clinicedc 2.0.26__py3-none-any.whl → 2.0.28__py3-none-any.whl

{clinicedc-2.0.26.dist-info → clinicedc-2.0.28.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: clinicedc
-Version: 2.0.26
+Version: 2.0.28
 Summary: A clinical trials data management framework built on Django
 Keywords: django,clinicedc,edc,clinical trials,research,data management,esource
 Author: Erik van Widenfelt, Jonathan Willitts

{clinicedc-2.0.26.dist-info → clinicedc-2.0.28.dist-info}/RECORD

@@ -593,9 +593,9 @@ edc_consent/modelform_mixins/consent_modelform_mixin/consent_modelform_mixin.py,
 edc_consent/modelform_mixins/consent_modelform_mixin/consent_modelform_validation_mixin.py,sha256=Wwo3l-pdFlLkK8q50GkaCyPUXtuPJXODqYfb3HF1jDw,9613
 edc_consent/modelform_mixins/consent_modelform_mixin/review_fields_modelform_mixin.py,sha256=HOiWpf8SnPaGMtRbKM6uAglbV1HmQWdzxSoyQW1ab2U,1922
 edc_consent/modelform_mixins/requires_consent_modelform_mixin.py,sha256=-rQAmOvl1fx8-lEUB6M4V7tqaTqDRxtid002EWYPIxM,2340
-edc_consent/models/__init__.py,sha256=hBdNWnac5MtlZATkOKZHUelMRn2M6jPCgGktCio5Wgk,282
+edc_consent/models/__init__.py,sha256=kTUrf6WlsKInX7jVuD3DyIqRW1OUaeSemflLLzWLV_I,278
 edc_consent/models/edc_permissions.py,sha256=f9PWQ1ZFz4rKT7wFpfr8anQ7mV6sCdNaWNMimPLGae8,338
-edc_consent/models/signals.py,sha256=vhLiZPwSinm_CXh-r9Ty_Xaja5okvqrSFCkDp6DHylc,3020
+edc_consent/models/signals.py,sha256=kjYIlFTcm395_z4h3wlBkYbcxzAjgqsea3_ik5rm6CM,3320
 edc_consent/navbars.py,sha256=Bqb2UfOCLL6yuT_fSvKYQymbBj7V6q9CwvmI-VdUmls,334
 edc_consent/site_consents.py,sha256=jQYufDBievxoyOlC0Q1Llxv9xYqCEyk58Q1Fg_cu3mY,16882
 edc_consent/stubs.py,sha256=ZXjNqT6nBHRFHCB5tCOzBC3ZdiiBR3IitygO3FldTZA,513
@@ -611,8 +611,8 @@ edc_consent/views/home_view.py,sha256=TRqEcysATqzVGTHPhn6HxPsWjIGAPDwYaCylIJOWM7
 edc_consent/wsgi.py,sha256=IuY8oXnc033507PBykHhWuZxUDpg4MaMvTmVSM6uJ54,390
 edc_constants/__init__.py,sha256=jHg-osFAN-UgMbnvV1MnQ0sD37lq0QisRbJ_oqrGUdw,84
 edc_constants/apps.py,sha256=H3gCke2ogPgCL2sSD44Nb56ZBurei4uXWEhcUTdIlYI,318
-edc_constants/choices.py,sha256=sTap6YDFb3ydlm4dLewt0E4X-q9lHCRHR5aDX28SdV4,19094
-edc_constants/constants.py,sha256=ZVHT0VazXzdt4cjt5wKRXu6mRNRY5JoDADDO3a4WOrc,5356
+edc_constants/choices.py,sha256=OvsfqZvb872tANzN0LMLgGLMkqaqRRb1FooXBcTr4cY,19638
+edc_constants/constants.py,sha256=Utlax5PHmnKXe0DQebnz7aEwlE1KM9ItUEET6jPqgN0,5585
 edc_constants/context_processor.py,sha256=JwfB03QXX9AFcVI_-ohdNVTGWpP2DDpH_t_kdiAe-7s,809
 edc_constants/date_constants.py,sha256=5XrhZHz0caO1qghW4_r2slDMVdHsz6QG8OfSo2mMKSg,616
 edc_constants/disease_constants.py,sha256=ZXzwomCaDMtrghHkAHdUUuNbZloIFn0lnG0-nZfdEvE,743
@@ -2794,8 +2794,8 @@ edc_randomization/model_mixins.py,sha256=BJe7eLxveTFNPIS7hz7796hSL0DFvTml03HmNih
 edc_randomization/models/__init__.py,sha256=iaJ6FM7VVqLpp8M-OjVWjohp4ELdxtPXqbEiT3iN5Tw,94
 edc_randomization/models/edc_permissions.py,sha256=f6P4zXxLQdTAbn2KnFlwfE86Lmzj7Ecp4JJ2F8mrwTc,286
 edc_randomization/models/randomization_list.py,sha256=Hd5yUSZ5HBKhNzYdlbJufab8U2x3Dzw8n4WXnYzJxyc,253
