meta-edc 1.1.13__py3-none-any.whl → 1.1.15__py3-none-any.whl

meta_ae/action_items.py

@@ -43,7 +43,7 @@ class AeFollowupAction(ActionWithNotification):
     name = AE_FOLLOWUP_ACTION
     display_name = "Submit AE Followup Report"
     notification_display_name = "AE Followup Report"
-    parent_action_names = [AE_INITIAL_ACTION, AE_FOLLOWUP_ACTION]
+    parent_action_names = (AE_INITIAL_ACTION, AE_FOLLOWUP_ACTION)
     reference_model = "meta_ae.aefollowup"
     related_reference_model = "meta_ae.aeinitial"
     related_reference_fk_attr = "ae_initial"
@@ -61,7 +61,7 @@ class AeFollowupAction(ActionWithNotification):
     priority = HIGH_PRIORITY
 
     def get_next_actions(self):
-        next_actions = []
+        next_actions = ()
 
         # add AE followup to next_actions if followup.
         next_actions = self.append_to_next_if_required(
@@ -98,14 +98,14 @@ class AeInitialAction(ActionWithNotification):
     name = AE_INITIAL_ACTION
     display_name = "Submit AE Initial Report"
     notification_display_name = "AE Initial Report"
-    parent_action_names = [
+    parent_action_names = (
         BLOOD_RESULTS_LIPIDS_ACTION,
         BLOOD_RESULTS_GLU_ACTION,
         BLOOD_RESULTS_LFT_ACTION,
         BLOOD_RESULTS_RFT_ACTION,
         BLOOD_RESULTS_FBC_ACTION,
         FOLLOWUP_EXAMINATION_ACTION,
-    ]
+    )
     reference_model = "meta_ae.aeinitial"
     show_link_to_changelist = True
     show_link_to_add = True
@@ -118,7 +118,7 @@ class AeInitialAction(ActionWithNotification):
 
         1. Add death report action if death
         """
-        next_actions = []
+        next_actions = ()
         deceased = (
             self.reference_obj.ae_grade == GRADE5 or self.reference_obj.sae_reason.name == DEAD
         )
@@ -156,20 +156,18 @@ class AeInitialAction(ActionWithNotification):
             required=self.reference_obj.ae_grade == GRADE4,
         )
         # add next AeTmgAction if G3 and is an SAE
-        next_actions = self.append_to_next_if_required(
+        return self.append_to_next_if_required(
             next_actions=next_actions,
             action_name=AE_TMG_ACTION,
             required=(self.reference_obj.ae_grade == GRADE3 and self.reference_obj.sae == YES),
         )
 
-        return next_actions
-
 
 class AeSusarAction(ActionWithNotification):
     name = AE_SUSAR_ACTION
     display_name = "Submit AE SUSAR Report"
     notification_display_name = "AE SUSAR Report"
-    parent_action_names = [AE_INITIAL_ACTION]
+    parent_action_names = (AE_INITIAL_ACTION,)
     reference_model = "meta_ae.aesusar"
     related_reference_model = "meta_ae.aeinitial"
     related_reference_fk_attr = "ae_initial"
@@ -184,7 +182,7 @@ class AeTmgAction(ActionWithNotification):
     name = AE_TMG_ACTION
     display_name = "TMG AE Report pending"
     notification_display_name = "TMG AE Report"
-    parent_action_names = [AE_INITIAL_ACTION, AE_FOLLOWUP_ACTION, AE_TMG_ACTION]
+    parent_action_names = (AE_INITIAL_ACTION, AE_FOLLOWUP_ACTION, AE_TMG_ACTION)
     reference_model = "meta_ae.aetmg"
     related_reference_model = "meta_ae.aeinitial"
     related_reference_fk_attr = "ae_initial"
@@ -204,13 +202,13 @@ class DeathReportAction(PregnancyActionItemMixin, ActionWithNotification):
     display_name = "Submit Death Report"
     notification_display_name = "Death Report"
     reference_model = "meta_ae.deathreport"
-    parent_action_names = [AE_INITIAL_ACTION, AE_FOLLOWUP_ACTION]
+    parent_action_names = (AE_INITIAL_ACTION, AE_FOLLOWUP_ACTION)
     show_link_to_changelist = True
     show_link_to_add = True
     admin_site_name = "meta_ae_admin"
     priority = HIGH_PRIORITY
     singleton = True
-    dirty_fields = ["cause_of_death"]
+    dirty_fields = ("cause_of_death",)
 
