ci_mariadb.py
@@ -0,0 +1,35 @@
+# SECURITY WARNING: keep the secret key used in production secret!
+SECRET_KEY = "Paste long random string here" # Insert long random string
+
+# SECURITY WARNING: don't run with debug turned on in production!
+DEBUG = True
+
+# Database
+# https://docs.djangoproject.com/en/1.10/ref/settings/#databases
+
+DATABASES = {
+ "default": {
+ "ENGINE": "django.db.backends.mysql",
+ "NAME": "smash",
+ "USER": "runner",
+ "PASSWORD": "password",
+ "HOST": "mariadb",
+ "PORT": "",
+ "TEST": {
+ "NAME": "dbtest",
+ },
+ }
+}
+
+STATIC_ROOT = (
+ "/tmp/static" # Warning! `/tmp` directory can be flushed in any moment; use a persistent one; e.g. ~/tmp/static
+)
+MEDIA_ROOT = (
+ "/tmp/media" # Warning! `/tmp` directory can be flushed in any moment; use a persistent one, e.g. ~/tmp/media
+)
+UPLOAD_ROOT = "/tmp/upload"
+ETL_ROOT = "/tmp/etl"
+
+STATICFILES_STORAGE = "django.contrib.staticfiles.storage.StaticFilesStorage"
+
+ALLOWED_HOSTS = ["127.0.0.1", "localhost"]
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 82d46b071491f2f523491e3a2ab196fcec63262c..a577b36cdca50a526db9e8700a582a1a5710b24b 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,10 +1,9 @@
-coverage==7.3.2
+coverage==7.6.1
django-debug-toolbar==4.2.0
fakeldap==0.6.6
Faker==19.13.0
mock==5.1.0
-mockito==1.4.0
parameterized==0.9.0
pycodestyle==2.11.1
-pylint==3.0.2
+pylint==3.3.1
pylint_django==2.5.5
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index f651e25d83f1b34700cea736b071787eca38dd05..1ab039f81732573c411d21377e23a997a4f31025 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,68 +1,35 @@
pycurl==7.45.2
-asn1crypto==1.5.1
Babel==2.13.1
-backports.functools-lru-cache==1.6.6
-certifi==2023.7.22
-cffi==1.16.0
-chardet==5.2.0
-coverage==7.3.2
-cryptography==41.0.5
-cycler==0.12.1
+certifi==2024.8.30
Django==3.2.22
-django_auth_ldap==4.6.0
-django-cleanup==8.0.0
-django-common-helpers==0.9.2
+django_auth_ldap==4.8.0
+django-cron==0.6.0
+django-cleanup==9.0.0
django-cron==0.6.0
django-excel==0.0.10
-django-formtools==2.4.1
django-npm==1.0.0
-django-otp==1.2.4
+django-otp==1.5.4
django-phonenumber-field==6.4.0
django-stronghold==0.4.0
-django-two-factor-auth==1.15.5
-enum34==1.1.10
-funcsigs==1.0.2
-gunicorn==21.2.0
-idna==3.4
-ipaddress==1.0.23
-kiwisolver==1.4.5
-lml==0.1.0
+django-two-factor-auth==1.16.0
+gunicorn==23.0.0
luhn==0.2.0
-lxml==4.9.3
-matplotlib==3.8.1
-mockito==1.4.0
+matplotlib==3.9.2
+mockito==1.5.1
+mysqlclient==2.2.4
nexmo==2.5.2
-numpy==1.26.1
-pandas==2.1.2
-packaging==23.2
+numpy==1.26.4
+pandas==2.2.3
django-datatables-view==1.20.0
-phonenumberslite==8.13.24
-Pillow==10.1.0
+phonenumberslite==8.13.46
psycopg2==2.9.9
-pycparser==2.21
-pyexcel==0.7.0
-pyexcel-io==0.6.6
-pyexcel-webio==0.1.4
-pyexcel-xls==0.7.0
-PyJWT==2.8.0
-pyparsing==3.1.1
python-dateutil==2.8.2
-python-docx==1.0.1
-pytz==2023.3.post1
-py==1.10.0
+python-docx==1.1.2
+pytz==2024.2
pytest==7.4.3
-qrcode==7.4.2
-requests==2.31.0
+pyexcel-xls==0.7.0
six==1.16.0
-sqlparse==0.4.4
-subprocess32==3.5.4
-text-unidecode==1.3
-texttable==1.7.0
timeout-decorator==0.5.0
-urllib3==2.0.7
-whitenoise==6.6.0
-xlrd==2.0.1
-wheel==0.41.3
-xlwt==1.3.0
+whitenoise==6.7.0
parameterized==0.9.0
setuptools==68.2.2
diff --git a/smash/smash/settings.py b/smash/smash/settings.py
index 53366991ed9bfea8a41a5ea7d788f979333c82d7..12e6fc6b411a20ef64351e023c6f51102f91ec4b 100644
--- a/smash/smash/settings.py
+++ b/smash/smash/settings.py
@@ -11,18 +11,29 @@ https://docs.djangoproject.com/en/1.10/ref/settings/
"""
import functools
+import logging
import os
import ldap
from django_auth_ldap.config import LDAPSearch
from django.contrib.staticfiles import storage
+logger = logging.getLogger(__name__)
+
# Build paths inside the project like this: os.path.join(BASE_DIR, ...)
BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
PROJECT_PATH = os.path.abspath(os.path.dirname(__file__))
# Quick-start development settings - unsuitable for production
# See https://docs.djangoproject.com/en/1.10/howto/deployment/checklist/
+# To run the unit tests we need a redcap instance.
+# UL
+REDCAP_TEST_API_TOKEN = os.environ.get('REDCAP_TEST_API_TOKEN', None)
+REDCAP_TEST_URL = os.environ.get('REDCAP_TEST_URL', None)
+
+if REDCAP_TEST_API_TOKEN is None or REDCAP_TEST_URL is None:
+ logging.warning('Environment variables REDCAP_TEST_API_TOKEN or REDCAP_TEST_URL does not exist. Unit tests for redcap will fail without them having proper values.')
+
COPYRIGHT_NOTE = "2024 Bioinformatics Core, Luxembourg Centre for Systems Biomedicine"
DEBUG = True
diff --git a/smash/web/__init__.py b/smash/web/__init__.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..a5faf6259d3efda9ac2dc277bdc29872cee556a5 100644
--- a/smash/web/__init__.py
+++ b/smash/web/__init__.py
@@ -0,0 +1,16 @@
+from functools import wraps
+
+
+def disable_for_loaddata(signal_handler):
+ """
+ Decorator that turns off signal handlers when loading fixture data.
+ https://docs.djangoproject.com/en/3.2/ref/django-admin/#what-s-a-fixture
+ """
+
+ @wraps(signal_handler)
+ def wrapper(*args, **kwargs):
+ if "raw" in kwargs and kwargs["raw"]:
+ return
+ signal_handler(*args, **kwargs)
+
+ return wrapper
diff --git a/smash/web/api_views/serialization_utils.py b/smash/web/api_views/serialization_utils.py
index d919b7bd26de4c9e5f7a867ef11d14c63dd5f188..3f9cee1e19426bb73238ea253ac4b8cbf9cdfd95 100644
--- a/smash/web/api_views/serialization_utils.py
+++ b/smash/web/api_views/serialization_utils.py
@@ -21,7 +21,7 @@ def bool_to_yes_no_null(val: bool):
def str_to_yes_no(val: str):
- if val.lower() == 'true':
+ if val.lower() == "true":
return "YES"
else:
return "NO"
@@ -30,7 +30,7 @@ def str_to_yes_no(val: str):
def str_to_yes_no_null(val: str):
if val is None:
return None
- if val.lower() == 'true':
+ if val.lower() == "true":
return "YES"
else:
return "NO"
@@ -52,7 +52,7 @@ def location_to_str(location):
def serialize_date(date):
if date is not None:
- result = date.strftime('%Y-%m-%d')
+ result = date.strftime("%Y-%m-%d")
else:
result = ""
return result
@@ -60,15 +60,23 @@ def serialize_date(date):
def serialize_datetime(date):
if date is not None:
- result = date.strftime('%Y-%m-%d %H:%M')
+ result = date.strftime("%Y-%m-%d %H:%M")
else:
result = ""
return result
-def add_column(result: List, name: str, field_name: str, column_list: object, param_filter: Optional[str],
- columns_used_in_study: Optional[object] = None, visible_param: Optional[bool] = None,
- sortable: Optional[bool] = True, add_param: Optional[bool] = True):
+def add_column(
+ result: List,
+ name: str,
+ field_name: str,
+ column_list: object,
+ param_filter: Optional[str],
+ columns_used_in_study: Optional[object] = None,
+ visible_param: Optional[bool] = None,
+ sortable: Optional[bool] = True,
+ add_param: Optional[bool] = True,
+):
add = add_param
if columns_used_in_study:
add = getattr(columns_used_in_study, field_name)
@@ -79,21 +87,30 @@ def add_column(result: List, name: str, field_name: str, column_list: object, pa
visible = True
else:
visible = getattr(column_list, field_name)
- result.append({
- "type": field_name,
- "name": name,
- "filter": param_filter,
- "visible": visible,
- "sortable": sortable
- })
+ result.append(
+ {
+ "type": field_name,
+ "name": name,
+ "filter": param_filter,
+ "visible": visible,
+ "sortable": sortable,
+ }
+ )
def get_filters_for_data_table_request(request_data):
filters = []
column_id = 0
- while request_data.get("columns[" + str(column_id) + "][search][value]", "unknown") != "unknown":
- val = request_data.get("columns[" + str(column_id) + "][search][value]", "unknown")
+ while (
+ request_data.get("columns[" + str(column_id) + "][search][value]", "unknown")
+ != "unknown"
+ ):
+ val = request_data.get(
+ "columns[" + str(column_id) + "][search][value]", "unknown"
+ )
if val != "":
- filters.append([request_data.get("columns[" + str(column_id) + "][data]"), val])
+ filters.append(
+ [request_data.get("columns[" + str(column_id) + "][data]"), val]
+ )
column_id += 1
return filters
diff --git a/smash/web/auth.py b/smash/web/auth.py
index 8fc88205e85212f77d25d1b3cbda6118f59ce6a3..bf8c54958f8c7becc4f2347c411ce1a4140a4b4d 100644
--- a/smash/web/auth.py
+++ b/smash/web/auth.py
@@ -8,9 +8,8 @@ logger = logging.getLogger(__name__)
def do_login(request):
- user_login = request.POST.get('username', 'none')
- user = authenticate(username=user_login,
- password=request.POST.get('password', 'none'))
+ user_login = request.POST.get("username", "none")
+ user = authenticate(username=user_login, password=request.POST.get("password", "none"))
if user is not None:
login(request, user)
return True, "ok"
@@ -31,15 +30,15 @@ def do_logout(request):
def user_logged_in_callback(sender, request, user, **kwargs): # pylint: disable=unused-argument
# to cover more complex cases:
# http://stackoverflow.com/questions/4581789/how-do-i-get-user-ip-address-in-django
- ip = request.META.get('REMOTE_ADDR')
- logger.info('login user: %s via ip: %s', user, ip)
+ ip = request.META.get("REMOTE_ADDR")
+ logger.info("login user: %s via ip: %s", user, ip)
@receiver(user_logged_out)
def user_logged_out_callback(sender, request, user, **kwargs): # pylint: disable=unused-argument
- ip = request.META.get('REMOTE_ADDR')
+ ip = request.META.get("REMOTE_ADDR")
- logger.info('logout user: %s via ip: %s', user, ip)
+ logger.info("logout user: %s via ip: %s", user, ip)
@receiver(user_login_failed)
diff --git a/smash/web/importer/etl_common.py b/smash/web/importer/etl_common.py
index dc3ba581ad46ba3633222abcee36373ddcaeab3d..e1d0191489635190a56d8bdaad92b7569965520f 100644
--- a/smash/web/importer/etl_common.py
+++ b/smash/web/importer/etl_common.py
@@ -44,45 +44,65 @@ class EtlCommon:
return new_value
return new_value
- def create_provenance_and_change_data(self, object_to_change: models.Model, field_name: str, new_value: object,
- object_type: Type[models.Model]) -> Optional[Provenance]:
+ def create_provenance_and_change_data(
+ self,
+ object_to_change: models.Model,
+ field_name: str,
+ new_value: object,
+ object_type: Type[models.Model],
+ ) -> Optional[Provenance]:
old_value = getattr(object_to_change, field_name)
if old_value != new_value:
setattr(object_to_change, field_name, new_value)
- return self.create_provenance(field_name, new_value, object_to_change, object_type, old_value)
+ return self.create_provenance(
+ field_name, new_value, object_to_change, object_type, old_value
+ )
return None
- def create_provenance(self, field_name: str, new_value: object, object_to_change: models.Model,
- object_type: Type[models.Model], old_value: object) -> Provenance:
+ def create_provenance(
+ self,
+ field_name: str,
+ new_value: object,
+ object_to_change: models.Model,
+ object_type: Type[models.Model],
+ old_value: object,
+ ) -> Provenance:
description = f'{field_name} changed from "{old_value}" to "{new_value}"'
- p = Provenance(modified_table=object_type._meta.db_table,
- modified_table_id=object_to_change.id,
- modification_author=self.etl_data.import_worker,
- previous_value=old_value,
- new_value=new_value,
- modification_description=description,
- modified_field=field_name,
- )
+ p = Provenance(
+ modified_table=object_type._meta.db_table,
+ modified_table_id=object_to_change.id,
+ modification_author=self.etl_data.import_worker,
+ previous_value=old_value,
+ new_value=new_value,
+ modification_description=description,
+ modified_field=field_name,
+ )
p.save()
return p
- def create_provenance_for_new_object(self, object_type: Type[models.Model], new_object: models.Model) -> list:
+ def create_provenance_for_new_object(
+ self, object_type: Type[models.Model], new_object: models.Model
+ ) -> list:
result = []
for field in object_type._meta.get_fields():
- if field.get_internal_type() == "CharField" or \
- field.get_internal_type() == "DateField" or \
- field.get_internal_type() == "IntegerField" or \
- field.get_internal_type() == "DateTimeField" or \
- field.get_internal_type() == "BooleanField":
+ if (
+ field.get_internal_type() == "CharField"
+ or field.get_internal_type() == "DateField"
+ or field.get_internal_type() == "IntegerField"
+ or field.get_internal_type() == "DateTimeField"
+ or field.get_internal_type() == "BooleanField"
+ ):
new_value = getattr(new_object, field.name)
if new_value is not None and new_value != "":
- p = self.create_provenance(field.name, new_value, new_object, object_type, '')
+ p = self.create_provenance(
+ field.name, new_value, new_object, object_type, ""
+ )
result.append(p)
return result
@staticmethod
def remove_bom(line) -> str:
if isinstance(line, str):
- return line[3:] if line.encode('utf8').startswith(codecs.BOM_UTF8) else line
+ return line[3:] if line.encode("utf8").startswith(codecs.BOM_UTF8) else line
else:
return line[3:] if line.startswith(codecs.BOM_UTF8) else line
diff --git a/smash/web/management/commands/holidays.py b/smash/web/management/commands/holidays.py
index 8804121a0d32d5c66889642e7459a5ad31983a72..c8b1878292a34ab7719fcdd89f85ee9c4eca3f74 100644
--- a/smash/web/management/commands/holidays.py
+++ b/smash/web/management/commands/holidays.py
@@ -14,27 +14,47 @@ def get_ascension_day(easter_sunday):
class Command(BaseCommand):
- help = 'import holidays for the specified years'
+ help = "import holidays for the specified years"
def add_arguments(self, parser):
- parser.add_argument('year', nargs='+', type=int)
+ parser.add_argument("year", nargs="+", type=int)
def handle(self, *args, **options):
for location in Location.objects.exclude(name="Flying Team").all():
- for year in options['year']:
- self.stdout.write(f"importing holidays for year {year} and location {location}")
+ for year in options["year"]:
+ self.stdout.write(
+ f"importing holidays for year {year} and location {location}"
+ )
# new years day
self.create_holiday(year, 1, 1, "New Years Day", location)
# easter monday
easter_sunday = get_easter_sunday_date(year)
easter_monday = get_easter_monday(easter_sunday)
- self.create_holiday(year, easter_monday.month, easter_monday.day, "Easter Monday", location)
+ self.create_holiday(
+ year,
+ easter_monday.month,
+ easter_monday.day,
+ "Easter Monday",
+ location,
+ )
# ascension day
ascension_day = get_ascension_day(easter_sunday)
- self.create_holiday(year, ascension_day.month, ascension_day.day, "Ascension Day", location)
+ self.create_holiday(
+ year,
+ ascension_day.month,
+ ascension_day.day,
+ "Ascension Day",
+ location,
+ )
# pentecost monday
pentecost_day = get_pentecost_day(easter_sunday)
- self.create_holiday(year, pentecost_day.month, pentecost_day.day, "Pentecost Monday", location)
+ self.create_holiday(
+ year,
+ pentecost_day.month,
+ pentecost_day.day,
+ "Pentecost Monday",
+ location,
+ )
# labour day
self.create_holiday(year, 5, 1, "Labour Day", location)
# national day
@@ -49,22 +69,33 @@ class Command(BaseCommand):
def create_holiday(self, year, month, day, comment, location):
# check if already exists:
- count = Appointment.objects.filter(datetime_when__year=year, datetime_when__month=month, datetime_when__day=day,
- location=location, comment=comment).count()
+ count = Appointment.objects.filter(
+ datetime_when__year=year,
+ datetime_when__month=month,
+ datetime_when__day=day,
+ location=location,
+ comment=comment,
+ ).count()
if count != 0:
self.stdout.write(
- f'an holiday with the same description already exists for the same day: {comment}')
+ f"an holiday with the same description already exists for the same day: {comment}"
+ )
return
holiday = Appointment()
- holiday.datetime_when = datetime.datetime(year=year, month=month, day=day, hour=9)
+ holiday.datetime_when = datetime.datetime(
+ year=year, month=month, day=day, hour=9
+ )
holiday.location = location
holiday.length = 60 * 8
holiday.comment = comment
holiday.visit_id = None
holiday.save()
- appointment_type_other, _ = AppointmentType.objects.get_or_create(code='OTHER',
- defaults={'default_duration': 60})
- link = AppointmentTypeLink(appointment=holiday, appointment_type=appointment_type_other)
+ appointment_type_other, _ = AppointmentType.objects.get_or_create(
+ code="OTHER", defaults={"default_duration": 60}
+ )
+ link = AppointmentTypeLink(
+ appointment=holiday, appointment_type=appointment_type_other
+ )
link.save()
diff --git a/smash/web/migrations/0001_initial.py b/smash/web/migrations/0001_initial.py
index 545ed4a1da48b3249d8e711983d73b08b80c46ab..688877651ca5d2fe8a1190cd40f39c0522e83418 100644
--- a/smash/web/migrations/0001_initial.py
+++ b/smash/web/migrations/0001_initial.py
@@ -29,7 +29,7 @@ class Migration(migrations.Migration):
fields=[
("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
("code", models.CharField(max_length=20, verbose_name="Appointment code")),
- ("description", models.CharField(max_length=2000, verbose_name="Appointment description")),
+ ("description", models.TextField(max_length=2000, verbose_name="Appointment description")),
("default_duration", models.IntegerField(verbose_name="Default duration (in minutes)")),
("rest_time", models.IntegerField(verbose_name="Suggested rest time")),
],
@@ -125,7 +125,7 @@ class Migration(migrations.Migration):
),
),
("main_pseudonym", models.CharField(max_length=45, verbose_name="Pseudonym")),
- ("comments", models.CharField(max_length=2000, verbose_name="Comments")),
+ ("comments", models.TextField(max_length=2000, verbose_name="Comments")),
("date_added", models.DateField(auto_now=True, verbose_name="Added on")),
("referral", models.CharField(max_length=128, null=True, verbose_name="Referred by")),
("diagnosis", models.CharField(max_length=128, null=True, verbose_name="Diagnosis")),
diff --git a/smash/web/migrations/0001_version-1-0-0.py b/smash/web/migrations/0001_version-1-0-0.py