     def get_next_actions(self):
         """Adds 1 DEATHReportTMG if not yet created and
@@ -242,7 +240,7 @@ class DeathReportTmgAction(ActionWithNotification):
     name = DEATH_REPORT_TMG_ACTION
     display_name = "TMG Death Report pending"
     notification_display_name = "TMG Death Report"
-    parent_action_names = [DEATH_REPORT_ACTION, DEATH_REPORT_TMG_ACTION]
+    parent_action_names = (DEATH_REPORT_ACTION, DEATH_REPORT_TMG_ACTION)
     reference_model = "meta_ae.deathreporttmg"
     related_reference_model = "meta_ae.deathreport"
     related_reference_fk_attr = "death_report"
@@ -301,12 +299,11 @@ class DeathReportTmgAction(ActionWithNotification):
                 )
                 .count()
                 < 2
+            ) and (
+                self.reference_obj.cause_of_death
+                != self.related_action_item.reference_obj.cause_of_death
             ):
-                if (
-                    self.reference_obj.cause_of_death
-                    != self.related_action_item.reference_obj.cause_of_death
-                ):
-                    next_actions = ["self"]
+                next_actions = ["self"]
         return next_actions
 
 

meta_ae/templatetags/meta_ae_extras.py

@@ -24,6 +24,6 @@ def format_ae_description(context, ae_initial, wrap_length):
     context["OTHER"] = OTHER
     context["YES"] = YES
     context["ae_initial"] = ae_initial
-    context["sae_reason"] = mark_safe(formatted_sae_reason)  # nosec B308, B703
-    context["ae_description"] = mark_safe(formatted_ae_description)  # nosec B308, B703
+    context["sae_reason"] = mark_safe(formatted_sae_reason)  # nosec B308, B703  # noqa: S308
+    context["ae_description"] = mark_safe(formatted_ae_description)  # nosec B308, B703  # noqa: S308
     return context

meta_analytics/dataframes/get_last_imp_visits_df.py

@@ -62,8 +62,8 @@ def get_last_imp_visits_df(
     df_off = df_off.set_index("subject_identifier")
 
     df_meds = df_meds.set_index("subject_identifier")
-    df_final = pd.merge(
-        df_meds, df_off, left_index=True, right_index=True, how="outer"
+    df_final = df_meds.merge(
+        df_off, left_index=True, right_index=True, how="outer"
     ).reset_index()
 
     # merge with RandomizationList if lot_obj

meta_analytics/tables/enrolled/glucose.py

@@ -24,5 +24,4 @@ class GlucoseTable(Table):
         df_tmp = df_tmp.reset_index()
         gender_tbl = GenderTable(main_df=df_tmp).table_df
         age_tbl = AgeTable(main_df=df_tmp).table_df
-        self.table_df = pd.concat([self.table_df, gender_tbl, age_tbl])
-        self.table_df.reset_index(drop=True, inplace=True)
+        self.table_df = pd.concat([self.table_df, gender_tbl, age_tbl]).reset_index(drop=True)

meta_consent/models/subject_consent_v1.py

@@ -5,7 +5,6 @@ from .subject_consent import SubjectConsent
 
 
 class SubjectConsentV1(SubjectConsent):
-
     objects = ConsentObjectsByCdefManager()
     on_site = CurrentSiteByCdefManager()
     history = HistoricalRecords()

meta_dashboard/view_utils/subject_screening_button.py

@@ -42,7 +42,7 @@ class SubjectScreeningButton(BaseSubjectScreeningButton):
 
 @dataclass
 class SubjectScreeningPartOneButton(SubjectScreeningButton):
-    model_obj: ScreeningPartOne = None
+    model_obj: ScreeningPartOne | None = None
     model_cls: type[ScreeningPartOne] = field(default=ScreeningPartOne)
 
     @property
@@ -52,7 +52,7 @@ class SubjectScreeningPartOneButton(SubjectScreeningButton):
 