index 251793ee9a7b8c4a8748cdb02693b5a8e922e99a..beb180f00eeb90635d1df801f6c162712f737e76 100644
--- a/smash/web/migrations/0001_version-1-0-0.py
+++ b/smash/web/migrations/0001_version-1-0-0.py
@@ -6,6 +6,7 @@ import django.core.validators
import django.db.models.deletion
from django.conf import settings
from django.db import migrations, models
+from django.db import connection
from web.models.appointment_list import APPOINTMENT_LIST_UNFINISHED
from web.models.constants import (
@@ -1596,7 +1597,7 @@ class Migration(migrations.Migration):
fields=[
("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
("code", models.CharField(max_length=20, verbose_name="Code")),
- ("description", models.CharField(blank=True, max_length=1024, verbose_name="Description")),
+ ("description", models.TextField(blank=True, max_length=1024, verbose_name="Description")),
("study", models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="web.study")),
],
),
@@ -1673,7 +1674,7 @@ class Migration(migrations.Migration):
fields=[
("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
("code", models.CharField(max_length=20, verbose_name="Appointment code")),
- ("description", models.CharField(max_length=2000, verbose_name="Appointment description")),
+ ("description", models.TextField(max_length=2000, verbose_name="Appointment description")),
("default_duration", models.IntegerField(verbose_name="Default duration (in minutes)")),
("rest_time", models.IntegerField(default=0, verbose_name="Suggested rest time")),
(
@@ -1694,11 +1695,11 @@ class Migration(migrations.Migration):
verbose_name="Type of worker required for appointment",
),
),
- ("calendar_color", models.CharField(default="#cfc600", max_length=2000, verbose_name="Calendar color")),
+ ("calendar_color", models.TextField(default="#cfc600", max_length=2000, verbose_name="Calendar color")),
("calendar_color_priority", models.IntegerField(default=1, verbose_name="Calendar color priority")),
(
"calendar_font_color",
- models.CharField(default="#00000", max_length=2000, verbose_name="Calendar font color"),
+ models.TextField(default="#00000", max_length=2000, verbose_name="Calendar font color"),
),
("can_be_parallelized", models.BooleanField(default=False, verbose_name="Can be parallelized")),
],
@@ -2157,7 +2158,7 @@ class Migration(migrations.Migration):
max_length=20,
),
),
- ("possible_values", models.CharField(blank=True, default="", max_length=1024, null=True)),
+ ("possible_values", models.TextField(blank=True, default="", max_length=1024, null=True)),
("default_value", models.CharField(blank=True, max_length=256, null=True)),
("readonly", models.BooleanField(default=False)),
("required", models.BooleanField(default=False)),
@@ -2177,7 +2178,7 @@ class Migration(migrations.Migration):
name="CustomStudySubjectValue",
fields=[
("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
- ("value", models.CharField(blank=True, max_length=2048, null=True)),
+ ("value", models.TextField(blank=True, max_length=2048, null=True)),
(
"study_subject",
models.ForeignKey(
@@ -2371,15 +2372,15 @@ class Migration(migrations.Migration):
name="Provenance",
fields=[
("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
- ("modified_table", models.CharField(max_length=1024, null=True, verbose_name="Modified table")),
+ ("modified_table", models.CharField(max_length=128, null=True, verbose_name="Modified table")),
("modified_table_id", models.IntegerField(default=0, null=True, verbose_name="Modified table row")),
("modification_date", models.DateTimeField(auto_now_add=True, verbose_name="Modified on")),
(
"previous_value",
- models.CharField(blank=True, max_length=2048, null=True, verbose_name="Previous Value"),
+ models.TextField(blank=True, max_length=2048, null=True, verbose_name="Previous Value"),
),
- ("new_value", models.CharField(blank=True, max_length=2048, null=True, verbose_name="New Value")),
- ("modification_description", models.CharField(max_length=20480, verbose_name="Description")),
+ ("new_value", models.TextField(blank=True, max_length=2048, null=True, verbose_name="New Value")),
+ ("modification_description", models.TextField(max_length=20480, verbose_name="Description")),
(
"modification_author",
models.ForeignKey(
@@ -2389,10 +2390,10 @@ class Migration(migrations.Migration):
verbose_name="Worker who modified the row",
),
),
- ("modified_field", models.CharField(blank="", max_length=1024, verbose_name="Modified field")),
+ ("modified_field", models.CharField(blank="", max_length=128, verbose_name="Modified field")),
(
"request_path",
- models.CharField(blank=True, max_length=20480, null=True, verbose_name="Request Path"),
+ models.TextField(blank=True, max_length=20480, null=True, verbose_name="Request Path"),
),
("request_ip_addr", models.GenericIPAddressField(null=True, verbose_name="Request IP Address")),
],
@@ -2566,7 +2567,7 @@ class Migration(migrations.Migration):
("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
("type", models.CharField(editable=False, max_length=50, verbose_name="Type")),
("name", models.CharField(editable=False, max_length=255, verbose_name="Name")),
- ("value", models.CharField(max_length=1024, verbose_name="Value")),
+ ("value", models.TextField(max_length=1024, verbose_name="Value")),
(
"value_type",
models.CharField(
@@ -2703,7 +2704,7 @@ class Migration(migrations.Migration):
("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
("table_name", models.CharField(blank=True, default="", max_length=128)),
("column_name", models.CharField(blank=True, default="", max_length=128)),
- ("csv_column_name", models.CharField(blank=True, default="", max_length=1024)),
+ ("csv_column_name", models.TextField(blank=True, default="", max_length=1024)),
("enabled", models.BooleanField(default=True)),
(
"etl_data",
@@ -2992,3 +2993,6 @@ class Migration(migrations.Migration):
migrations.RunPython(configuration_items__0171),
migrations.RunPython(configuration_items__0176),
]
+
+ if connection.vendor == "mysql":
+ operations = [migrations.RunSQL("SET SESSION sql_mode='ANSI_QUOTES';")] + operations
diff --git a/smash/web/migrations/0014_auto_20170220_0812.py b/smash/web/migrations/0014_auto_20170220_0812.py
index 190888eddad882ffef72c0ac8f43c4b86d55610e..8073a8f299e9f0d9aca48dd34baa41e2a7110868 100644
--- a/smash/web/migrations/0014_auto_20170220_0812.py
+++ b/smash/web/migrations/0014_auto_20170220_0812.py
@@ -36,7 +36,7 @@ class Migration(migrations.Migration):
migrations.AlterField(
model_name="subject",
name="comments",
- field=models.CharField(blank=True, max_length=2000, verbose_name="Comments"),
+ field=models.TextField(blank=True, max_length=2000, verbose_name="Comments"),
),
migrations.AlterField(
model_name="subject",
diff --git a/smash/web/migrations/0017_auto_20170301_1600.py b/smash/web/migrations/0017_auto_20170301_1600.py
index 77814d62961c638605d9d8ed25e06f524e696a1d..b9018c9abb351be55fb6667fbd024a9d3debb481 100644
--- a/smash/web/migrations/0017_auto_20170301_1600.py
+++ b/smash/web/migrations/0017_auto_20170301_1600.py
@@ -8,43 +8,43 @@ from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
- ('web', '0016_auto_20170228_1652'),
+ ("web", "0016_auto_20170228_1652"),
]
operations = [
migrations.AddField(
- model_name='appointment',
- name='comment',
- field=models.CharField(blank=True, max_length=1024, null=True, verbose_name='Comment'),
+ model_name="appointment",
+ name="comment",
+ field=models.TextField(blank=True, max_length=1024, null=True, verbose_name="Comment"),
),
migrations.AddField(
- model_name='appointmenttype',
- name='calendar_color',
- field=models.CharField(default='#cfc600', max_length=2000, verbose_name='Calendar color'),
+ model_name="appointmenttype",
+ name="calendar_color",
+ field=models.TextField(default="#cfc600", max_length=2000, verbose_name="Calendar color"),
),
migrations.AddField(
- model_name='appointmenttype',
- name='calendar_color_priority',
- field=models.IntegerField(default=1, verbose_name='Calendar color priority'),
+ model_name="appointmenttype",
+ name="calendar_color_priority",
+ field=models.IntegerField(default=1, verbose_name="Calendar color priority"),
),
migrations.AddField(
- model_name='appointmenttype',
- name='calendar_font_color',
- field=models.CharField(default='#00000', max_length=2000, verbose_name='Calendar color'),
+ model_name="appointmenttype",
+ name="calendar_font_color",
+ field=models.TextField(default="#00000", max_length=2000, verbose_name="Calendar color"),
),
migrations.AlterField(
- model_name='appointment',
- name='is_finished',
- field=models.BooleanField(default=False, editable=False, verbose_name='Has the appointment ended?'),
+ model_name="appointment",
+ name="is_finished",
+ field=models.BooleanField(default=False, editable=False, verbose_name="Has the appointment ended?"),
),
migrations.AlterField(
- model_name='subject',
- name='dead',
- field=models.BooleanField(default=False, editable=False, verbose_name='Dead'),
+ model_name="subject",
+ name="dead",
+ field=models.BooleanField(default=False, editable=False, verbose_name="Dead"),
),
migrations.AlterField(
- model_name='subject',
- name='resigned',
- field=models.BooleanField(default=False, editable=False, verbose_name='Resigned'),
+ model_name="subject",
+ name="resigned",
+ field=models.BooleanField(default=False, editable=False, verbose_name="Resigned"),
),
]
diff --git a/smash/web/migrations/0090_vouchertype_vouchertypeprice.py b/smash/web/migrations/0090_vouchertype_vouchertypeprice.py
index 57c52c5a706f8b5ac583e4367c799b8ed24b629b..76e6d8bdc810049cb6480af11453158492a10ab2 100644
--- a/smash/web/migrations/0090_vouchertype_vouchertypeprice.py
+++ b/smash/web/migrations/0090_vouchertype_vouchertypeprice.py
@@ -9,27 +9,27 @@ import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
- ('web', '0089_unfinshed_appointment_list'),
+ ("web", "0089_unfinshed_appointment_list"),
]
operations = [
migrations.CreateModel(
- name='VoucherType',
+ name="VoucherType",
fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('code', models.CharField(max_length=20, verbose_name='Code')),
- ('description', models.CharField(blank=True, max_length=1024, verbose_name='Description')),
- ('study', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='web.Study')),
+ ("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
+ ("code", models.CharField(max_length=20, verbose_name="Code")),
+ ("description", models.TextField(blank=True, max_length=1024, verbose_name="Description")),
+ ("study", models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="web.Study")),
],
),
migrations.CreateModel(
- name='VoucherTypePrice',
+ name="VoucherTypePrice",
fields=[
- ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
- ('price', models.DecimalField(decimal_places=2, max_digits=6, verbose_name='Price')),
- ('start_date', models.DateField(verbose_name='Start date')),
- ('end_date', models.DateField(verbose_name='End date')),
- ('voucher_type', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='web.VoucherType')),
+ ("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
+ ("price", models.DecimalField(decimal_places=2, max_digits=6, verbose_name="Price")),
+ ("start_date", models.DateField(verbose_name="Start date")),
+ ("end_date", models.DateField(verbose_name="End date")),
+ ("voucher_type", models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to="web.VoucherType")),
],
),
]
diff --git a/smash/web/migrations/0097_auto_20171211_1616.py b/smash/web/migrations/0097_auto_20171211_1616.py
index 9ae00ede5a5b0508d61b648430ef65cf7478827c..715aee1fd5cb4369ab85da3b221819fc139da265 100644
--- a/smash/web/migrations/0097_auto_20171211_1616.py
+++ b/smash/web/migrations/0097_auto_20171211_1616.py
@@ -95,7 +95,7 @@ class Migration(migrations.Migration):
migrations.AddField(
model_name="studysubject",
name="screening",
- field=models.CharField(blank=True, max_length=1024, null=True, verbose_name="Screening"),
+ field=models.TextField(blank=True, max_length=1024, null=True, verbose_name="Screening"),
),
migrations.AddField(
model_name="studysubject",
@@ -112,7 +112,7 @@ class Migration(migrations.Migration):
migrations.AlterField(
model_name="studysubject",
name="diagnosis",
- field=models.CharField(blank=True, max_length=1024, null=True, verbose_name="Diagnosis"),
+ field=models.TextField(blank=True, max_length=1024, null=True, verbose_name="Diagnosis"),
),
migrations.AlterField(
model_name="voucher",
diff --git a/smash/web/migrations/0141_auto_20200319_1040.py b/smash/web/migrations/0141_auto_20200319_1040.py
index 1ec81c4fa0c40d903297532068676e1b987c3ec2..12f552a6f96c5ca64ed17f2bad92bf74071a6387 100644
--- a/smash/web/migrations/0141_auto_20200319_1040.py
+++ b/smash/web/migrations/0141_auto_20200319_1040.py
@@ -8,13 +8,13 @@ from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
- ('web', '0140_auto_20190528_0953'),
+ ("web", "0140_auto_20190528_0953"),
]
operations = [
migrations.AlterField(
- model_name='appointmenttype',
- name='calendar_font_color',
- field=models.CharField(default='#00000', max_length=2000, verbose_name='Calendar font color'),
+ model_name="appointmenttype",
+ name="calendar_font_color",
+ field=models.TextField(default="#00000", max_length=2000, verbose_name="Calendar font color"),
),
]
diff --git a/smash/web/migrations/0142_provenance.py b/smash/web/migrations/0142_provenance.py
index eb818bfcbd81506d18322e88cf0e7c93c95b9b51..1bbd6a42e320b06401abd8227e13ac820e8f5754 100644
--- a/smash/web/migrations/0142_provenance.py
+++ b/smash/web/migrations/0142_provenance.py
@@ -16,15 +16,15 @@ class Migration(migrations.Migration):
name="Provenance",
fields=[
("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
- ("modified_table", models.CharField(max_length=1024, verbose_name="Modified table")),
- ("modified_table_id", models.CharField(max_length=1024, verbose_name="Modified table row")),
+ ("modified_table", models.CharField(max_length=128, verbose_name="Modified table")),
+ ("modified_table_id", models.IntegerField(default=0, null=True, verbose_name="Modified table row")),
("modification_date", models.DateTimeField(verbose_name="Modified on")),
(
"previous_value",
- models.CharField(blank=True, max_length=2048, null=True, verbose_name="Previous Value"),
+ models.TextField(blank=True, max_length=2048, null=True, verbose_name="Previous Value"),
),
- ("new_value", models.CharField(blank=True, max_length=2048, null=True, verbose_name="New Value")),
- ("modification_description", models.CharField(max_length=2048, verbose_name="Description")),
+ ("new_value", models.TextField(blank=True, max_length=2048, null=True, verbose_name="New Value")),
+ ("modification_description", models.TextField(max_length=2048, verbose_name="Description")),
(
"modification_author",
models.ForeignKey(
diff --git a/smash/web/migrations/0144_auto_20200319_1221.py b/smash/web/migrations/0144_auto_20200319_1221.py
index e8b8c4bfdeb810ed9d57b6d3172d1098ab9cbc78..d7c3e07ce9e67ba8992d09dc6a2768887f9eada2 100644
--- a/smash/web/migrations/0144_auto_20200319_1221.py
+++ b/smash/web/migrations/0144_auto_20200319_1221.py
@@ -8,19 +8,19 @@ from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
- ('web', '0143_auto_20200319_1121'),
+ ("web", "0143_auto_20200319_1121"),
]
operations = [
migrations.AddField(
- model_name='provenance',
- name='modified_field',
- field=models.CharField(default='', max_length=1024, verbose_name='Modified field'),
+ model_name="provenance",
+ name="modified_field",
+ field=models.TextField(default="", max_length=1024, verbose_name="Modified field"),
preserve_default=False,
),
migrations.AlterField(
- model_name='provenance',
- name='modification_description',
- field=models.CharField(max_length=20480, verbose_name='Description'),
+ model_name="provenance",
+ name="modification_description",
+ field=models.TextField(max_length=20480, verbose_name="Description"),
),
]
diff --git a/smash/web/migrations/0145_auto_20200319_1404.py b/smash/web/migrations/0145_auto_20200319_1404.py
index 21dfc1004facf6f15a6d8fdd4454cf275112825d..8353bfa7c3be7ad72a67e1278642df39848cdb7f 100644
--- a/smash/web/migrations/0145_auto_20200319_1404.py
+++ b/smash/web/migrations/0145_auto_20200319_1404.py
@@ -8,13 +8,13 @@ from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
- ('web', '0144_auto_20200319_1221'),
+ ("web", "0144_auto_20200319_1221"),
]
operations = [
migrations.AlterField(
- model_name='provenance',
- name='modified_field',
- field=models.CharField(blank='', max_length=1024, verbose_name='Modified field'),
+ model_name="provenance",
+ name="modified_field",
+ field=models.TextField(blank="", max_length=1024, verbose_name="Modified field"),
),
]
diff --git a/smash/web/migrations/0148_auto_20200319_1301.py b/smash/web/migrations/0148_auto_20200319_1301.py
index 0d9ecd0e3b6720ee41082ba333d972cfbf0e312d..3c4b96684ddf0f4e1e994a000be2541cfa22180b 100644
--- a/smash/web/migrations/0148_auto_20200319_1301.py
+++ b/smash/web/migrations/0148_auto_20200319_1301.py
@@ -7,17 +7,17 @@ from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
- ('web', '0147_auto_20200320_0931'),
+ ("web", "0147_auto_20200320_0931"),
]
operations = [
migrations.AlterModelOptions(
- name='appointmenttypelink',
- options={'permissions': [('view_daily_planning', 'Can see daily planning')]},
+ name="appointmenttypelink",
+ options={"permissions": [("view_daily_planning", "Can see daily planning")]},
),
migrations.AlterField(
- model_name='appointmenttype',
- name='calendar_font_color',
- field=models.CharField(default='#00000', max_length=2000, verbose_name='Calendar font color'),
+ model_name="appointmenttype",
+ name="calendar_font_color",
+ field=models.TextField(default="#00000", max_length=2000, verbose_name="Calendar font color"),
),
]
diff --git a/smash/web/migrations/0162_auto_20200416_1212.py b/smash/web/migrations/0162_auto_20200416_1212.py
index 231b4fa2e2530b832ac05af08ccb2e875e9e86dd..4114d664b5bb98eb85d84ff322d45702f949a2ba 100644
--- a/smash/web/migrations/0162_auto_20200416_1212.py
+++ b/smash/web/migrations/0162_auto_20200416_1212.py
@@ -8,18 +8,18 @@ from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
- ('web', '0161_auto_20200416_0736'),
+ ("web", "0161_auto_20200416_0736"),
]
operations = [
migrations.AlterField(
- model_name='configurationitem',
- name='value',
- field=models.CharField(max_length=1024, verbose_name='Value'),
+ model_name="configurationitem",
+ name="value",
+ field=models.TextField(max_length=1024, verbose_name="Value"),
),
migrations.AlterField(
- model_name='subject',
- name='next_of_keen_name',
- field=models.CharField(blank=True, max_length=255, verbose_name='Next of keen'),
+ model_name="subject",
+ name="next_of_keen_name",
+ field=models.CharField(blank=True, max_length=255, verbose_name="Next of keen"),
),
]
diff --git a/smash/web/migrations/0168_rename_radcap_field.py b/smash/web/migrations/0168_rename_radcap_field.py
index 37be8307a63d50b0248938df0d12d3df8d6aa438..bbec2ef46c3427638dab73a497332cb4b840ce4d 100644
--- a/smash/web/migrations/0168_rename_radcap_field.py
+++ b/smash/web/migrations/0168_rename_radcap_field.py
@@ -28,14 +28,14 @@ class Migration(migrations.Migration):
operations = [
migrations.RunSQL(
- "update web_configurationitem set type = '"
+ "update web_configurationitem, set type = '"
+ RED_CAP_KIT_ID_FIELD_TYPE
+ "' where type = '"
+ RED_CAP_SAMPLE_DATE_FIELD_TYPE
+ "';"
),
migrations.RunSQL(
- "update web_configurationitem set name = 'Redcap field for sample kit id in the visit' where type = '"
+ "update web_configurationitem, set name = 'Redcap field for sample kit id in the visit' where type = '"
+ RED_CAP_KIT_ID_FIELD_TYPE
+ "';"
),
diff --git a/smash/web/migrations/0173_auto_20201105_1142.py b/smash/web/migrations/0173_auto_20201105_1142.py
index 74e66773d22e0c801421ca5c425c7708fd6d2aa0..b20401e89bdb9439bd4ff16d8653917469ba23fd 100644
--- a/smash/web/migrations/0173_auto_20201105_1142.py
+++ b/smash/web/migrations/0173_auto_20201105_1142.py
@@ -12,7 +12,7 @@ class Migration(migrations.Migration):
migrations.AlterField(
model_name="provenance",
name="modified_table",
- field=models.CharField(max_length=1024, null=True, verbose_name="Modified table"),
+ field=models.TextField(max_length=1024, null=True, verbose_name="Modified table"),
),
migrations.AlterField(
model_name="provenance",
diff --git a/smash/web/migrations/0174_auto_20201105_1157.py b/smash/web/migrations/0174_auto_20201105_1157.py
index fdb995fec343f8d80b5af2fd26c832a6488e208e..a14890dc4b1f8fb6af8cca3b5ec6673acc6a69f1 100644
--- a/smash/web/migrations/0174_auto_20201105_1157.py
+++ b/smash/web/migrations/0174_auto_20201105_1157.py
@@ -12,6 +12,6 @@ class Migration(migrations.Migration):
migrations.AddField(
model_name="provenance",
name="request_path",
- field=models.CharField(blank=True, max_length=20480, null=True, verbose_name="Request Path"),
+ field=models.TextField(blank=True, max_length=20480, null=True, verbose_name="Request Path"),
)
]
diff --git a/smash/web/migrations/0177_customstudysubjectfield_customstudysubjectvalue.py b/smash/web/migrations/0177_customstudysubjectfield_customstudysubjectvalue.py
index 053afbc6db84ede5d570f4094df5338999a79ce8..9284b02930abc3dca02e6836fde5cd931a32b65a 100644
--- a/smash/web/migrations/0177_customstudysubjectfield_customstudysubjectvalue.py
+++ b/smash/web/migrations/0177_customstudysubjectfield_customstudysubjectvalue.py
@@ -29,7 +29,7 @@ class Migration(migrations.Migration):
max_length=20,
),
),
- ("possible_values", models.CharField(blank=True, default="", max_length=1024, null=True)),
+ ("possible_values", models.TextField(blank=True, default="", max_length=1024, null=True)),
("default_value", models.CharField(blank=True, max_length=20, null=True)),
("readonly", models.BooleanField(default=False)),
("required", models.BooleanField(default=False)),
@@ -49,7 +49,7 @@ class Migration(migrations.Migration):
name="CustomStudySubjectValue",
fields=[
("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
- ("value", models.CharField(blank=True, max_length=2048, null=True)),
+ ("value", models.TextField(blank=True, max_length=2048, null=True)),
(
"study_subject",
models.ForeignKey(
diff --git a/smash/web/migrations/0178_auto_20201116_1250.py b/smash/web/migrations/0178_auto_20201116_1250.py
index 91febe10fabdb42e82726f4c02d8ab0dad3e08af..da37d7a941837d1d2bc8bd6d479f328bf1a1425c 100644
--- a/smash/web/migrations/0178_auto_20201116_1250.py
+++ b/smash/web/migrations/0178_auto_20201116_1250.py
@@ -118,7 +118,7 @@ class Migration(migrations.Migration):
migrations.AlterField(
model_name="appointmenttype",
name="calendar_font_color",
- field=models.CharField(default="#00000", max_length=2000, verbose_name="Calendar font color"),
+ field=models.TextField(default="#00000", max_length=2000, verbose_name="Calendar font color"),
),
migrations.AlterField(
model_name="availability",
@@ -166,7 +166,7 @@ class Migration(migrations.Migration):
migrations.AlterField(
model_name="configurationitem",
name="value",
- field=models.CharField(max_length=1024, verbose_name="Value"),
+ field=models.TextField(max_length=1024, verbose_name="Value"),
),
migrations.AlterField(
model_name="contactattempt",
@@ -774,22 +774,22 @@ class Migration(migrations.Migration):
migrations.AlterField(
model_name="provenance",
name="modification_description",
- field=models.CharField(max_length=20480, verbose_name="Description"),
+ field=models.TextField(max_length=20480, verbose_name="Description"),
),
migrations.AlterField(
model_name="provenance",
name="modified_field",
- field=models.CharField(blank="", max_length=1024, verbose_name="Modified field"),
+ field=models.TextField(blank="", max_length=1024, verbose_name="Modified field"),
),
migrations.AlterField(
model_name="provenance",
name="new_value",
- field=models.CharField(blank=True, max_length=2048, null=True, verbose_name="New Value"),
+ field=models.TextField(blank=True, max_length=2048, null=True, verbose_name="New Value"),
),
migrations.AlterField(
model_name="provenance",
name="previous_value",
- field=models.CharField(blank=True, max_length=2048, null=True, verbose_name="Previous Value"),
+ field=models.TextField(blank=True, max_length=2048, null=True, verbose_name="Previous Value"),
),
migrations.AlterField(
model_name="study",
@@ -1248,7 +1248,7 @@ class Migration(migrations.Migration):
migrations.AlterField(
model_name="studysubject",
name="diagnosis",
- field=models.CharField(blank=True, max_length=1024, null=True, verbose_name="Diagnosis"),
+ field=models.TextField(blank=True, max_length=1024, null=True, verbose_name="Diagnosis"),
),
migrations.AlterField(
model_name="studysubject",
@@ -1341,7 +1341,7 @@ class Migration(migrations.Migration):
migrations.AlterField(
model_name="studysubject",
name="screening",
- field=models.CharField(blank=True, max_length=1024, null=True, verbose_name="Screening"),
+ field=models.TextField(blank=True, max_length=1024, null=True, verbose_name="Screening"),
),
migrations.AlterField(
model_name="studysubject",
@@ -1889,7 +1889,7 @@ class Migration(migrations.Migration):
migrations.AlterField(
model_name="vouchertype",
name="description",
- field=models.CharField(blank=True, max_length=1024, verbose_name="Description"),
+ field=models.TextField(blank=True, max_length=1024, verbose_name="Description"),
),
migrations.AlterField(
model_name="vouchertypeprice",
diff --git a/smash/web/migrations/0184_visitimportdata.py b/smash/web/migrations/0184_visitimportdata.py
index 366d3b1b119aca08bc3aa38559257340bdd4aa3f..1b90921513dba56a63999bae0a261675c9855863 100644
--- a/smash/web/migrations/0184_visitimportdata.py
+++ b/smash/web/migrations/0184_visitimportdata.py
@@ -140,7 +140,7 @@ class Migration(migrations.Migration):
("id", models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name="ID")),
("table_name", models.CharField(blank=True, default="", max_length=128)),
("column_name", models.CharField(blank=True, default="", max_length=128)),
- ("csv_column_name", models.CharField(blank=True, default="", max_length=1024)),
+ ("csv_column_name", models.TextField(blank=True, default="", max_length=1024)),
("enabled", models.BooleanField(default=True)),
(
"etl_data",
diff --git a/smash/web/migrations/0215_alter_studysubject_referral_letter.py b/smash/web/migrations/0215_alter_studysubject_referral_letter.py
new file mode 100644
index 0000000000000000000000000000000000000000..532b2c10e05e5e432e11df7c2d4e5479eb2598f7
--- /dev/null
+++ b/smash/web/migrations/0215_alter_studysubject_referral_letter.py
@@ -0,0 +1,25 @@
+# Generated by Django 3.2.22 on 2024-07-30 06:09
+
+import django.core.files.storage
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ("web", "0214_merge_20240404_0917"),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name="studysubject",
+ name="referral_letter",
+ field=models.FileField(
+ blank=True,
+ null=True,
+ storage=django.core.files.storage.FileSystemStorage(location="/tmp/upload"),
+ upload_to="referral_letters",
+ verbose_name="Referral letter",
+ ),
+ ),
+ ]
diff --git a/smash/web/migrations/0216_auto_20240730_0621.py b/smash/web/migrations/0216_auto_20240730_0621.py
new file mode 100644
index 0000000000000000000000000000000000000000..cc86d63259d3cb4a8752f9b6055e33a3abfe7d9b
--- /dev/null
+++ b/smash/web/migrations/0216_auto_20240730_0621.py
@@ -0,0 +1,85 @@
+# Generated by Django 3.2.22 on 2024-07-30 06:21
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ("web", "0215_alter_studysubject_referral_letter"),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name="appointmenttype",
+ name="calendar_color",
+ field=models.TextField(default="#cfc600", max_length=2000, verbose_name="Calendar color"),
+ ),
+ migrations.AlterField(
+ model_name="appointmenttype",
+ name="calendar_font_color",
+ field=models.TextField(default="#00000", max_length=2000, verbose_name="Calendar font color"),
+ ),
+ migrations.AlterField(
+ model_name="appointmenttype",
+ name="description",
+ field=models.TextField(max_length=2000, verbose_name="Appointment description"),
+ ),
+ migrations.AlterField(
+ model_name="configurationitem",
+ name="value",
+ field=models.TextField(max_length=1024, verbose_name="Value"),
+ ),
+ migrations.AlterField(
+ model_name="customstudysubjectfield",
+ name="possible_values",
+ field=models.TextField(blank=True, default="", max_length=1024, null=True),
+ ),
+ migrations.AlterField(
+ model_name="customstudysubjectvalue",
+ name="value",
+ field=models.TextField(blank=True, max_length=2048, null=True),
+ ),
+ migrations.AlterField(
+ model_name="etlcolumnmapping",
+ name="csv_column_name",
+ field=models.TextField(blank=True, default="", max_length=1024),
+ ),
+ migrations.AlterField(
+ model_name="etldata",
+ name="run_at_times",
+ field=models.TextField(
+ blank=True, default="", max_length=1024, verbose_name="At what time automatic import should run"
+ ),
+ ),
+ migrations.AlterField(
+ model_name="provenance",
+ name="modification_description",
+ field=models.TextField(max_length=20480, verbose_name="Description"),
+ ),
+ migrations.AlterField(
+ model_name="provenance",
+ name="modified_field",
+ field=models.CharField(blank="", max_length=128, verbose_name="Modified field"),
+ ),
+ migrations.AlterField(
+ model_name="provenance",
+ name="modified_table",
+ field=models.CharField(max_length=128, null=True, verbose_name="Modified table"),
+ ),
+ migrations.AlterField(
+ model_name="provenance",
+ name="new_value",
+ field=models.TextField(blank=True, max_length=2048, null=True, verbose_name="New Value"),
+ ),
+ migrations.AlterField(
+ model_name="provenance",
+ name="previous_value",
+ field=models.TextField(blank=True, max_length=2048, null=True, verbose_name="Previous Value"),
+ ),
+ migrations.AlterField(
+ model_name="provenance",
+ name="request_path",
+ field=models.TextField(blank=True, max_length=20480, null=True, verbose_name="Request Path"),
+ ),
+ ]
diff --git a/smash/web/migrations/0217_alter_vouchertype_description.py b/smash/web/migrations/0217_alter_vouchertype_description.py
new file mode 100644
index 0000000000000000000000000000000000000000..eadca30d52af9a7fda1cd48986639fd5e6103e73
--- /dev/null
+++ b/smash/web/migrations/0217_alter_vouchertype_description.py
@@ -0,0 +1,18 @@
+# Generated by Django 3.2.22 on 2024-07-30 07:16
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('web', '0216_auto_20240730_0621'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='vouchertype',
+ name='description',
+ field=models.CharField(blank=True, max_length=1024, verbose_name='Description'),
+ ),
+ ]
diff --git a/smash/web/models/appointment_type.py b/smash/web/models/appointment_type.py
index 3514afa477bd767d807fe109b4ff921dc4b33ce9..6fa48352951a59ee10a88fc18317a823cbf88e27 100644
--- a/smash/web/models/appointment_type.py
+++ b/smash/web/models/appointment_type.py
@@ -6,52 +6,26 @@ from .constants import APPOINTMENT_TYPE_DEFAULT_COLOR, APPOINTMENT_TYPE_DEFAULT_
class AppointmentType(models.Model):
class Meta:
- app_label = 'web'
- ordering = ['description']
+ app_label = "web"
+ ordering = ["description"]
- required_equipment = models.ManyToManyField("web.Item",
- verbose_name='Required equipment',
- blank=True
- )
- code = models.CharField(max_length=20,
- verbose_name='Appointment code'
- )
- description = models.CharField(max_length=2000,
- verbose_name='Appointment description'
- )
- default_duration = models.IntegerField(
- verbose_name='Default duration (in minutes)'
+ required_equipment = models.ManyToManyField("web.Item", verbose_name="Required equipment", blank=True)
+ code = models.CharField(max_length=20, verbose_name="Appointment code")
+ description = models.TextField(max_length=2000, verbose_name="Appointment description")
+ default_duration = models.IntegerField(verbose_name="Default duration (in minutes)")
+ calendar_color_priority = models.IntegerField(verbose_name="Calendar color priority", default=1)
+ calendar_color = models.TextField(
+ max_length=2000, verbose_name="Calendar color", default=APPOINTMENT_TYPE_DEFAULT_COLOR
)
- calendar_color_priority = models.IntegerField(
- verbose_name='Calendar color priority',
- default=1
+ calendar_font_color = models.TextField(
+ max_length=2000, verbose_name="Calendar font color", default=APPOINTMENT_TYPE_DEFAULT_FONT_COLOR
)
- calendar_color = models.CharField(max_length=2000,
- verbose_name='Calendar color',
- default=APPOINTMENT_TYPE_DEFAULT_COLOR
- )
- calendar_font_color = models.CharField(max_length=2000,
- verbose_name='Calendar font color',
- default=APPOINTMENT_TYPE_DEFAULT_FONT_COLOR
- )
- rest_time = models.IntegerField(
- verbose_name='Suggested rest time',
- default=0
+ rest_time = models.IntegerField(verbose_name="Suggested rest time", default=0)
+ can_be_parallelized = models.BooleanField(verbose_name="Can be parallelized", default=False)
+ REQ_ROLE_CHOICES = (("DOCTOR", "Doctor"), ("NURSE", "Nurse"), ("PSYCHOLOGIST", "Psychologist"), ("ANY", "Any"))
+ required_worker = models.CharField(
+ max_length=20, choices=REQ_ROLE_CHOICES, verbose_name="Type of worker required for appointment", default="ANY"
)
- can_be_parallelized = models.BooleanField(
- verbose_name='Can be parallelized',
- default=False
- )
- REQ_ROLE_CHOICES = (
- ('DOCTOR', 'Doctor'),
- ('NURSE', 'Nurse'),
- ('PSYCHOLOGIST', 'Psychologist'),
- ('ANY', 'Any')
- )
- required_worker = models.CharField(max_length=20, choices=REQ_ROLE_CHOICES,
- verbose_name='Type of worker required for appointment',
- default='ANY'
- )
def __str__(self):
return self.description
diff --git a/smash/web/models/configuration_item.py b/smash/web/models/configuration_item.py
index a38cba7ce76980de662e831c9f0e54a522c95a41..f3fded7fb661fd251df2c79011246867f5e2381f 100644
--- a/smash/web/models/configuration_item.py
+++ b/smash/web/models/configuration_item.py
@@ -6,11 +6,20 @@ from django.core.validators import validate_email
from django.db import models
from web.utils import strtobool
-from web.models.constants import CANCELLED_APPOINTMENT_COLOR_CONFIGURATION_TYPE, \
- NO_SHOW_APPOINTMENT_COLOR_CONFIGURATION_TYPE, KIT_EMAIL_HOUR_CONFIGURATION_TYPE, \
- KIT_EMAIL_DAY_OF_WEEK_CONFIGURATION_TYPE, KIT_DAILY_EMAIL_TIME_FORMAT_TYPE, KIT_DAILY_EMAIL_DAYS_PERIOD_TYPE, \
- VALUE_TYPE_CHOICES, VALUE_TYPE_TEXT, DEFAULT_FROM_EMAIL, VIRUS_EMAIL_HOUR_CONFIGURATION_TYPE, \
- KIT_RECIPIENT_EMAIL_CONFIGURATION_TYPE, VISIT_SHOW_VISIT_NUMBER_FROM_ZERO
+from web.models.constants import (
+ CANCELLED_APPOINTMENT_COLOR_CONFIGURATION_TYPE,
+ NO_SHOW_APPOINTMENT_COLOR_CONFIGURATION_TYPE,
+ KIT_EMAIL_HOUR_CONFIGURATION_TYPE,
+ KIT_EMAIL_DAY_OF_WEEK_CONFIGURATION_TYPE,
+ KIT_DAILY_EMAIL_TIME_FORMAT_TYPE,
+ KIT_DAILY_EMAIL_DAYS_PERIOD_TYPE,
+ VALUE_TYPE_CHOICES,
+ VALUE_TYPE_TEXT,
+ DEFAULT_FROM_EMAIL,
+ VIRUS_EMAIL_HOUR_CONFIGURATION_TYPE,
+ KIT_RECIPIENT_EMAIL_CONFIGURATION_TYPE,
+ VISIT_SHOW_VISIT_NUMBER_FROM_ZERO,
+)
def is_valid_email(value: str) -> bool:
@@ -23,36 +32,29 @@ def is_valid_email(value: str) -> bool:
class ConfigurationItem(models.Model):
class Meta:
- app_label = 'web'
+ app_label = "web"
- type = models.CharField(max_length=50,
- verbose_name='Type',
- editable=False
- )
- name = models.CharField(max_length=255,
- verbose_name='Name',
- editable=False
- )
+ type = models.CharField(max_length=50, verbose_name="Type", editable=False)
+ name = models.CharField(max_length=255, verbose_name="Name", editable=False)
- value = models.CharField(max_length=1024,
- verbose_name='Value',
- )
- value_type = models.CharField(max_length=32,