 @dataclass
 class SubjectScreeningPartTwoButton(SubjectScreeningButton):
-    model_obj: ScreeningPartTwo = None
+    model_obj: ScreeningPartTwo | None = None
     model_cls: type[ScreeningPartTwo] = field(default=ScreeningPartTwo)
 
     @property
@@ -84,7 +84,7 @@ class SubjectScreeningPartTwoButton(SubjectScreeningButton):
 
 @dataclass
 class SubjectScreeningPartThreeButton(SubjectScreeningButton):
-    model_obj: ScreeningPartThree = None
+    model_obj: ScreeningPartThree | None = None
     model_cls: type[ScreeningPartThree] = field(default=ScreeningPartThree)
 
     @property

meta_edc/admin.py

@@ -18,7 +18,7 @@ class AdminSite(DjangoAdminSite):
     index_title = "Site administration"
     site_url = "/administration/"
 
-    def __init__(self, **kwargs):
+    def __init__(self, **kwargs):  # noqa: ARG002
         super().__init__(name="meta_edc")
 
 

meta_edc/celery.py

@@ -1,4 +1,5 @@
 import os
+import sys
 
 from celery import Celery
 
@@ -13,4 +14,4 @@ app.autodiscover_tasks()
 
 @app.task(bind=True)
 def debug_task(self):
-    print(f"Request: {self.request!r}")
+    sys.stdout.write(f"Request: {self.request!r}\n")

meta_edc/celery_live.py

@@ -1,4 +1,5 @@
 import os
+import sys
 
 from celery import Celery
 
@@ -15,4 +16,4 @@ app.autodiscover_tasks()
 
 @app.task(bind=True)
 def debug_task(self):
-    print(f"Request: {self.request!r}")
+    sys.stdout.write(f"Request: {self.request!r}\n")

meta_edc/celery_uat.py

@@ -1,4 +1,5 @@
 import os
+import sys
 
 from celery import Celery
 
@@ -21,4 +22,4 @@ app.autodiscover_tasks()
 
 @app.task(bind=True)
 def debug_task(self):
-    print(f"Request: {self.request!r}")
+    sys.stdout.write(f"Request: {self.request!r}\n")

meta_edc/meta_version.py

@@ -3,11 +3,11 @@ PHASE_THREE = 3
 PHASE_THREE_ONLY = "PHASE_THREE_ONLY"
 
 
-class InvalidMetaVersion(Exception):
+class InvalidMetaVersion(Exception):  # noqa: N818
     pass
 
 
 def get_meta_version():
-    from django.conf import settings
+    from django.conf import settings  # noqa: PLC0415
 
     return settings.META_PHASE

meta_edc/navbars.py

@@ -12,19 +12,21 @@ from meta_dashboard.navbars import navbar as meta_dashboard_navbar
 
 navbar = Navbar(name=settings.APP_NAME)
 
-navbar_item = copy([item for item in lab_navbar.navbar_items if item.name == "specimens"][0])
+navbar_item = copy(next(item for item in lab_navbar.navbar_items if item.name == "specimens"))
 navbar_item.active = False
 navbar_item.label = "Specimens"
 navbar.register(navbar_item)
 
 navbar.register(
-    [item for item in meta_dashboard_navbar.navbar_items if item.name == "screened_subject"][0]
+    next(
+        item for item in meta_dashboard_navbar.navbar_items if item.name == "screened_subject"
+    )
 )
 
 navbar.register(
-    [item for item in meta_dashboard_navbar.navbar_items if item.name == "consented_subject"][
-        0
-    ]
+    next(
+        item for item in meta_dashboard_navbar.navbar_items if item.name == "consented_subject"
+    )
 )
 
 for navbar_item in review_navbar.navbar_items:

meta_edc/settings/defaults.py

@@ -2,7 +2,7 @@ import os
 import sys
 from importlib.metadata import version
 from pathlib import Path
-from urllib.parse import quote
+from urllib.parse import quote, urljoin
 