- choices=VALUE_TYPE_CHOICES,
- verbose_name='Value type',
- default=VALUE_TYPE_TEXT
- )
+ value = models.TextField(
+ max_length=1024,
+ verbose_name="Value",
+ )
+ value_type = models.CharField(
+ max_length=32, choices=VALUE_TYPE_CHOICES, verbose_name="Value type", default=VALUE_TYPE_TEXT
+ )
def __str__(self):
return f"{self.name} {self.value}"
@staticmethod
- def is_valid(item: 'ConfigurationItem') -> bool:
+ def is_valid(item: "ConfigurationItem") -> bool:
message = ConfigurationItem.validation_error(item)
return message == ""
@staticmethod
- def validation_error(item: 'ConfigurationItem') -> str:
+ def validation_error(item: "ConfigurationItem") -> str:
pattern = None
if item.type in (CANCELLED_APPOINTMENT_COLOR_CONFIGURATION_TYPE, NO_SHOW_APPOINTMENT_COLOR_CONFIGURATION_TYPE):
pattern = "^#[0-9a-fA-F]+$"
@@ -66,7 +68,7 @@ class ConfigurationItem(models.Model):
pattern = "^(%Y-%m-%d|%Y-%m-%d %H:%M)$"
if item.type == KIT_RECIPIENT_EMAIL_CONFIGURATION_TYPE:
for email in item.value.split(";"):
- if email != '' and not is_valid_email(email):
+ if email != "" and not is_valid_email(email):
return f"Email {email} address is invalid"
if item.type == DEFAULT_FROM_EMAIL:
diff --git a/smash/web/models/custom_data/custom_study_subject_field.py b/smash/web/models/custom_data/custom_study_subject_field.py
index 9d754d61041e4f09987faeb3d627390516414d90..5664f821636eba80232e71c240ffafa9c91a02ac 100644
--- a/smash/web/models/custom_data/custom_study_subject_field.py
+++ b/smash/web/models/custom_data/custom_study_subject_field.py
@@ -9,7 +9,7 @@ class CustomStudySubjectField(models.Model):
name = models.CharField(max_length=64, null=False, blank=False)
type = models.CharField(max_length=20, choices=CUSTOM_FIELD_TYPE, null=False, blank=False)
- possible_values = models.CharField(max_length=1024, null=True, blank=True, default='')
+ possible_values = models.TextField(max_length=1024, null=True, blank=True, default="")
default_value = models.CharField(max_length=256, null=True, blank=True)
readonly = models.BooleanField(default=False)
@@ -20,12 +20,7 @@ class CustomStudySubjectField(models.Model):
tracked = models.BooleanField(default=False)
- study = models.ForeignKey("web.Study",
- verbose_name='Study',
- editable=False,
- null=False,
- on_delete=models.CASCADE
- )
+ study = models.ForeignKey("web.Study", verbose_name="Study", editable=False, null=False, on_delete=models.CASCADE)
def get_study_subject_field_id(study_subject_field: CustomStudySubjectField) -> str:
diff --git a/smash/web/models/custom_data/custom_study_subject_value.py b/smash/web/models/custom_data/custom_study_subject_value.py
index 6398dfe615cdbcb1e5d07ae20a179f5348e46830..0967f117bab3c46a0f46660f2227250cb580c3fb 100644
--- a/smash/web/models/custom_data/custom_study_subject_value.py
+++ b/smash/web/models/custom_data/custom_study_subject_value.py
@@ -4,17 +4,11 @@ from django.db import models
class CustomStudySubjectValue(models.Model):
- value = models.CharField(max_length=2048, null=True, blank=True)
-
- study_subject_field = models.ForeignKey("web.CustomStudySubjectField",
- verbose_name='Custom Field',
- editable=False,
- null=False,
- on_delete=models.CASCADE
- )
- study_subject = models.ForeignKey("web.StudySubject",
- verbose_name='Study',
- editable=False,
- null=False,
- on_delete=models.CASCADE
- )
+ value = models.TextField(max_length=2048, null=True, blank=True)
+
+ study_subject_field = models.ForeignKey(
+ "web.CustomStudySubjectField", verbose_name="Custom Field", editable=False, null=False, on_delete=models.CASCADE
+ )
+ study_subject = models.ForeignKey(
+ "web.StudySubject", verbose_name="Study", editable=False, null=False, on_delete=models.CASCADE
+ )
diff --git a/smash/web/models/etl/etl_column_mapping.py b/smash/web/models/etl/etl_column_mapping.py
index 9bc36b991eede5b48ffef5e0bbadeb246cf49a96..a08674ac2dc6dce724a338a7646eaad603b3c3a6 100644
--- a/smash/web/models/etl/etl_column_mapping.py
+++ b/smash/web/models/etl/etl_column_mapping.py
@@ -7,33 +7,19 @@ logger = logging.getLogger(__name__)
class EtlColumnMapping(models.Model):
- etl_data = models.ForeignKey("web.EtlData",
- verbose_name='Importer',
- editable=False,
- null=False,
- on_delete=models.CASCADE,
- related_name="column_mappings"
- )
-
- table_name = models.CharField(max_length=128,
- default='',
- null=False,
- blank=True
- )
-
- column_name = models.CharField(max_length=128,
- default='',
- null=False,
- blank=True
- )
-
- csv_column_name = models.CharField(max_length=1024,
- default='',
- null=False,
- blank=True
- )
-
- enabled = models.BooleanField(default=True,
- null=False,
- blank=False
- )
+ etl_data = models.ForeignKey(
+ "web.EtlData",
+ verbose_name="Importer",
+ editable=False,
+ null=False,
+ on_delete=models.CASCADE,
+ related_name="column_mappings",
+ )
+
+ table_name = models.CharField(max_length=128, default="", null=False, blank=True)
+
+ column_name = models.CharField(max_length=128, default="", null=False, blank=True)
+
+ csv_column_name = models.TextField(max_length=1024, default="", null=False, blank=True)
+
+ enabled = models.BooleanField(default=True, null=False, blank=False)
diff --git a/smash/web/models/etl/etl_data.py b/smash/web/models/etl/etl_data.py
index 9316adb93a6b3337f74496ef00c265fbd9b5c4c2..f3cbd22ad12c509babf5c13cc8171e42362e951a 100644
--- a/smash/web/models/etl/etl_data.py
+++ b/smash/web/models/etl/etl_data.py
@@ -13,48 +13,32 @@ logger = logging.getLogger(__name__)
class EtlData(models.Model):
- study = models.ForeignKey("web.Study",
- verbose_name='Study',
- editable=False,
- null=False,
- on_delete=models.CASCADE
- )
-
- filename = models.CharField(max_length=128,
- verbose_name='File used for automatic import',
- default='',
- null=False,
- blank=True
- )
- run_at_times = models.CharField(max_length=1024,
- verbose_name='At what time automatic import should run',
- default='',
- null=False,
- blank=True
- )
-
- csv_delimiter = models.CharField(max_length=1,
- verbose_name='CSV delimiter',
- default=',',
- null=False,
- blank=False
- )
- date_format = models.CharField(max_length=20,
- verbose_name='Date format',
- default='%Y-%m-%d',
- null=False,
- blank=False
- )
+ study = models.ForeignKey("web.Study", verbose_name="Study", editable=False, null=False, on_delete=models.CASCADE)
+
+ filename = models.CharField(
+ max_length=128, verbose_name="File used for automatic import", default="", null=False, blank=True
+ )
+ run_at_times = models.TextField(
+ max_length=1024, verbose_name="At what time automatic import should run", default="", null=False, blank=True
+ )
+
+ csv_delimiter = models.CharField(max_length=1, verbose_name="CSV delimiter", default=",", null=False, blank=False)
+ date_format = models.CharField(
+ max_length=20, verbose_name="Date format", default="%Y-%m-%d", null=False, blank=False
+ )
def set_column_mapping(self, object_type: Type[models.Model], column_name: str, csv_column_name: str):
for entry in self.column_mappings.all():
- if entry.table_name == object_type._meta.db_table and \
- entry.column_name == column_name:
+ if entry.table_name == object_type._meta.db_table and entry.column_name == column_name:
entry.csv_column_name = csv_column_name
entry.save()
return
- EtlColumnMapping.objects.create(etl_data=self, table_name=object_type._meta.db_table, column_name=column_name,
- csv_column_name=csv_column_name)
+ EtlColumnMapping.objects.create(
+ etl_data=self,
+ table_name=object_type._meta.db_table,
+ column_name=column_name,
+ csv_column_name=csv_column_name,
+ )
def get_absolute_file_path(self) -> str:
return os.path.join(settings.ETL_ROOT, self.filename)
diff --git a/smash/web/models/privacy_notice.py b/smash/web/models/privacy_notice.py
index 62e7fc177dfa2d87c05feedbf21f3cfcf66a78b4..03a68bbc4c3efc0df028d72b600ad2ff83d090f6 100644
--- a/smash/web/models/privacy_notice.py
+++ b/smash/web/models/privacy_notice.py
@@ -5,19 +5,20 @@ from django.db import models
from django.dispatch import receiver
from web.templatetags.filters import basename
+from web import disable_for_loaddata
class PrivacyNotice(models.Model):
- name = models.CharField(max_length=255, verbose_name='Name')
- created_at = models.DateTimeField(auto_now_add=True, verbose_name='Created at')
- updated_at = models.DateTimeField(auto_now=True, verbose_name='Updated at')
- summary = models.CharField(max_length=255, verbose_name='Summary', blank=False, null=False)
- document = models.FileField(upload_to='privacy_notices/',
- verbose_name='Study Privacy Notice file',
- null=False, editable=True)
+ name = models.CharField(max_length=255, verbose_name="Name")
+ created_at = models.DateTimeField(auto_now_add=True, verbose_name="Created at")
+ updated_at = models.DateTimeField(auto_now=True, verbose_name="Updated at")
+ summary = models.CharField(max_length=255, verbose_name="Summary", blank=False, null=False)
+ document = models.FileField(
+ upload_to="privacy_notices/", verbose_name="Study Privacy Notice file", null=False, editable=True
+ )
def __str__(self):
- return f'{self.name} ({basename(self.document.url)})'
+ return f"{self.name} ({basename(self.document.url)})"
@property
def all_studies(self):
@@ -26,7 +27,9 @@ class PrivacyNotice(models.Model):
# These two auto-delete files from filesystem when they are unneeded:
+
@receiver(models.signals.post_delete, sender=PrivacyNotice)
+@disable_for_loaddata
def auto_delete_file_on_delete(sender, instance: PrivacyNotice, **kwargs): # pylint: disable=unused-argument
"""
Deletes file from filesystem
@@ -38,6 +41,7 @@ def auto_delete_file_on_delete(sender, instance: PrivacyNotice, **kwargs): # py
@receiver(models.signals.pre_save, sender=PrivacyNotice)
+@disable_for_loaddata
def auto_delete_file_on_change(sender, instance: PrivacyNotice, **kwargs): # pylint: disable=unused-argument
"""
Deletes old file from filesystem
diff --git a/smash/web/models/provenance.py b/smash/web/models/provenance.py
index 8739b6a3abee7287f888dd56a9379d5e25fff592..ae91de57b9ef398479bc3c0b60dbb8178961a65a 100644
--- a/smash/web/models/provenance.py
+++ b/smash/web/models/provenance.py
@@ -4,48 +4,31 @@ from django.db import models
class Provenance(models.Model):
class Meta:
- app_label = 'web'
- index_together = ['modified_table', 'modified_table_id', 'modification_date']
+ app_label = "web"
+ index_together = ["modified_table", "modified_table_id", "modification_date"]
- modified_table = models.CharField(max_length=1024,
- verbose_name='Modified table',
- blank=False, null=True
- )
+ modified_table = models.CharField(max_length=128, verbose_name="Modified table", blank=False, null=True)
- modified_table_id = models.IntegerField(default=0, verbose_name='Modified table row', blank=False, null=True)
+ modified_table_id = models.IntegerField(default=0, verbose_name="Modified table row", blank=False, null=True)
- modification_date = models.DateTimeField(
- verbose_name='Modified on',
- null=False, blank=False,
- auto_now_add=True
- )
+ modification_date = models.DateTimeField(verbose_name="Modified on", null=False, blank=False, auto_now_add=True)
- modification_author = models.ForeignKey("web.Worker",
- verbose_name='Worker who modified the row',
- null=True, blank=False, on_delete=models.deletion.CASCADE
- )
+ modification_author = models.ForeignKey(
+ "web.Worker",
+ verbose_name="Worker who modified the row",
+ null=True,
+ blank=False,
+ on_delete=models.deletion.CASCADE,
+ )
- modified_field = models.CharField(max_length=1024,
- verbose_name='Modified field',
- blank='', null=False
- )
+ modified_field = models.CharField(max_length=128, verbose_name="Modified field", blank="", null=False)
- previous_value = models.CharField(max_length=2048,
- verbose_name='Previous Value',
- blank=True, null=True)
+ previous_value = models.TextField(max_length=2048, verbose_name="Previous Value", blank=True, null=True)
- new_value = models.CharField(max_length=2048,
- verbose_name='New Value',
- blank=True, null=True)
+ new_value = models.TextField(max_length=2048, verbose_name="New Value", blank=True, null=True)
- modification_description = models.CharField(max_length=20480,
- verbose_name='Description',
- blank=False, null=False
- )
+ modification_description = models.TextField(max_length=20480, verbose_name="Description", blank=False, null=False)
- request_path = models.CharField(max_length=20480,
- verbose_name='Request Path',
- blank=True, null=True
- )
+ request_path = models.TextField(max_length=20480, verbose_name="Request Path", blank=True, null=True)
- request_ip_addr = models.GenericIPAddressField(verbose_name='Request IP Address', null=True)
+ request_ip_addr = models.GenericIPAddressField(verbose_name="Request IP Address", null=True)
diff --git a/smash/web/models/study_subject.py b/smash/web/models/study_subject.py
index 49d87c7509d0059335cfc3f190f1cadfea008ee9..f7ecc3be65a470b18d6b56bcf8b2dab1e0dbb835 100644
--- a/smash/web/models/study_subject.py
+++ b/smash/web/models/study_subject.py
@@ -10,6 +10,7 @@ from django.dispatch import receiver
from web.models import Appointment, Location, Provenance, Visit, VoucherType
from web.models.constants import BOOL_CHOICES, FILE_STORAGE
from web.models.custom_data import CustomStudySubjectField, CustomStudySubjectValue
+from web import disable_for_loaddata
logger = logging.getLogger(__name__)
@@ -214,16 +215,12 @@ class StudySubject(models.Model):
def custom_data_values(self):
# find the custom fields that have not yet been populated into the study subject
# https://docs.djangoproject.com/en/3.2/ref/models/querysets/#filteredrelation-objects
- fields = (
- CustomStudySubjectField.objects
- .annotate(
- t=FilteredRelation(
- "customstudysubjectvalue",
- condition=Q(customstudysubjectvalue__study_subject=self),
- )
+ fields = CustomStudySubjectField.objects.annotate(
+ t=FilteredRelation(
+ "customstudysubjectvalue",
+ condition=Q(customstudysubjectvalue__study_subject=self),
)
- .filter(t__study_subject_field__isnull=True, study=self.study)
- )
+ ).filter(t__study_subject_field__isnull=True, study=self.study)
for field in fields:
CustomStudySubjectValue.objects.create(
@@ -273,6 +270,7 @@ class StudySubject(models.Model):
# SIGNALS
@receiver(post_save, sender=StudySubject)
+@disable_for_loaddata
def set_as_resigned_or_excluded_or_endpoint_reached(sender, instance, **kwargs): # pylint: disable=unused-argument
if instance.excluded:
instance.mark_as_excluded()
diff --git a/smash/web/models/subject.py b/smash/web/models/subject.py
index c704304db4cc058faa5fcc33e9063c01e4968ebd..3838ab81664eb61048912a7b1b7c13d29c998ce3 100644
--- a/smash/web/models/subject.py
+++ b/smash/web/models/subject.py
@@ -7,6 +7,7 @@ from django.dispatch import receiver
from .constants import SEX_CHOICES, COUNTRY_OTHER_ID
from web.models import Country, Visit, Appointment, Provenance
+from web import disable_for_loaddata
from . import Language
logger = logging.getLogger(__name__)
@@ -14,121 +15,69 @@ logger = logging.getLogger(__name__)
class Subject(models.Model):
class Meta:
- app_label = 'web'
+ app_label = "web"
permissions = [
("export_subjects", "Can export subject data to excel/csv"),
]
@property
def provenances(self):
- return Provenance.objects.filter(modified_table=Subject._meta.db_table, modified_table_id=self.id)\
- .order_by('-modification_date')
-
- sex = models.CharField(max_length=1,
- choices=SEX_CHOICES,
- verbose_name='Sex'
- )
-
- first_name = models.CharField(max_length=50,
- verbose_name='First name'
- )
-
- social_security_number = models.CharField(max_length=50,
- verbose_name='Social security number',
- blank=True,
- )
-
- last_name = models.CharField(max_length=50,
- verbose_name='Last name'
- )
-
- languages = models.ManyToManyField(Language,
- blank=True,
- verbose_name='Known languages'
- )
-
- default_written_communication_language = models.ForeignKey(Language,
- null=True,
- blank=True,
- related_name="subjects_written_communication",
- verbose_name='Default language for document generation',
- on_delete=models.SET_NULL
- )
- phone_number = models.CharField(max_length=64,
- null=True,
- blank=True,
- verbose_name='Phone number'
- )
-
- phone_number_2 = models.CharField(max_length=64,
- null=True,
- blank=True,
- verbose_name='Phone number 2'
- )
-
- phone_number_3 = models.CharField(max_length=64,
- null=True,
- blank=True,
- verbose_name='Phone number 3'
- )
-
- email = models.EmailField(
- null=True,
+ return Provenance.objects.filter(modified_table=Subject._meta.db_table, modified_table_id=self.id).order_by(
+ "-modification_date"
+ )
+
+ sex = models.CharField(max_length=1, choices=SEX_CHOICES, verbose_name="Sex")
+
+ first_name = models.CharField(max_length=50, verbose_name="First name")
+
+ social_security_number = models.CharField(
+ max_length=50,
+ verbose_name="Social security number",
blank=True,
- verbose_name='E-mail'
)
- date_born = models.DateField(
+ last_name = models.CharField(max_length=50, verbose_name="Last name")
+
+ languages = models.ManyToManyField(Language, blank=True, verbose_name="Known languages")
+
+ default_written_communication_language = models.ForeignKey(
+ Language,
null=True,
blank=True,
- verbose_name='Date of birth (YYYY-MM-DD)'
+ related_name="subjects_written_communication",
+ verbose_name="Default language for document generation",
+ on_delete=models.SET_NULL,
)
+ phone_number = models.CharField(max_length=64, null=True, blank=True, verbose_name="Phone number")
+
+ phone_number_2 = models.CharField(max_length=64, null=True, blank=True, verbose_name="Phone number 2")
+
+ phone_number_3 = models.CharField(max_length=64, null=True, blank=True, verbose_name="Phone number 3")
+
+ email = models.EmailField(null=True, blank=True, verbose_name="E-mail")
- address = models.CharField(max_length=255,
- blank=True,
- verbose_name='Address'
- )
-
- postal_code = models.CharField(max_length=7,
- blank=True,
- verbose_name='Postal code'
- )
-
- city = models.CharField(max_length=50,
- blank=True,
- verbose_name='City'
- )
-
- country = models.ForeignKey(Country,
- null=False,
- blank=False,
- default=COUNTRY_OTHER_ID,
- verbose_name='Country', on_delete=models.CASCADE
- )
-
- next_of_kin_name = models.CharField(max_length=255,
- blank=True,
- verbose_name='Next of kin'
- )
-
- next_of_kin_phone = models.CharField(max_length=50,
- blank=True,
- verbose_name='Next of kin phone'
- )
-
- next_of_kin_address = models.TextField(max_length=2000,
- blank=True,
- verbose_name='Next of kin address'
- )
-
- dead = models.BooleanField(
- verbose_name='Deceased',
- default=False,
- editable=True
+ date_born = models.DateField(null=True, blank=True, verbose_name="Date of birth (YYYY-MM-DD)")
+
+ address = models.CharField(max_length=255, blank=True, verbose_name="Address")
+
+ postal_code = models.CharField(max_length=7, blank=True, verbose_name="Postal code")
+
+ city = models.CharField(max_length=50, blank=True, verbose_name="City")
+
+ country = models.ForeignKey(
+ Country, null=False, blank=False, default=COUNTRY_OTHER_ID, verbose_name="Country", on_delete=models.CASCADE
)
+ next_of_kin_name = models.CharField(max_length=255, blank=True, verbose_name="Next of kin")
+
+ next_of_kin_phone = models.CharField(max_length=50, blank=True, verbose_name="Next of kin phone")
+
+ next_of_kin_address = models.TextField(max_length=2000, blank=True, verbose_name="Next of kin address")
+
+ dead = models.BooleanField(verbose_name="Deceased", default=False, editable=True)
+
def pretty_address(self):
- return f'{self.address} ({self.postal_code}), {self.city}. {self.country}'
+ return f"{self.address} ({self.postal_code}), {self.city}. {self.country}"
def mark_as_dead(self):
self.dead = True
@@ -142,8 +91,9 @@ class Subject(models.Model):
visit.save()
def finish_all_appointments(self):
- appointments = Appointment.objects.filter(visit__subject__subject=self,
- status=Appointment.APPOINTMENT_STATUS_SCHEDULED)
+ appointments = Appointment.objects.filter(
+ visit__subject__subject=self, status=Appointment.APPOINTMENT_STATUS_SCHEDULED
+ )
for appointment in appointments:
appointment.status = Appointment.APPOINTMENT_STATUS_CANCELLED
appointment.save()
@@ -154,13 +104,17 @@ class Subject(models.Model):
# SIGNALS
@receiver(post_save, sender=Subject)
+@disable_for_loaddata
def set_as_deceased(sender, instance, **kwargs): # pylint: disable=unused-argument
if instance.dead:
- p = Provenance(modified_table=Subject._meta.db_table,
- modified_table_id=instance.id, modification_author=None,
- previous_value=instance.dead, new_value=True,
- modification_description=f'Subject "{instance}" marked as dead',
- modified_field='dead',
- )
+ p = Provenance(
+ modified_table=Subject._meta.db_table,
+ modified_table_id=instance.id,
+ modification_author=None,
+ previous_value=instance.dead,
+ new_value=True,
+ modification_description=f'Subject "{instance}" marked as dead',
+ modified_field="dead",
+ )
instance.mark_as_dead()
p.save()
diff --git a/smash/web/models/visit.py b/smash/web/models/visit.py
index 47fe940691c7b2b845bb508b3466238a6e1f8a2b..c45661e194e6700dce0f7a704990ec5172ef32de 100644
--- a/smash/web/models/visit.py
+++ b/smash/web/models/visit.py
@@ -8,61 +8,65 @@ from django.db.models.signals import post_save
from django.dispatch import receiver
from web.models.constants import BOOL_CHOICES
+from web import disable_for_loaddata
logger = logging.getLogger(__name__)
class Visit(models.Model):
class Meta:
- app_label = 'web'
+ app_label = "web"
- subject = models.ForeignKey("web.StudySubject", on_delete=models.CASCADE, verbose_name='Subject'
- )
- datetime_begin = models.DateTimeField(
- verbose_name='Visit starts at'
+ subject = models.ForeignKey(
+ "web.StudySubject", on_delete=models.CASCADE, verbose_name="Subject"
)
+ datetime_begin = models.DateTimeField(verbose_name="Visit starts at")
datetime_end = models.DateTimeField(
- verbose_name='Visit ends at'
+ verbose_name="Visit ends at"
) # Deadline before which all appointments need to be scheduled
- is_finished = models.BooleanField(
- verbose_name='Has ended',
- default=False
+ is_finished = models.BooleanField(verbose_name="Has ended", default=False)
+ post_mail_sent = models.BooleanField(
+ choices=BOOL_CHOICES, verbose_name="Post mail sent", default=False
+ )
+ appointment_types = models.ManyToManyField(
+ "web.AppointmentType",
+ verbose_name="Requested appointments",
+ blank=True,
)
- post_mail_sent = models.BooleanField(choices=BOOL_CHOICES,
- verbose_name='Post mail sent',
- default=False
- )
- appointment_types = models.ManyToManyField("web.AppointmentType",
- verbose_name='Requested appointments',
- blank=True,
- )
# this value is automatically computed by signal handled by
# update_visit_number method
- visit_number = models.IntegerField(
- verbose_name='Visit number',
- default=1
- )
+ visit_number = models.IntegerField(verbose_name="Visit number", default=1)
@property
def next_visit(self):
- return Visit.objects.filter(subject=self.subject, visit_number=self.visit_number + 1) \
- .order_by('datetime_begin', 'datetime_end').first()
+ return (
+ Visit.objects.filter(
+ subject=self.subject, visit_number=self.visit_number + 1
+ )
+ .order_by("datetime_begin", "datetime_end")
+ .first()
+ )
@property
def future_visits(self):
- return Visit.objects.filter(subject=self.subject).filter(visit_number__gt=self.visit_number) \
- .order_by('datetime_begin', 'datetime_end')
+ return (
+ Visit.objects.filter(subject=self.subject)
+ .filter(visit_number__gt=self.visit_number)
+ .order_by("datetime_begin", "datetime_end")
+ )
def __str__(self):
- start = self.datetime_begin.strftime('%Y-%m-%d')
- end = self.datetime_end.strftime('%Y-%m-%d')
- finished = '✓' if self.is_finished else ''
- return f'#{self.visit_number:02} ' \
- f'| {start} / {end} ' \
- f'| {self.subject.subject.first_name} {self.subject.subject.last_name} ' \
- f'| {finished}'
+ start = self.datetime_begin.strftime("%Y-%m-%d")
+ end = self.datetime_end.strftime("%Y-%m-%d")
+ finished = "✓" if self.is_finished else ""
+ return (
+ f"#{self.visit_number:02} "
+ f"| {start} / {end} "
+ f"| {self.subject.subject.first_name} {self.subject.subject.last_name} "
+ f"| {finished}"
+ )
def mark_as_finished(self):
self.is_finished = True
@@ -82,46 +86,68 @@ class Visit(models.Model):
if create_follow_up:
if self.subject.visit_used_to_compute_followup_date is not None:
- visit_started = self.subject.visit_used_to_compute_followup_date.datetime_begin
- start_number = self.subject.visit_used_to_compute_followup_date.visit_number
+ visit_started = (
+ self.subject.visit_used_to_compute_followup_date.datetime_begin
+ )
+ start_number = (
+ self.subject.visit_used_to_compute_followup_date.visit_number
+ )
else:
- visit_started = Visit.objects.filter(subject=self.subject, visit_number=1).first().datetime_begin
+ visit_started = (
+ Visit.objects.filter(subject=self.subject, visit_number=1)
+ .first()
+ .datetime_begin
+ )
start_number = 1
follow_up_number = Visit.objects.filter(subject=self.subject).count() + 1
study = self.subject.study
- args = {self.subject.type.follow_up_delta_units: self.subject.type.follow_up_delta_time}
+ args = {
+ self.subject.type.follow_up_delta_units: self.subject.type.follow_up_delta_time
+ }
- time_to_next_visit = relativedelta(**args) * (follow_up_number - start_number)
+ time_to_next_visit = relativedelta(**args) * (
+ follow_up_number - start_number
+ )
- logger.warning('new visit: %s %s %s', args, relativedelta(**args), time_to_next_visit)
+ logger.warning(
+ "new visit: %s %s %s", args, relativedelta(**args), time_to_next_visit
+ )
Visit.objects.create(
subject=self.subject,
datetime_begin=visit_started + time_to_next_visit,
- datetime_end=visit_started + time_to_next_visit + relativedelta(
- months=study.default_visit_duration_in_months)
+ datetime_end=visit_started
+ + time_to_next_visit
+ + relativedelta(months=study.default_visit_duration_in_months),
)
def unfinish(self):
# if ValueError messages are changed, change test/view/test_visit.py
# check visit is indeed finished
if not self.is_finished:
- raise ValueError('The visit is not finished.')
+ raise ValueError("The visit is not finished.")
# check if there are some unfinished visits before this visit
- unfinished_visits = Visit.objects.filter(subject=self.subject,
- is_finished=False, datetime_begin__lt=self.datetime_begin).count()
+ unfinished_visits = Visit.objects.filter(
+ subject=self.subject,
+ is_finished=False,
+ datetime_begin__lt=self.datetime_begin,
+ ).count()
if unfinished_visits > 0:
- raise ValueError("Visit can't be unfinished. There is at least one unfinished visit.")
+ raise ValueError(
+ "Visit can't be unfinished. There is at least one unfinished visit."
+ )
# check that there is only one future visit
future_visits = self.future_visits
if len(future_visits) > 1:
- raise ValueError("Visit can't be unfinished. "
- "Only visits with one immediate future visit (without appointments) can be unfinished.")
+ raise ValueError(
+ "Visit can't be unfinished. "
+ "Only visits with one immediate future visit (without appointments) can be unfinished."
+ )
elif len(future_visits) == 1:
# check that the future visit has no appointments
# remove visit if it has no appointments
@@ -132,7 +158,9 @@ class Visit(models.Model):
self.subject.save()
next_visit.delete()
else:
- raise ValueError("Visit can't be unfinished. The next visit has appointments.")
+ raise ValueError(
+ "Visit can't be unfinished. The next visit has appointments."
+ )
else:
# this can happen when there is no auto follow up visit
@@ -143,33 +171,58 @@ class Visit(models.Model):
@receiver(post_save, sender=Visit)
-def check_visit_number(sender, instance, created, **kwargs): # pylint: disable=unused-argument
+@disable_for_loaddata
+def check_visit_number(
+ sender, instance, created, **kwargs
+): # pylint: disable=unused-argument
# no other solution to ensure the visit_number is in chronological order than to sort the whole list if there are
# future visits
visit = instance
- if visit.subject is not None: # not sure if select_for_update has an effect, the tests work as well without it
+ if (
+ visit.subject is not None
+ ): # not sure if select_for_update has an effect, the tests work as well without it
# new visit, sort only future visit respect to the new one
if created:
- visits_before = Visit.objects.select_for_update().filter(subject=visit.subject) \
- .filter(datetime_begin__lt=visit.datetime_begin).count()
+ visits_before = (
+ Visit.objects.select_for_update()
+ .filter(subject=visit.subject)
+ .filter(datetime_begin__lt=visit.datetime_begin)
+ .count()
+ )
# we need to sort the future visits respect to the new one, if any
- visits = Visit.objects.select_for_update().filter(subject=visit.subject) \
- .filter(datetime_begin__gte=visit.datetime_begin).order_by('datetime_begin', 'id')
+ visits = (
+ Visit.objects.select_for_update()
+ .filter(subject=visit.subject)
+ .filter(datetime_begin__gte=visit.datetime_begin)
+ .order_by("datetime_begin", "id")
+ )
with transaction.atomic(): # not sure if it has an effect, the tests work as well without it
for i, v in enumerate(visits):
- expected_visit_number = (visits_before + i + 1)
+ expected_visit_number = visits_before + i + 1
if v.visit_number != expected_visit_number:
# does not rise post_save, we avoid recursion
- Visit.objects.filter(id=v.id).update(visit_number=expected_visit_number)
- if v.id == visit.id: # if the iteration visit is the same that the instance that produced the
+ Visit.objects.filter(id=v.id).update(
+ visit_number=expected_visit_number
+ )
+ if (
+ v.id == visit.id
+ ): # if the iteration visit is the same that the instance that produced the
# signal call this ensures that the upper saved object is also updated, otherwise,
# refresh_from_db should be called
visit.visit_number = v.visit_number
else:
# if visits are modified, then, check everything
- visits = Visit.objects.select_for_update().filter(subject=visit.subject).order_by('datetime_begin', 'id')
+ visits = (
+ Visit.objects.select_for_update()
+ .filter(subject=visit.subject)
+ .order_by("datetime_begin", "id")
+ )
with transaction.atomic():
for i, v in enumerate(visits):
- expected_visit_number = (i + 1)
- if v.visit_number != expected_visit_number: # update only those with wrong numbers
- Visit.objects.filter(id=v.id).update(visit_number=expected_visit_number)
+ expected_visit_number = i + 1
+ if (
+ v.visit_number != expected_visit_number
+ ): # update only those with wrong numbers
+ Visit.objects.filter(id=v.id).update(
+ visit_number=expected_visit_number
+ )
diff --git a/smash/web/officeAvailability.py b/smash/web/officeAvailability.py
index f7a154194f7e27517f79e674776c8470f4540344..21590071cd576aec1879b0b28b3637191f46fb81 100644
--- a/smash/web/officeAvailability.py
+++ b/smash/web/officeAvailability.py
@@ -29,7 +29,15 @@ class OfficeAvailability:
Docs: https://pandas.pydata.org/pandas-docs/stable/generated/pandas.date_range.html
"""
- def __init__(self, name, start=None, end=None, office_start="8:00", office_end="18:00", minimum_slot="1T"):
+ def __init__(
+ self,
+ name,
+ start=None,
+ end=None,
+ office_start="8:00",
+ office_end="18:00",
+ minimum_slot="1T",
+ ):
self.business_hours = None
today_midnight = get_today_midnight_date()
@@ -49,8 +57,12 @@ class OfficeAvailability:
self.office_start = office_start
self.office_end = office_end
self.minimum_slot = minimum_slot
- self.range = pd.date_range(start=self.start, end=self.end, freq=self.minimum_slot)
- logger.debug("Name: %s. Min index: %s. Max index: %s", self.name, self.start, self.end)
+ self.range = pd.date_range(
+ start=self.start, end=self.end, freq=self.minimum_slot
+ )
+ logger.debug(
+ "Name: %s. Min index: %s. Max index: %s", self.name, self.start, self.end
+ )
self.availability = pd.Series(index=self.range, data=0) # initialize range at 0
def _get_duration(self):
@@ -66,7 +78,11 @@ class OfficeAvailability:
"""
availability_range = availability_range.round(self.minimum_slot)
if only_working_hours:
- availability_range = availability_range.to_series().between_time(self.office_start, self.office_end).index
+ availability_range = (
+ availability_range.to_series()
+ .between_time(self.office_start, self.office_end)
+ .index
+ )
self.availability[availability_range] = 1
def remove_availability(self, availability_range, only_working_hours=False):
@@ -76,7 +92,11 @@ class OfficeAvailability:
"""
availability_range = availability_range.round(self.minimum_slot)
if only_working_hours:
- availability_range = availability_range.to_series().between_time(self.office_start, self.office_end).index
+ availability_range = (
+ availability_range.to_series()
+ .between_time(self.office_start, self.office_end)
+ .index
+ )
self.availability[availability_range] = 0
def _ensure_dates_are_in_bounds(self, given_start, given_end):
@@ -101,7 +121,9 @@ class OfficeAvailability:
return start, end
- def consider_this(self, appointment_availability_or_holiday, only_working_hours=False):
+ def consider_this(
+ self, appointment_availability_or_holiday, only_working_hours=False
+ ):
"""
:appointment_availability_or_holiday can be an object from the following classes: Availability, Holiday,
Appointment, AppointmentTypeLink.
@@ -132,9 +154,16 @@ class OfficeAvailability:
start = appointment_availability_or_holiday.available_from
end = appointment_availability_or_holiday.available_till
weekday = appointment_availability_or_holiday.day_number
- logger.debug("Considering Availability from %s to %s for weekday %d", start, end, weekday)
+ logger.debug(
+ "Considering Availability from %s to %s for weekday %d",
+ start,
+ end,
+ weekday,
+ )
# selects the weekdays and then the specific hours
- portion = self.availability[self.availability.index.weekday == (weekday - 1)].between_time(start, end)
+ portion = self.availability[
+ self.availability.index.weekday == (weekday - 1)
+ ].between_time(start, end)
set_to = 1
elif isinstance(appointment_availability_or_holiday, Holiday):
start = appointment_availability_or_holiday.datetime_start
@@ -143,27 +172,41 @@ class OfficeAvailability:
# from 1960 to 2120 creating a huge pd.Range)
logger.debug(
"Considering %s from %s to %s",
- "Extra Availability" if appointment_availability_or_holiday.kind == AVAILABILITY_EXTRA else "Holiday",
+ (
+ "Extra Availability"
+ if appointment_availability_or_holiday.kind == AVAILABILITY_EXTRA
+ else "Holiday"
+ ),
start,
end,
)
try:
start, end = self._ensure_dates_are_in_bounds(start, end)
except ValueError:
- logger.debug("Holiday range does not overlap the availability range. Ignoring Holiday.")
+ logger.debug(
+ "Holiday range does not overlap the availability range. Ignoring Holiday."
+ )
return
portion = self.availability[
pd.date_range(start=start, end=end, freq=self.minimum_slot)
] # select the specific range
- set_to = 1 if appointment_availability_or_holiday.kind == AVAILABILITY_EXTRA else 0
+ set_to = (
+ 1
+ if appointment_availability_or_holiday.kind == AVAILABILITY_EXTRA
+ else 0
+ )
elif isinstance(appointment_availability_or_holiday, Appointment):
start = appointment_availability_or_holiday.datetime_when
- end = start + datetime.timedelta(minutes=appointment_availability_or_holiday.length)
+ end = start + datetime.timedelta(
+ minutes=appointment_availability_or_holiday.length
+ )
logger.debug("Considering General Appointment from %s to %s", start, end)
try:
start, end = self._ensure_dates_are_in_bounds(start, end)
except ValueError:
- logger.debug("Appointment range does not overlap the availability range. Ignoring Appointment.")