 import django
 import environ
@@ -48,7 +48,7 @@ else:
 # copy your .env file from .envs/ to BASE_DIR
 if "test" in sys.argv:
     env.read_env(ENV_DIR / ".env-tests")
-    print(f"Reading env from {(BASE_DIR /'.env-tests')}")  # noqa
+    print(f"Reading env from {(BASE_DIR / '.env-tests')}")  # noqa
 else:
     if not (ENV_DIR / ".env").exists():
         raise FileExistsError(f"Environment file does not exist. Got `{(ENV_DIR / '.env')}`")
@@ -550,7 +550,7 @@ if env("AWS_ENABLED"):
     AWS_LOCATION = env.str("AWS_LOCATION")
     AWS_IS_GZIPPED = True
     STORAGES = {"staticfiles": {"BACKEND": "storages.backends.s3boto3.S3Boto3Storage"}}
-    STATIC_URL = f"{os.path.join(AWS_S3_CUSTOM_DOMAIN, AWS_LOCATION)}/"
+    STATIC_URL = urljoin(AWS_S3_CUSTOM_DOMAIN, AWS_LOCATION)
     STATIC_ROOT = ""
 elif DEBUG:
     STATIC_URL = env.str("DJANGO_STATIC_URL")

meta_edc/urls.py

@@ -10,7 +10,7 @@ from edc_utils.paths_for_urlpatterns import paths_for_urlpatterns
 from .views import HomeView
 
 
-def trigger_error(request):
+def trigger_error(request):  # noqa: ARG001
     division_by_zero = 1 / 0  # noqa
 
 

meta_edc/utils.py

@@ -1,9 +1,11 @@
+import sys
+
 from django.core.exceptions import ImproperlyConfigured
 
 
 def confirm_meta_version(phase):
     response = input(f"This is meta phase {phase}. Type 2 or 3 to continue: ")
     if response not in ["2", "3"]:
-        print("settings load has been halted.")
+        sys.stdout.write("settings load has been halted.\n")
         raise ImproperlyConfigured("Check settings.META_PHASE")
     return int(response)

{meta_edc-1.1.13.dist-info → meta_edc-1.1.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: meta-edc
-Version: 1.1.13
+Version: 1.1.15
 Summary: META Trial EDC (https://www.isrctn.com/ISRCTN76157257)
 Keywords: django,clinicedc,META EDC,EDC,clinical trials,META Trial,ISRCTN76157257
 Author: Erik van Widenfelt, Jonathan Willitts
@@ -15,13 +15,12 @@ Classifier: Intended Audience :: Science/Research
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Dist: clinicedc>=2.0.13
-Requires-Dist: edc-he>=1.1.0
-Requires-Dist: edc-microscopy>=1.1.1
-Requires-Dist: edc-mnsi>=1.1.3
-Requires-Dist: edc-phq9>=1.0.1
-Requires-Dist: edc-qol>=1.1.2
-Requires-Dist: psycopg2>=2.9.10
+Requires-Dist: clinicedc>=2.0.26
+Requires-Dist: edc-he>=1.2.0
+Requires-Dist: edc-microscopy>=1.2.0
+Requires-Dist: edc-mnsi>=1.2.0
+Requires-Dist: edc-phq9>=1.1.0
+Requires-Dist: edc-qol>=1.2.0
 Requires-Python: >=3.12, <3.14
 Description-Content-Type: text/x-rst
 
@@ -89,8 +88,8 @@ Assuming you are logged into the account ``myaccount``:
     mkdir ~/edc && \
     cd ~/edc && \
     uv venv && \
-    uv pip install -U meta-edc==1.1.12 && \
-    wget https://raw.githubusercontent.com/meta-trial/meta-edc/1.1.12/manage.py && \
+    uv pip install -U meta-edc==1.1.14 && \
+    wget https://raw.githubusercontent.com/meta-trial/meta-edc/1.1.14/manage.py && \
     uv pip freeze | grep meta-edc
 
 Copy your ``.env`` file to ``~/.etc``.
@@ -140,7 +139,7 @@ From the above example:
 
     cd ~/edc && \
     uv venv --clear && \
-    uv pip install -U meta-edc==1.1.12 && \
+    uv pip install -U meta-edc==1.1.14 && \
     wget -O manage.py https://raw.githubusercontent.com/meta-trial/meta-edc/1.1.10/manage.py && \
     uv pip freeze | grep meta-edc && \
     python manage.py check