+ logger.debug(
+ "Appointment range does not overlap the availability range. Ignoring Appointment."
+ )
return
portion = self.availability[
pd.date_range(start=start, end=end, freq=self.minimum_slot)
@@ -187,7 +230,9 @@ class OfficeAvailability:
] # select the specific range
set_to = 0
else:
- logger.error("Expected Availability, Holiday, Appointment or AppointmentTypeLink objects.")
+ logger.error(
+ "Expected Availability, Holiday, Appointment or AppointmentTypeLink objects."
+ )
raise TypeError
if only_working_hours:
@@ -195,7 +240,8 @@ class OfficeAvailability:
# limit portion to be changed to the bounds of the object time space (solution 1 of the aforementioned problem)
portion = portion[
- (self.availability.index.min() <= portion.index) & (portion.index <= self.availability.index.max())
+ (self.availability.index.min() <= portion.index)
+ & (portion.index <= self.availability.index.max())
]
self.availability[portion.index] = set_to
@@ -219,18 +265,25 @@ class OfficeAvailability:
10000 loops each)
"""
if only_working_hours:
- availability = self.availability.between_time(self.office_start, self.office_end)
+ availability = self.availability.between_time(
+ self.office_start, self.office_end
+ )
else:
availability = self.availability
- return availability.mean() * 100 # better to isolate the operation in case we change it later
+ return (
+ availability.mean() * 100
+ ) # better to isolate the operation in case we change it later
def is_available(self, only_working_hours=False):
"""
Returns True if on the selected period is available at least 50% of the time
Otherwise returns False
"""
- return self.get_availability_percentage(only_working_hours=only_working_hours) > 50.0
+ return (
+ self.get_availability_percentage(only_working_hours=only_working_hours)
+ > 50.0
+ )
def plot_availability(self):
"""
@@ -244,7 +297,12 @@ class OfficeAvailability:
mask = business_hours.between_time(self.office_start, self.office_end).index
business_hours[mask] = 1
axes = business_hours.plot(
- kind="area", alpha=0.33, color="#1190D8", label="Business Hours", legend=True, ax=axes
+ kind="area",
+ alpha=0.33,
+ color="#1190D8",
+ label="Business Hours",
+ legend=True,
+ ax=axes,
)
# calculate good xticks
@@ -293,4 +351,6 @@ class OfficeAvailability:
axes.set_xlabel("Date & Time")
fig.tight_layout()
- fig.savefig(f"{self.name}_{self.start.strftime('%Y%m%d%H%M')}_{self.end.strftime('%Y%m%d%H%M')}.pdf")
+ fig.savefig(
+ f"{self.name}_{self.start.strftime('%Y%m%d%H%M')}_{self.end.strftime('%Y%m%d%H%M')}.pdf"
+ )
diff --git a/smash/web/statistics.py b/smash/web/statistics.py
index 75991b35fca4b40715fd8fd4e8f3119bc63151af..bd3eb875fab49207d0cb1f07dd1f86836ff0e0a9 100644
--- a/smash/web/statistics.py
+++ b/smash/web/statistics.py
@@ -10,7 +10,7 @@ from django.db.models import Q, Count
from web.migration_functions import is_sqlite_db
from .models import AppointmentType, Appointment, Visit, SubjectType
-__author__ = 'Valentin Grouès'
+__author__ = "Valentin Grouès"
def extract_month_sql(field_name):
@@ -31,59 +31,94 @@ QUERY_VISITS_RANKS = """
SELECT DISTINCT(visit_number) AS rank FROM web_visit
"""
-QUERY_APPOINTMENTS_COUNT = """
+QUERY_APPOINTMENTS_COUNT = (
+ """
SELECT count(*) FROM web_appointment LEFT JOIN (SELECT id, subject_id as web_visit_subject_id,
visit_number AS rnk FROM web_visit)
a ON a.id = web_appointment.visit_id
LEFT JOIN web_studysubject ON web_studysubject.id = web_visit_subject_id
WHERE a.rnk = %s
-AND """ + extract_month_sql("web_appointment.datetime_when") + """ = %s
-AND """ + extract_year_sql("web_appointment.datetime_when") + """ = %s
+AND """
+ + extract_month_sql("web_appointment.datetime_when")
+ + """ = %s
+AND """
+ + extract_year_sql("web_appointment.datetime_when")
+ + """ = %s
"""
+)
-QUERY_VISITS_ENDED_COUNT = """
+QUERY_VISITS_ENDED_COUNT = (
+ """
SELECT count(*) FROM (SELECT id, subject_id as web_visit_subject_id, datetime_begin, datetime_end,
visit_number AS rnk FROM web_visit) a
LEFT JOIN web_studysubject ON web_studysubject.id = web_visit_subject_id
WHERE a.rnk = %s
-AND """ + extract_month_sql("a.datetime_end") + """ = %s
-AND """ + extract_year_sql("a.datetime_end") + """ = %s
+AND """
+ + extract_month_sql("a.datetime_end")
+ + """ = %s
+AND """
+ + extract_year_sql("a.datetime_end")
+ + """ = %s
"""
+)
-QUERY_VISITS_STARTED_COUNT = """
+QUERY_VISITS_STARTED_COUNT = (
+ """
SELECT count(*) FROM (SELECT id, subject_id as web_visit_subject_id, datetime_begin, datetime_end,
visit_number AS rnk FROM web_visit) a
LEFT JOIN web_studysubject ON web_studysubject.id = web_visit_subject_id
WHERE a.rnk = %s
-AND """ + extract_month_sql("a.datetime_begin") + """ = %s
-AND """ + extract_year_sql("a.datetime_begin") + """ = %s
+AND """
+ + extract_month_sql("a.datetime_begin")
+ + """ = %s
+AND """
+ + extract_year_sql("a.datetime_begin")
+ + """ = %s
"""
+)
-QUERY_APPOINTMENTS = """
+QUERY_APPOINTMENTS = (
+ """
SELECT types.appointment_type_id, web_appointment.status, count(*) FROM web_appointment
LEFT JOIN (SELECT id, subject_id as web_visit_subject_id, visit_number AS rnk
FROM web_visit) a ON a.id = web_appointment.visit_id LEFT JOIN web_appointmenttypelink types
ON types.appointment_id = web_appointment.id
LEFT JOIN web_studysubject ON web_studysubject.id = web_visit_subject_id
WHERE a.rnk = %s
-AND """ + extract_month_sql("web_appointment.datetime_when") + """ = %s
-AND """ + extract_year_sql("web_appointment.datetime_when") + """ = %s
+AND """
+ + extract_month_sql("web_appointment.datetime_when")
+ + """ = %s
+AND """
+ + extract_year_sql("web_appointment.datetime_when")
+ + """ = %s
{}
-GROUP BY TYPES.appointment_type_id, web_appointment.status
+GROUP BY types.appointment_type_id, web_appointment.status
"""
+)
class StatisticsManager:
def __init__(self):
- self.appointment_types = {appointment_type.id: appointment_type for appointment_type in
- AppointmentType.objects.all()}
- self.statuses_list = Appointment.objects.filter().values_list('status', flat=True).distinct().order_by(
- 'status').all()
- self.statuses_labels = [Appointment.APPOINTMENT_STATUS_CHOICES.get(status, status.title()) for status in
- self.statuses_list]
+ self.appointment_types = {
+ appointment_type.id: appointment_type
+ for appointment_type in AppointmentType.objects.all()
+ }
+ self.statuses_list = (
+ Appointment.objects.filter()
+ .values_list("status", flat=True)
+ .distinct()
+ .order_by("status")
+ .all()
+ )
+ self.statuses_labels = [
+ Appointment.APPOINTMENT_STATUS_CHOICES.get(status, status.title())
+ for status in self.statuses_list
+ ]
self.visits_ranks = self._get_visits_ranks()
- def get_statistics_for_month(self, month, year, subject_type: SubjectType = None, visit=None):
+ def get_statistics_for_month(
+ self, month, year, subject_type: SubjectType = None, visit=None
+ ):
"""
Build dict with statistics for a given month of a given year.
Statistics include:
@@ -108,15 +143,21 @@ class StatisticsManager:
if visit is not None:
visit = int(visit)
- filters_month_year_appointments, filters_month_year_visits_ended, filters_month_year_visits_started = \
- self._build_filters(month, subject_type, year)
-
- number_of_appointments = self._get_number_of_appointments(filters_month_year_appointments, visit, month, year,
- subject_type)
- number_of_visits_started = self._get_number_visits_started(filters_month_year_visits_started, visit, month,
- year, subject_type)
- number_of_visits_ended = self._get_number_visits_ended(filters_month_year_visits_ended, visit, month, year,
- subject_type)
+ (
+ filters_month_year_appointments,
+ filters_month_year_visits_ended,
+ filters_month_year_visits_started,
+ ) = self._build_filters(month, subject_type, year)
+
+ number_of_appointments = self._get_number_of_appointments(
+ filters_month_year_appointments, visit, month, year, subject_type
+ )
+ number_of_visits_started = self._get_number_visits_started(
+ filters_month_year_visits_started, visit, month, year, subject_type
+ )
+ number_of_visits_ended = self._get_number_visits_ended(
+ filters_month_year_visits_ended, visit, month, year, subject_type
+ )
general_results["appointments"] = number_of_appointments
general_results["visits_started"] = number_of_visits_started
@@ -124,38 +165,70 @@ class StatisticsManager:
results["general"] = general_results
- results_appointments = self.get_appointments_per_type_and_status(filters_month_year_appointments, month,
- self.statuses_list, visit, year, subject_type)
+ results_appointments = self.get_appointments_per_type_and_status(
+ filters_month_year_appointments,
+ month,
+ self.statuses_list,
+ visit,
+ year,
+ subject_type,
+ )
results["appointments"] = results_appointments
results["statuses_list"] = self.statuses_labels
- appointment_types_values = list(map(attrgetter('code'), list(self.appointment_types.values())))
+ appointment_types_values = list(
+ map(attrgetter("code"), list(self.appointment_types.values()))
+ )
sorted_appointment_types_values = sorted(appointment_types_values)
results["appointments_types_list"] = sorted_appointment_types_values
return results
- def get_appointments_per_type_and_status(self, filters_month_year_appointments, month, statuses_list, visit, year,
- subject_type=None):
+ def get_appointments_per_type_and_status(
+ self,
+ filters_month_year_appointments,
+ month,
+ statuses_list,
+ visit,
+ year,
+ subject_type=None,
+ ):
if not visit:
results_appointments = {}
for appointment_type in list(self.appointment_types.values()):
- appointment_type_filters = copy.deepcopy(filters_month_year_appointments)
- appointment_type_filters.add(Q(appointment_types=appointment_type), Q.AND)
- results_appointment_set = Appointment.objects.filter(appointment_type_filters).values(
- 'status').order_by(
- 'status').annotate(
- Count('status'))
- results_appointment = [Appointment.objects.filter(appointment_type_filters).count()]
- results_appointment_per_status = {result['status']: result['status__count'] for result in
- results_appointment_set}
-
- results_appointment.extend([results_appointment_per_status.get(status, 0) for status in statuses_list])
+ appointment_type_filters = copy.deepcopy(
+ filters_month_year_appointments
+ )
+ appointment_type_filters.add(
+ Q(appointment_types=appointment_type), Q.AND
+ )
+ results_appointment_set = (
+ Appointment.objects.filter(appointment_type_filters)
+ .values("status")
+ .order_by("status")
+ .annotate(Count("status"))
+ )
+ results_appointment = [
+ Appointment.objects.filter(appointment_type_filters).count()
+ ]
+ results_appointment_per_status = {
+ result["status"]: result["status__count"]
+ for result in results_appointment_set
+ }
+
+ results_appointment.extend(
+ [
+ results_appointment_per_status.get(status, 0)
+ for status in statuses_list
+ ]
+ )
results_appointments[appointment_type.code] = results_appointment
else:
results_appointment_set = defaultdict(dict)
query = QUERY_APPOINTMENTS
subject_type_clause = ""
if subject_type is not None:
- subject_type_clause = f" AND web_studysubject.type_id = '{subject_type.id}'"
+ subject_type_clause = (
+ f" AND web_studysubject.type_id = '{subject_type.id}'"
+ )
query = query.format(subject_type_clause)
with connection.cursor() as cursor:
cursor.execute(query, [visit, month, year])
@@ -166,42 +239,86 @@ class StatisticsManager:
results_appointments = {}
for appointment_type in list(self.appointment_types.values()):
if appointment_type.id not in results_appointment_set:
- results_appointments[appointment_type.code] = [0 * i for i in range(0, len(statuses_list) + 1)]
+ results_appointments[appointment_type.code] = [
+ 0 * i for i in range(0, len(statuses_list) + 1)
+ ]
continue
- results_appointment_set_for_type = results_appointment_set[appointment_type.id]
+ results_appointment_set_for_type = results_appointment_set[
+ appointment_type.id
+ ]
total = [sum(results_appointment_set_for_type.values())]
- total.extend([results_appointment_set_for_type.get(status, 0) for status in statuses_list])
+ total.extend(
+ [
+ results_appointment_set_for_type.get(status, 0)
+ for status in statuses_list
+ ]
+ )
results_appointments[appointment_type.code] = total
return results_appointments
@staticmethod
- def _get_count_from_filters_or_sql(model, filters, query, visit, month, year, subject_type: SubjectType):
+ def _get_count_from_filters_or_sql(
+ model, filters, query, visit, month, year, subject_type: SubjectType
+ ):
if visit:
if subject_type is not None:
query += f" AND web_studysubject.type_id = '{subject_type.id}'"
with connection.cursor() as cursor:
- cursor.execute(
- query,
- [visit, month, year])
+ cursor.execute(query, [visit, month, year])
row = cursor.fetchone()
count = int(row[0])
else:
count = model.objects.filter(filters).count()
return count
- def _get_number_visits_started(self, filters_month_year_visits_started, visit, month, year,
- subject_type: SubjectType = None):
- return self._get_count_from_filters_or_sql(Visit, filters_month_year_visits_started, QUERY_VISITS_STARTED_COUNT,
- visit, month, year, subject_type)
-
- def _get_number_visits_ended(self, filters_month_year_visits_ended, visit, month, year,
- subject_type: SubjectType = None):
- return self._get_count_from_filters_or_sql(Visit, filters_month_year_visits_ended, QUERY_VISITS_ENDED_COUNT,
- visit, month, year, subject_type)
-
- def _get_number_of_appointments(self, filters, visit, month, year, subject_type: SubjectType = None):
- return self._get_count_from_filters_or_sql(Appointment, filters, QUERY_APPOINTMENTS_COUNT, visit, month, year,
- subject_type)
+ def _get_number_visits_started(
+ self,
+ filters_month_year_visits_started,
+ visit,
+ month,
+ year,
+ subject_type: SubjectType = None,
+ ):
+ return self._get_count_from_filters_or_sql(
+ Visit,
+ filters_month_year_visits_started,
+ QUERY_VISITS_STARTED_COUNT,
+ visit,
+ month,
+ year,
+ subject_type,
+ )
+
+ def _get_number_visits_ended(
+ self,
+ filters_month_year_visits_ended,
+ visit,
+ month,
+ year,
+ subject_type: SubjectType = None,
+ ):
+ return self._get_count_from_filters_or_sql(
+ Visit,
+ filters_month_year_visits_ended,
+ QUERY_VISITS_ENDED_COUNT,
+ visit,
+ month,
+ year,
+ subject_type,
+ )
+
+ def _get_number_of_appointments(
+ self, filters, visit, month, year, subject_type: SubjectType = None
+ ):
+ return self._get_count_from_filters_or_sql(
+ Appointment,
+ filters,
+ QUERY_APPOINTMENTS_COUNT,
+ visit,
+ month,
+ year,
+ subject_type,
+ )
@staticmethod
def _build_filters(month, subject_type, year):
@@ -223,7 +340,11 @@ class StatisticsManager:
filters_month_year_visits_ended.add(subject_type_filter, Q.AND)
subject_type_filter_appointments = Q(visit__subject__type=subject_type)
filters_month_year_appointments.add(subject_type_filter_appointments, Q.AND)
- return filters_month_year_appointments, filters_month_year_visits_ended, filters_month_year_visits_started
+ return (
+ filters_month_year_appointments,
+ filters_month_year_visits_ended,
+ filters_month_year_visits_started,
+ )
@staticmethod
def _get_visits_ranks():
diff --git a/smash/web/templates/_base.html b/smash/web/templates/_base.html
index c4a0863a1c611aa62ec9f83b7cf23201951a226b..3c75a7588ad9327438d41f38965c353f427c64a2 100644
--- a/smash/web/templates/_base.html
+++ b/smash/web/templates/_base.html
@@ -258,7 +258,7 @@ desired effect
{% block footer %}
<!-- To the right -->
<div class="pull-right hidden-xs">
- Version: <strong>1.4.4</strong>
+ Version: <strong>1.4.5</strong>
</div>
<!-- Default to the left -->
diff --git a/smash/web/tests/api_views/test_flying_team.py b/smash/web/tests/api_views/test_flying_team.py
index f735413e8806a27c492bf051b47230c412282afa..e07eb6ab19c0fca591684b59f0ba337d4242f377 100644
--- a/smash/web/tests/api_views/test_flying_team.py
+++ b/smash/web/tests/api_views/test_flying_team.py
@@ -12,17 +12,17 @@ class TestFlyingTeamApi(LoggedInTestCase):
def test_flying_teams(self):
flying_team_name = "some flying_team"
- response = self.client.get(reverse('web.api.flying_teams'))
+ response = self.client.get(reverse("web.api.flying_teams"))
self.assertEqual(response.status_code, 200)
create_flying_team(flying_team_name)
- response = self.client.get(reverse('web.api.flying_teams'))
- flying_teams = json.loads(response.content)['flying_teams']
+ response = self.client.get(reverse("web.api.flying_teams"))
+ flying_teams = json.loads(response.content)["flying_teams"]
found = False
for flying_team in flying_teams:
- if flying_team['name'] == flying_team_name:
+ if flying_team["name"] == flying_team_name:
found = True
self.assertTrue(found)
diff --git a/smash/web/tests/forms/test_CustomStudySubjectFieldAddForm.py b/smash/web/tests/forms/test_CustomStudySubjectFieldAddForm.py
index a96a7aff4f62f6d1c046be6f825416d44df43907..e1aaa3eb45c5d1e5431d222f2c60da69bde09dbe 100644
--- a/smash/web/tests/forms/test_CustomStudySubjectFieldAddForm.py
+++ b/smash/web/tests/forms/test_CustomStudySubjectFieldAddForm.py
@@ -2,37 +2,60 @@ from django.test import TestCase
from parameterized import parameterized
from web.forms.custom_study_subject_field_forms import CustomStudySubjectFieldAddForm
-from web.models.constants import CUSTOM_FIELD_TYPE_TEXT, CUSTOM_FIELD_TYPE_BOOLEAN, CUSTOM_FIELD_TYPE_INTEGER, \
- CUSTOM_FIELD_TYPE_DOUBLE, CUSTOM_FIELD_TYPE_DATE, CUSTOM_FIELD_TYPE_SELECT_LIST, CUSTOM_FIELD_TYPE_FILE
+from web.models.constants import (
+ CUSTOM_FIELD_TYPE_TEXT,
+ CUSTOM_FIELD_TYPE_BOOLEAN,
+ CUSTOM_FIELD_TYPE_INTEGER,
+ CUSTOM_FIELD_TYPE_DOUBLE,
+ CUSTOM_FIELD_TYPE_DATE,
+ CUSTOM_FIELD_TYPE_SELECT_LIST,
+ CUSTOM_FIELD_TYPE_FILE,
+)
from web.models.custom_data import CustomStudySubjectField
from web.tests.functions import get_test_study
class CustomStudySubjectFieldAddFormTest(TestCase):
- @parameterized.expand([
- ('text', CUSTOM_FIELD_TYPE_TEXT, 'bla', True),
- ('bool valid', CUSTOM_FIELD_TYPE_BOOLEAN, 'True', True),
- ('bool invalid', CUSTOM_FIELD_TYPE_BOOLEAN, 'bla', False),
- ('int valid', CUSTOM_FIELD_TYPE_INTEGER, '102', True),
- ('int invalid', CUSTOM_FIELD_TYPE_INTEGER, 'bla', False),
- ('double valid', CUSTOM_FIELD_TYPE_DOUBLE, '202.25', True),
- ('double invalid', CUSTOM_FIELD_TYPE_DOUBLE, 'bla', False),
- ('date valid', CUSTOM_FIELD_TYPE_DATE, '2021-01-20', True),
- ('date invalid', CUSTOM_FIELD_TYPE_DATE, 'bla', False),
- ('select list valid', CUSTOM_FIELD_TYPE_SELECT_LIST, 'abc', True, 'abc;def;xyz'),
- ('select list invalid', CUSTOM_FIELD_TYPE_SELECT_LIST, 'bla', False, 'abc;def'),
- ('file', CUSTOM_FIELD_TYPE_FILE, None, True),
- ('file invalid', CUSTOM_FIELD_TYPE_FILE, 'tmp', False),
- ('text', CUSTOM_FIELD_TYPE_TEXT, 'bla', True, True),
- ])
- def test_add_field(self, _, field_type, default_value, valid, possible_values='', tracked=False):
+ @parameterized.expand(
+ [
+ ("text", CUSTOM_FIELD_TYPE_TEXT, "bla", True),
+ ("bool valid", CUSTOM_FIELD_TYPE_BOOLEAN, "True", True),
+ ("bool invalid", CUSTOM_FIELD_TYPE_BOOLEAN, "bla", False),
+ ("int valid", CUSTOM_FIELD_TYPE_INTEGER, "102", True),
+ ("int invalid", CUSTOM_FIELD_TYPE_INTEGER, "bla", False),
+ ("double valid", CUSTOM_FIELD_TYPE_DOUBLE, "202.25", True),
+ ("double invalid", CUSTOM_FIELD_TYPE_DOUBLE, "bla", False),
+ ("date valid", CUSTOM_FIELD_TYPE_DATE, "2021-01-20", True),
+ ("date invalid", CUSTOM_FIELD_TYPE_DATE, "bla", False),
+ (
+ "select list valid",
+ CUSTOM_FIELD_TYPE_SELECT_LIST,
+ "abc",
+ True,
+ "abc;def;xyz",
+ ),
+ (
+ "select list invalid",
+ CUSTOM_FIELD_TYPE_SELECT_LIST,
+ "bla",
+ False,
+ "abc;def",
+ ),
+ ("file", CUSTOM_FIELD_TYPE_FILE, None, True),
+ ("file invalid", CUSTOM_FIELD_TYPE_FILE, "tmp", False),
+ ("text", CUSTOM_FIELD_TYPE_TEXT, "bla", True, True),
+ ]
+ )
+ def test_add_field(
+ self, _, field_type, default_value, valid, possible_values="", tracked=False
+ ):
sample_data = {
- 'default_value': default_value,
- 'name': '1. name',
- 'type': field_type,
- 'possible_values': possible_values,
- 'tracked': tracked,
+ "default_value": default_value,
+ "name": "1. name",
+ "type": field_type,
+ "possible_values": possible_values,
+ "tracked": tracked,
}
form = CustomStudySubjectFieldAddForm(sample_data, study=get_test_study())
@@ -40,7 +63,9 @@ class CustomStudySubjectFieldAddFormTest(TestCase):
self.assertTrue(form.is_valid())
field = form.save()
- self.assertEqual(1, CustomStudySubjectField.objects.filter(id=field.id).count())
+ self.assertEqual(
+ 1, CustomStudySubjectField.objects.filter(id=field.id).count()
+ )
self.assertEqual(default_value, field.default_value)
self.assertEqual(tracked, field.tracked)
else:
diff --git a/smash/web/tests/forms/test_CustomStudySubjectFieldEditForm.py b/smash/web/tests/forms/test_CustomStudySubjectFieldEditForm.py
index cdbd8aa67710d2f5f70f9f32299e07eeacec1792..a9dd10e22530fb376b708ac881e9224241154282 100644
--- a/smash/web/tests/forms/test_CustomStudySubjectFieldEditForm.py
+++ b/smash/web/tests/forms/test_CustomStudySubjectFieldEditForm.py
@@ -2,39 +2,64 @@ from django.test import TestCase
from parameterized import parameterized
from web.forms.custom_study_subject_field_forms import CustomStudySubjectFieldEditForm
-from web.models.constants import CUSTOM_FIELD_TYPE_TEXT, CUSTOM_FIELD_TYPE_BOOLEAN, CUSTOM_FIELD_TYPE_INTEGER, \
- CUSTOM_FIELD_TYPE_DOUBLE, CUSTOM_FIELD_TYPE_DATE, CUSTOM_FIELD_TYPE_SELECT_LIST, CUSTOM_FIELD_TYPE_FILE
+from web.models.constants import (
+ CUSTOM_FIELD_TYPE_TEXT,
+ CUSTOM_FIELD_TYPE_BOOLEAN,
+ CUSTOM_FIELD_TYPE_INTEGER,
+ CUSTOM_FIELD_TYPE_DOUBLE,
+ CUSTOM_FIELD_TYPE_DATE,
+ CUSTOM_FIELD_TYPE_SELECT_LIST,
+ CUSTOM_FIELD_TYPE_FILE,
+)
from web.models.custom_data import CustomStudySubjectField
from web.tests.functions import get_test_study
class CustomStudySubjectFieldEditFormTest(TestCase):
- @parameterized.expand([
- ('text', CUSTOM_FIELD_TYPE_TEXT, 'bla', True),
- ('bool valid', CUSTOM_FIELD_TYPE_BOOLEAN, 'True', True),
- ('bool invalid', CUSTOM_FIELD_TYPE_BOOLEAN, 'bla', False),
- ('int valid', CUSTOM_FIELD_TYPE_INTEGER, '911', True),
- ('int invalid', CUSTOM_FIELD_TYPE_INTEGER, 'bla', False),
- ('double valid', CUSTOM_FIELD_TYPE_DOUBLE, '821.45', True),
- ('double invalid', CUSTOM_FIELD_TYPE_DOUBLE, 'bla', False),
- ('date valid', CUSTOM_FIELD_TYPE_DATE, '2020-10-04', True),
- ('date invalid', CUSTOM_FIELD_TYPE_DATE, 'bla', False),
- ('select list valid', CUSTOM_FIELD_TYPE_SELECT_LIST, 'abc', True, 'abc;def;xyz'),
- ('select list invalid', CUSTOM_FIELD_TYPE_SELECT_LIST, 'bla', False, 'abc;def'),
- ('file', CUSTOM_FIELD_TYPE_FILE, None, True),
- ('file invalid', CUSTOM_FIELD_TYPE_FILE, 'tmp', False),
- ('text', CUSTOM_FIELD_TYPE_TEXT, 'bla', True, True),
- ])
- def test_edit_field(self, _, field_type, default_value, valid, possible_values='', tracked=False):
- field = CustomStudySubjectField.objects.create(study=get_test_study(), default_value="", type=field_type)
+ @parameterized.expand(
+ [
+ ("text", CUSTOM_FIELD_TYPE_TEXT, "bla", True),
+ ("bool valid", CUSTOM_FIELD_TYPE_BOOLEAN, "True", True),
+ ("bool invalid", CUSTOM_FIELD_TYPE_BOOLEAN, "bla", False),
+ ("int valid", CUSTOM_FIELD_TYPE_INTEGER, "911", True),
+ ("int invalid", CUSTOM_FIELD_TYPE_INTEGER, "bla", False),
+ ("double valid", CUSTOM_FIELD_TYPE_DOUBLE, "821.45", True),
+ ("double invalid", CUSTOM_FIELD_TYPE_DOUBLE, "bla", False),
+ ("date valid", CUSTOM_FIELD_TYPE_DATE, "2020-10-04", True),
+ ("date invalid", CUSTOM_FIELD_TYPE_DATE, "bla", False),
+ (
+ "select list valid",
+ CUSTOM_FIELD_TYPE_SELECT_LIST,
+ "abc",
+ True,
+ "abc;def;xyz",
+ ),
+ (
+ "select list invalid",
+ CUSTOM_FIELD_TYPE_SELECT_LIST,
+ "bla",
+ False,
+ "abc;def",
+ ),
+ ("file", CUSTOM_FIELD_TYPE_FILE, None, True),
+ ("file invalid", CUSTOM_FIELD_TYPE_FILE, "tmp", False),
+ ("text", CUSTOM_FIELD_TYPE_TEXT, "bla", True, True),
+ ]
+ )
+ def test_edit_field(
+ self, _, field_type, default_value, valid, possible_values="", tracked=False
+ ):
+ field = CustomStudySubjectField.objects.create(
+ study=get_test_study(), default_value="", type=field_type
+ )
sample_data = {
- 'default_value': default_value,
- 'name': '1. name',
- 'type': field_type,
- 'possible_values': possible_values,
- 'tracked': tracked,
+ "default_value": default_value,
+ "name": "1. name",
+ "type": field_type,
+ "possible_values": possible_values,
+ "tracked": tracked,
}
form = CustomStudySubjectFieldEditForm(sample_data, instance=field)
diff --git a/smash/web/tests/functions.py b/smash/web/tests/functions.py
index 51d91ea3e089bcc4d87e9c376fc83cef3ab18d39..759e14f05782511adcd1be3799190419bc3a7b5a 100644
--- a/smash/web/tests/functions.py
+++ b/smash/web/tests/functions.py
@@ -6,14 +6,46 @@ from typing import Union
from django.contrib.auth.models import Permission
from django.contrib.auth import get_user_model
from django.utils.timezone import make_aware, is_aware
-
-from web.models import Location, AppointmentType, StudySubject, Worker, Visit, Appointment, ConfigurationItem, \
- Language, ContactAttempt, FlyingTeam, Availability, Subject, Study, StudyColumns, StudyNotificationParameters, \
- VoucherType, VoucherTypePrice, Voucher, Room, Item, WorkerStudyRole, StudyRedCapColumns, EtlColumnMapping, \
- SubjectImportData, SubjectType
-from web.models.constants import REDCAP_TOKEN_CONFIGURATION_TYPE, REDCAP_BASE_URL_CONFIGURATION_TYPE, \
- SEX_CHOICES_MALE, CONTACT_TYPES_PHONE, \
- MONDAY_AS_DAY_OF_WEEK, COUNTRY_AFGHANISTAN_ID, VOUCHER_STATUS_NEW, GLOBAL_STUDY_ID, DEFAULT_LOCALE_NAME
+from django.conf import settings
+
+from web.models import (
+ Location,
+ AppointmentType,
+ StudySubject,
+ Worker,
+ Visit,
+ Appointment,
+ ConfigurationItem,
+ Language,
+ ContactAttempt,
+ FlyingTeam,
+ Availability,
+ Subject,
+ Study,
+ StudyColumns,
+ StudyNotificationParameters,
+ VoucherType,
+ VoucherTypePrice,
+ Voucher,
+ Room,
+ Item,
+ WorkerStudyRole,
+ StudyRedCapColumns,
+ EtlColumnMapping,
+ SubjectImportData,
+ SubjectType,
+)
+from web.models.constants import (
+ REDCAP_TOKEN_CONFIGURATION_TYPE,
+ REDCAP_BASE_URL_CONFIGURATION_TYPE,
+ SEX_CHOICES_MALE,
+ CONTACT_TYPES_PHONE,
+ MONDAY_AS_DAY_OF_WEEK,
+ COUNTRY_AFGHANISTAN_ID,
+ VOUCHER_STATUS_NEW,
+ GLOBAL_STUDY_ID,
+ DEFAULT_LOCALE_NAME,
+)
from web.models.worker_study_role import ROLE_CHOICES_DOCTOR, WORKER_VOUCHER_PARTNER
from web.redcap_connector import RedcapSubject
from web.views.notifications import get_today_midnight_date
@@ -37,10 +69,12 @@ def create_voucher_type():
def create_voucher_type_price():
- return VoucherTypePrice.objects.create(voucher_type=create_voucher_type(),
- price=12.34,
- start_date=get_today_midnight_date(),
- end_date=get_today_midnight_date())
+ return VoucherTypePrice.objects.create(
+ voucher_type=create_voucher_type(),
+ price=12.34,
+ start_date=get_today_midnight_date(),
+ end_date=get_today_midnight_date(),
+ )
def create_empty_study_columns():
@@ -68,8 +102,12 @@ def create_study(name="test"):
study_columns = StudyColumns.objects.create()
notification_parameters = StudyNotificationParameters.objects.create()
redcap_columns = StudyRedCapColumns.objects.create()
- return Study.objects.create(name=name, columns=study_columns, notification_parameters=notification_parameters,
- redcap_columns=redcap_columns)
+ return Study.objects.create(
+ name=name,
+ columns=study_columns,
+ notification_parameters=notification_parameters,
+ redcap_columns=redcap_columns,
+ )
TEST_ID_COUNTER = 0
@@ -90,14 +128,16 @@ def create_voucher(study_subject=None, partner=None, worker=None):
if worker is None:
worker = create_worker()
number = str(get_test_id())
- return Voucher.objects.create(number=number,
- study_subject=study_subject,
- issue_date=get_today_midnight_date(),
- expiry_date=get_today_midnight_date(),
- voucher_type=create_voucher_type(),
- usage_partner=partner,
- issue_worker=worker,
- status=VOUCHER_STATUS_NEW)
+ return Voucher.objects.create(
+ number=number,
+ study_subject=study_subject,
+ issue_date=get_today_midnight_date(),
+ expiry_date=get_today_midnight_date(),
+ voucher_type=create_voucher_type(),
+ usage_partner=partner,
+ issue_worker=worker,
+ status=VOUCHER_STATUS_NEW,
+ )
def create_empty_notification_parameters():
@@ -158,7 +198,7 @@ def get_test_study() -> Study:
return create_study("test-study")
-def create_appointment_type(code='C', default_duration=10, description='test'):
+def create_appointment_type(code="C", default_duration=10, description="test"):
return AppointmentType.objects.create(
code=code,
default_duration=default_duration,
@@ -172,13 +212,14 @@ def create_contact_attempt(subject=None, worker=None):
if worker is None:
worker = create_worker()
- return ContactAttempt.objects.create(subject=subject,
- worker=worker,
- type=CONTACT_TYPES_PHONE,
- datetime_when=get_today_midnight_date(),
- success=True,
- comment="Successful contact attempt",
- )
+ return ContactAttempt.objects.create(
+ subject=subject,
+ worker=worker,
+ type=CONTACT_TYPES_PHONE,
+ datetime_when=get_today_midnight_date(),
+ success=True,
+ comment="Successful contact attempt",
+ )
def create_subject():
@@ -186,12 +227,16 @@ def create_subject():
first_name="Piotr",
last_name="Gawron",
sex=SEX_CHOICES_MALE,
- country_id=COUNTRY_AFGHANISTAN_ID
+ country_id=COUNTRY_AFGHANISTAN_ID,
)
-def create_study_subject(subject_id: int = 1, subject: Subject = None, nd_number: str = 'ND0001',
- study: Study = None) -> StudySubject:
+def create_study_subject(
+ subject_id: int = 1,
+ subject: Subject = None,
+ nd_number: str = "ND0001",
+ study: Study = None,
+) -> StudySubject:
if study is None:
study = get_test_study()
if subject is None:
@@ -201,9 +246,11 @@ def create_study_subject(subject_id: int = 1, subject: Subject = None, nd_number
type=get_control_subject_type(),
screening_number="piotr's number" + str(subject_id),
study=study,
- subject=subject
+ subject=subject,
)
- if nd_number is not None: # null value in column "nd_number" violates not-null constraint
+ if (
+ nd_number is not None
+ ): # null value in column "nd_number" violates not-null constraint
study_subject.nd_number = nd_number
study_subject.save()
@@ -211,25 +258,27 @@ def create_study_subject(subject_id: int = 1, subject: Subject = None, nd_number
def get_control_subject_type() -> SubjectType:
- return SubjectType.objects.filter(name='CONTROL').first()
+ return SubjectType.objects.filter(name="CONTROL").first()
def get_patient_subject_type() -> SubjectType:
- return SubjectType.objects.filter(name='PATIENT').first()
+ return SubjectType.objects.filter(name="PATIENT").first()
-def create_study_subject_with_multiple_screening_numbers(subject_id=1, subject=None, screening_number=None):
+def create_study_subject_with_multiple_screening_numbers(
+ subject_id=1, subject=None, screening_number=None
+):
if subject is None:
subject = create_subject()
if screening_number is None:
- screening_number = f'E-00{subject_id}; L-00{subject_id}'
+ screening_number = f"E-00{subject_id}; L-00{subject_id}"
return StudySubject.objects.create(
default_location=get_test_location(),
type=get_control_subject_type(),
screening_number=screening_number,
study=get_test_study(),
- subject=subject
+ subject=subject,
)
@@ -239,15 +288,16 @@ def create_red_cap_subject():
return result
-def create_user(username: str = None, password: str = None, email: str = 'jacob@bla') -> get_user_model():
+def create_user(
+ username: str = None, password: str = None, email: str = "jacob@bla"
+) -> get_user_model():
if username is None:
- username = 'piotr'
+ username = "piotr"
if password is None:
- password = 'top_secret'
+ password = "top_secret"
user = get_user_model().objects.create_user(
- username=username,
- email=email,
- password=password)
+ username=username, email=email, password=password
+ )
create_worker(user)
return user
@@ -262,63 +312,75 @@ def add_permissions_to_worker(worker, codenames):
def create_worker(user=None, with_test_location=False):
worker = Worker.objects.create(
- first_name='piotr',
+ first_name="piotr",
last_name="gawron",
- email='jacob@bla.com',
+ email="jacob@bla.com",
user=user,
specialization="spec",
unit="LCSB",
- phone_number="0123456789"
+ phone_number="0123456789",
)
if with_test_location:
worker.locations.set([get_test_location()])
worker.save()
WorkerStudyRole.objects.create(
- worker=worker, study_id=GLOBAL_STUDY_ID, name=ROLE_CHOICES_DOCTOR)
+ worker=worker, study_id=GLOBAL_STUDY_ID, name=ROLE_CHOICES_DOCTOR
+ )
return worker
def create_voucher_partner():
worker = Worker.objects.create(
- first_name='piotr',
+ first_name="piotr",
last_name="gawron",
- email='jacob@bla.com',
+ email="jacob@bla.com",
specialization="spec",
unit="LCSB",
- phone_number="0123456789"
+ phone_number="0123456789",
)
WorkerStudyRole.objects.create(
- worker=worker, study_id=GLOBAL_STUDY_ID, name=WORKER_VOUCHER_PARTNER)
+ worker=worker, study_id=GLOBAL_STUDY_ID, name=WORKER_VOUCHER_PARTNER
+ )
return worker
-def create_availability(worker=None, available_from=None, available_till=None, day_number=MONDAY_AS_DAY_OF_WEEK):
+def create_availability(
+ worker=None,
+ available_from=None,
+ available_till=None,
+ day_number=MONDAY_AS_DAY_OF_WEEK,
+):
if available_from is None:
- available_from = '8:00'
+ available_from = "8:00"
if available_till is None:
- available_till = '18:00'
+ available_till = "18:00"
if worker is None:
worker = create_worker()
- availability = Availability.objects.create(person=worker,
- day_number=day_number,
- available_from=available_from,
- available_till=available_till,
- )
+ availability = Availability.objects.create(
+ person=worker,
+ day_number=day_number,
+ available_from=available_from,
+ available_till=available_till,
+ )
return availability
-def create_visit(subject: StudySubject = None, datetime_begin=None, datetime_end=None) -> Visit:
+def create_visit(
+ subject: StudySubject = None, datetime_begin=None, datetime_end=None
+) -> Visit:
if subject is None:
subject = create_study_subject()
if datetime_begin is None:
datetime_begin = get_today_midnight_date() + datetime.timedelta(days=-31)
if datetime_end is None:
datetime_end = get_today_midnight_date() + datetime.timedelta(days=31)
- return Visit.objects.create(datetime_begin=datetime_begin,
- datetime_end=datetime_end,
- subject=subject,
- is_finished=False)
+ return Visit.objects.create(
+ datetime_begin=datetime_begin,
+ datetime_end=datetime_end,
+ subject=subject,
+ is_finished=False,
+ )
def create_appointment(visit=None, when=None, length=30) -> Appointment:
@@ -339,7 +401,8 @@ def create_appointment(visit=None, when=None, length=30) -> Appointment:
length=length,
location=get_test_location(),
status=Appointment.APPOINTMENT_STATUS_SCHEDULED,
- datetime_when=when_datetime)
+ datetime_when=when_datetime,
+ )
def create_appointment_without_visit(when=None, length=30):
@@ -347,7 +410,8 @@ def create_appointment_without_visit(when=None, length=30):
length=length,
location=get_test_location(),
status=Appointment.APPOINTMENT_STATUS_SCHEDULED,
- datetime_when=when)
+ datetime_when=when,
+ )
def create_configuration_item():
@@ -366,19 +430,31 @@ def create_flying_team(place=None):
return result
-def create_item(name='Test item', is_fixed=False, disposable=False):
+def create_item(name="Test item", is_fixed=False, disposable=False):
item = Item(name=name, is_fixed=is_fixed, disposable=disposable)
item.save()
return item
-def create_room(owner='Test owner', city='Test city',
- address='Test address', equipment=None,
- floor=1, is_vehicle=False, room_number=1):
+def create_room(
+ owner="Test owner",
+ city="Test city",
+ address="Test address",
+ equipment=None,
+ floor=1,
+ is_vehicle=False,
+ room_number=1,
+):
if equipment is None:
equipment = []
- room = Room(owner=owner, city=city, address=address,
- floor=floor, is_vehicle=is_vehicle, room_number=room_number)
+ room = Room(
+ owner=owner,
+ city=city,
+ address=address,
+ floor=floor,
+ is_vehicle=is_vehicle,
+ room_number=room_number,
+ )
room.save()
room.equipment.set(equipment) # Cannot be made in constructor/with single save
room.save()
@@ -392,14 +468,14 @@ def create_language(name="French", locale=DEFAULT_LOCALE_NAME) -> Language:
def get_resource_path(filename):
- return os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', filename)
+ return os.path.join(os.path.dirname(os.path.realpath(__file__)), "data", filename)
def format_form_field(value):
if isinstance(value, datetime.date):
- return value.strftime('%Y-%m-%d')
+ return value.strftime("%Y-%m-%d")
elif isinstance(value, datetime.datetime):
- return value.strftime('%Y-%m-%d %H:%M')
+ return value.strftime("%Y-%m-%d %H:%M")
elif value is None:
return ""
else:
@@ -409,67 +485,92 @@ def format_form_field(value):
def prepare_test_redcap_connection():
Language.objects.create(name="Finnish").save()
Language.objects.create(name="Italian").save()
- token_item = ConfigurationItem.objects.filter(
- type=REDCAP_TOKEN_CONFIGURATION_TYPE)[0]
+ token_item = ConfigurationItem.objects.filter(type=REDCAP_TOKEN_CONFIGURATION_TYPE)[
+ 0
+ ]
# noinspection SpellCheckingInspection
- token_item.value = "5DC21D45E3A2E068659F11046EA88734"
+ token_item.value = settings.REDCAP_TEST_API_TOKEN
token_item.save()
url_item = ConfigurationItem.objects.filter(
- type=REDCAP_BASE_URL_CONFIGURATION_TYPE)[0]
- url_item.value = "https://luxparktest.lcsb.uni.lu/redcap/"
+ type=REDCAP_BASE_URL_CONFIGURATION_TYPE
+ )[0]
+ url_item.value = settings.REDCAP_TEST_URL
url_item.save()
def datetimeify_date(date: Union[datetime.date, str, bytes]) -> datetime.datetime:
- if isinstance(date, datetime.date): # If it's date, then just make sure that timezone support is there
+ if isinstance(
+ date, datetime.date
+ ): # If it's date, then just make sure that timezone support is there
if is_aware(date):
return date
else:
return make_aware(date)
if isinstance(date, bytes): # If it's bytes, then convert to string and carry on...
- date = date.decode('utf8')
- if isinstance(date, str): # If it's string, convert to datetime with timezone support
- return make_aware(datetime.datetime.strptime(date, '%Y-%m-%d'))
+ date = date.decode("utf8")
+ if isinstance(
+ date, str
+ ): # If it's string, convert to datetime with timezone support
+ return make_aware(datetime.datetime.strptime(date, "%Y-%m-%d"))
actual_type = str(type(date))
raise TypeError(
- f"Date should be either a subclass of 'datetime.date', string or bytes! But is: {actual_type} instead")
+ f"Date should be either a subclass of 'datetime.date', string or bytes! But is: {actual_type} instead"
+ )
def create_tns_column_mapping(subject_import_data: SubjectImportData):
- EtlColumnMapping.objects.create(etl_data=subject_import_data,
- column_name="nd_number",
- csv_column_name="donor_id",
- table_name=StudySubject._meta.db_table)
- EtlColumnMapping.objects.create(etl_data=subject_import_data,
- column_name="comments",
- csv_column_name="treatingphysician",
- table_name=StudySubject._meta.db_table)
- EtlColumnMapping.objects.create(etl_data=subject_import_data,
- column_name="first_name",
- csv_column_name="firstname",
- table_name=Subject._meta.db_table)
- EtlColumnMapping.objects.create(etl_data=subject_import_data,
- column_name="first_name",
- csv_column_name="sig_firstname",
- table_name=Subject._meta.db_table)
- EtlColumnMapping.objects.create(etl_data=subject_import_data,
- column_name="last_name",
- csv_column_name="lastname",
- table_name=Subject._meta.db_table)
- EtlColumnMapping.objects.create(etl_data=subject_import_data,
- column_name="last_name",
- csv_column_name="sig_lastname",
- table_name=Subject._meta.db_table)
- EtlColumnMapping.objects.create(etl_data=subject_import_data,
- column_name="phone_number",
- csv_column_name="phonenr",
- table_name=Subject._meta.db_table)
- EtlColumnMapping.objects.create(etl_data=subject_import_data,
- column_name="date_born",
- csv_column_name="dateofbirth",
- table_name=Subject._meta.db_table)
- EtlColumnMapping.objects.create(etl_data=subject_import_data,
- column_name="next_of_kin_name",
- csv_column_name="representative",
- table_name=Subject._meta.db_table)
+ EtlColumnMapping.objects.create(
+ etl_data=subject_import_data,
+ column_name="nd_number",
+ csv_column_name="donor_id",
+ table_name=StudySubject._meta.db_table,
+ )
+ EtlColumnMapping.objects.create(
+ etl_data=subject_import_data,
+ column_name="comments",
+ csv_column_name="treatingphysician",
+ table_name=StudySubject._meta.db_table,
+ )
+ EtlColumnMapping.objects.create(
+ etl_data=subject_import_data,
+ column_name="first_name",
+ csv_column_name="firstname",
+ table_name=Subject._meta.db_table,
+ )
+ EtlColumnMapping.objects.create(
+ etl_data=subject_import_data,
+ column_name="first_name",
+ csv_column_name="sig_firstname",
+ table_name=Subject._meta.db_table,
+ )
+ EtlColumnMapping.objects.create(
+ etl_data=subject_import_data,
+ column_name="last_name",
+ csv_column_name="lastname",
+ table_name=Subject._meta.db_table,
+ )
+ EtlColumnMapping.objects.create(
+ etl_data=subject_import_data,
+ column_name="last_name",
+ csv_column_name="sig_lastname",
+ table_name=Subject._meta.db_table,
+ )
+ EtlColumnMapping.objects.create(
+ etl_data=subject_import_data,
+ column_name="phone_number",
+ csv_column_name="phonenr",
+ table_name=Subject._meta.db_table,
+ )
+ EtlColumnMapping.objects.create(
+ etl_data=subject_import_data,
+ column_name="date_born",
+ csv_column_name="dateofbirth",
+ table_name=Subject._meta.db_table,
+ )
+ EtlColumnMapping.objects.create(
+ etl_data=subject_import_data,
+ column_name="next_of_kin_name",
+ csv_column_name="representative",
+ table_name=Subject._meta.db_table,
+ )
diff --git a/smash/web/tests/test_statistics.py b/smash/web/tests/test_statistics.py
index f48ead719afde2fe3eba98391c5e17c1101be3d6..869a3f6c8272d615a01d2b60216cc7ea900c5216 100644
--- a/smash/web/tests/test_statistics.py
+++ b/smash/web/tests/test_statistics.py
@@ -5,11 +5,15 @@ from django.test import TestCase
from web.models import Visit, AppointmentTypeLink
from web.statistics import get_previous_year_and_month_for_date, StatisticsManager
-from web.tests.functions import create_appointment, create_appointment_type, get_control_subject_type, \
- get_patient_subject_type
+from web.tests.functions import (
+ create_appointment,
+ create_appointment_type,
+ get_control_subject_type,
+ get_patient_subject_type,
+)
from web.views.notifications import get_today_midnight_date
-__author__ = 'Valentin Grouès'
+__author__ = "Valentin Grouès"
class TestStatistics(TestCase):
@@ -17,7 +21,9 @@ class TestStatistics(TestCase):
self.now = get_today_midnight_date()
self.appointment_type = create_appointment_type()
appointment = create_appointment(when=self.now)
- AppointmentTypeLink.objects.create(appointment=appointment, appointment_type=self.appointment_type)
+ AppointmentTypeLink.objects.create(
+ appointment=appointment, appointment_type=self.appointment_type
+ )
self.visit_start = appointment.visit.datetime_begin
self.visit_end = appointment.visit.datetime_end
appointment.save()
@@ -35,67 +41,112 @@ class TestStatistics(TestCase):
self.assertEqual(12, previous_month)
def test_get_statistics_for_month_one_appointment(self):
- statistics = self.statistics_manager.get_statistics_for_month(self.visit_start.month, self.visit_start.year)
- self.check_statistics(statistics, 1, 0, 0, {"C": [0, 0]}, ['Scheduled'])
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.visit_start.month, self.visit_start.year
+ )
+ self.check_statistics(statistics, 1, 0, 0, {"C": [0, 0]}, ["Scheduled"])
- statistics = self.statistics_manager.get_statistics_for_month(self.now.month, self.now.year)
- self.check_statistics(statistics, 0, 0, 1, {"C": [1, 1]}, ['Scheduled'])
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.now.month, self.now.year
+ )
+ self.check_statistics(statistics, 0, 0, 1, {"C": [1, 1]}, ["Scheduled"])
- statistics = self.statistics_manager.get_statistics_for_month(self.visit_end.month, self.visit_end.year)
- self.check_statistics(statistics, 0, 1, 0, {"C": [0, 0]}, ['Scheduled'])
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.visit_end.month, self.visit_end.year
+ )
+ self.check_statistics(statistics, 0, 1, 0, {"C": [0, 0]}, ["Scheduled"])
def test_get_statistics_for_month_one_appointment_visit(self):
- statistics = self.statistics_manager.get_statistics_for_month(self.now.month, self.now.year, visit="1")
- self.check_statistics(statistics, 0, 0, 1, {"C": [1, 1]}, ['Scheduled'])
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.now.month, self.now.year, visit="1"
+ )
+ self.check_statistics(statistics, 0, 0, 1, {"C": [1, 1]}, ["Scheduled"])
- statistics = self.statistics_manager.get_statistics_for_month(self.now.month, self.now.year, visit="2")
- self.check_statistics(statistics, 0, 0, 0, {"C": [0, 0]}, ['Scheduled'])
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.now.month, self.now.year, visit="2"
+ )
+ self.check_statistics(statistics, 0, 0, 0, {"C": [0, 0]}, ["Scheduled"])
def test_get_statistics_for_month_one_appointment_subject_type(self):
- statistics = self.statistics_manager.get_statistics_for_month(self.now.month, self.now.year,
- subject_type=get_control_subject_type())
- self.check_statistics(statistics, 0, 0, 1, {"C": [1, 1]}, ['Scheduled'])
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.now.month, self.now.year, subject_type=get_control_subject_type()
+ )
+ self.check_statistics(statistics, 0, 0, 1, {"C": [1, 1]}, ["Scheduled"])
- statistics = self.statistics_manager.get_statistics_for_month(self.now.month, self.now.year,
- subject_type=get_patient_subject_type())
- self.check_statistics(statistics, 0, 0, 0, {"C": [0, 0]}, ['Scheduled'])
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.now.month, self.now.year, subject_type=get_patient_subject_type()
+ )
+ self.check_statistics(statistics, 0, 0, 0, {"C": [0, 0]}, ["Scheduled"])
def test_get_statistics_for_month_one_appointment_subject_type_and_visit(self):
- statistics = self.statistics_manager.get_statistics_for_month(self.now.month, self.now.year,
- subject_type=get_control_subject_type(),
- visit='1')
- self.check_statistics(statistics, 0, 0, 1, {"C": [1, 1]}, ['Scheduled'])
-
- statistics = self.statistics_manager.get_statistics_for_month(self.now.month, self.now.year,
- subject_type=get_patient_subject_type(),
- visit='1')
- self.check_statistics(statistics, 0, 0, 0, {"C": [0, 0]}, ['Scheduled'])
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.now.month,
+ self.now.year,
+ subject_type=get_control_subject_type(),
+ visit="1",
+ )
+ self.check_statistics(statistics, 0, 0, 1, {"C": [1, 1]}, ["Scheduled"])
+
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.now.month,
+ self.now.year,
+ subject_type=get_patient_subject_type(),
+ visit="1",
+ )
+ self.check_statistics(statistics, 0, 0, 0, {"C": [0, 0]}, ["Scheduled"])
def test_get_statistics_for_month_multiple_visits(self):
- second_visit = Visit.objects.create(datetime_begin=self.now + datetime.timedelta(days=-32),
- datetime_end=self.now + datetime.timedelta(days=31),
- subject=self.subject,
- is_finished=False)
+ second_visit = Visit.objects.create(
+ datetime_begin=self.now + datetime.timedelta(days=-32),
+ datetime_end=self.now + datetime.timedelta(days=31),
+ subject=self.subject,
+ is_finished=False,
+ )
second_appointment = create_appointment(second_visit, when=self.now)
- AppointmentTypeLink.objects.create(appointment=second_appointment, appointment_type=self.appointment_type)
+ AppointmentTypeLink.objects.create(
+ appointment=second_appointment, appointment_type=self.appointment_type
+ )
second_appointment.status = "Cancelled"
second_appointment.save()
self.statistics_manager = StatisticsManager()
- statistics = self.statistics_manager.get_statistics_for_month(self.now.month, self.now.year)
- self.check_statistics(statistics, 0, 0, 2, {"C": [2, 1, 1]}, ['Cancelled', 'Scheduled'])
-
- statistics = self.statistics_manager.get_statistics_for_month(self.now.month, self.now.year, visit="1")
- self.check_statistics(statistics, 0, 0, 1, {"C": [1, 1, 0]}, ['Cancelled', 'Scheduled'])
-
- statistics = self.statistics_manager.get_statistics_for_month(self.now.month, self.now.year, visit="2")
- self.check_statistics(statistics, 0, 0, 1, {"C": [1, 0, 1]}, ['Cancelled', 'Scheduled'])
-
- def check_statistics(self, statistics, expected_visits_started, expected_visits_ended, expected_appointments_count,
- expected_appointments_details, expected_statuses):
- self.assertEqual(expected_visits_started, statistics['general']['visits_started'])
- self.assertEqual(expected_visits_ended, statistics['general']['visits_ended'])
- self.assertEqual(expected_statuses, statistics['statuses_list'])
- self.assertEqual(expected_appointments_count, statistics['general']['appointments'])
- self.assertEqual(expected_appointments_details, statistics['appointments'])
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.now.month, self.now.year
+ )
+ self.check_statistics(
+ statistics, 0, 0, 2, {"C": [2, 1, 1]}, ["Cancelled", "Scheduled"]
+ )
+
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.now.month, self.now.year, visit="1"
+ )
+ self.check_statistics(
+ statistics, 0, 0, 1, {"C": [1, 1, 0]}, ["Cancelled", "Scheduled"]
+ )
+
+ statistics = self.statistics_manager.get_statistics_for_month(
+ self.now.month, self.now.year, visit="2"
+ )
+ self.check_statistics(
+ statistics, 0, 0, 1, {"C": [1, 0, 1]}, ["Cancelled", "Scheduled"]
+ )
+
+ def check_statistics(
+ self,
+ statistics,
+ expected_visits_started,
+ expected_visits_ended,
+ expected_appointments_count,
+ expected_appointments_details,
+ expected_statuses,
+ ):
+ self.assertEqual(
+ expected_visits_started, statistics["general"]["visits_started"]
+ )
+ self.assertEqual(expected_visits_ended, statistics["general"]["visits_ended"])
+ self.assertEqual(expected_statuses, statistics["statuses_list"])
+ self.assertEqual(
+ expected_appointments_count, statistics["general"]["appointments"]
+ )
+ self.assertEqual(expected_appointments_details, statistics["appointments"])