-edc_randomization/randomization_list_importer.py,sha256=YZG5Z0faOD85UpIFLkwt9Hq-2IAyI43xGINdhzI5YKQ,12815
-edc_randomization/randomization_list_verifier.py,sha256=A0LRQkI-pMt9TaJ3kps5LncMJZaz5eMdRFDeI35fIGo,6918
+edc_randomization/randomization_list_importer.py,sha256=FzL7-Iq9GJEXoi_ggGKvk7fApfL_oxcI7eJJUXyc4GM,13076
+edc_randomization/randomization_list_verifier.py,sha256=o-niIHR6OapiAXbGeLzW03PVz5DdYKOidJIcWJwCalM,7069
 edc_randomization/randomizer.py,sha256=_LYZp7gmpOIkovCs7TfAt78wb_Kl4iV6I85YIxgQ5pg,12729
 edc_randomization/randomizers.py,sha256=JvMDAnsgvRZkl50Bawm2iLsyw3bfWfGwBafn54K5g44,297
 edc_randomization/site_randomizers.py,sha256=CcHRz_J6OlJ64-iNul_LOHM0ai6SbcX5AMDrFFMewDA,4390
@@ -3292,7 +3292,7 @@ edc_visit_schedule/schedule/schedule.py,sha256=ROUNin-k1oJVtx_wEXwlj5xrhTw3I_6Ve
 edc_visit_schedule/schedule/visit_collection.py,sha256=9OJKrLtx-H0eL9oo0dsRqYGPICiAMqEF4xIhhlinx0A,2033
 edc_visit_schedule/schedule/window.py,sha256=gsXW7z3P84h6kWX7e7CABmalyLGgbbIwe0Q6atIbyEI,5229
 edc_visit_schedule/simple_model_validator.py,sha256=5lMyVrrlAy4HxLmAqM3he7D2ssCJoyjAWDWnFmJwRT0,789
-edc_visit_schedule/site_visit_schedules.py,sha256=MeeJjyYludPlmjrYHmnx5D6t85DZrWvPyFMgidYbewE,13087
+edc_visit_schedule/site_visit_schedules.py,sha256=dtFDEWTXQWx1KTFJQQDh2Uv52Ht2Rq64QktkYTsGBIQ,12949
 edc_visit_schedule/subject_schedule.py,sha256=gai8sQ9nek3KEu27GL656twm0zKP3I3g510effNdIT8,16552
 edc_visit_schedule/system_checks.py,sha256=Gp5DXTThRCFXyZ3dlN2S8FJPz16weonpjedcy6XIIms,9300
 edc_visit_schedule/templates/edc_visit_schedule/home.html,sha256=RqtGsq6-zXi43jU0iSv24-xsIXXHkuiHjJvF-yqDyjA,1112
@@ -3407,7 +3407,7 @@ edc_vitals/models/fields/waist_circumference.py,sha256=fZcHFDdEwWLjIVLktKrFCD9UU
 edc_vitals/models/fields/weight.py,sha256=zo9_9e3Cpu0UqoRbWS-iDkcDo6fK80b1dDQy4x4MyxE,921
 edc_vitals/utils.py,sha256=vXid44KUXxeaSyund_y5MNXc5DFJs052_PwUAjszE2k,1384
 edc_vitals/validators.py,sha256=vNiElWMs0rRnHRNuVoPLRf0rW_C_0xcfUyep1Y_Si5s,156
-clinicedc-2.0.26.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-clinicedc-2.0.26.dist-info/WHEEL,sha256=-neZj6nU9KAMg2CnCY6T3w8J53nx1kFGw_9HfoSzM60,79
-clinicedc-2.0.26.dist-info/METADATA,sha256=GB5NgaBjnahJvCN28GDKHj2QxuoAECGn_cC7hmIs9cU,15787
-clinicedc-2.0.26.dist-info/RECORD,,
+clinicedc-2.0.28.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+clinicedc-2.0.28.dist-info/WHEEL,sha256=-neZj6nU9KAMg2CnCY6T3w8J53nx1kFGw_9HfoSzM60,79
+clinicedc-2.0.28.dist-info/METADATA,sha256=YUfHfAvlHlkygsCSkKKCoV_MMwqlVWaUKE72Gq2R6iA,15787
+clinicedc-2.0.28.dist-info/RECORD,,

edc_consent/models/__init__.py

@@ -1,11 +1,11 @@
 from .edc_permissions import EdcPermissions
 from .signals import (
     requires_consent_on_pre_save,
-    # update_appointment_from_consentext_post_save,
+    update_appointment_from_consentext_post_save,
 )
 
 __all__ = [
     "EdcPermissions",
     "requires_consent_on_pre_save",
-    # "update_appointment_from_consentext_post_save",
+    "update_appointment_from_consentext_post_save",
 ]

edc_consent/models/signals.py

@@ -1,9 +1,14 @@
-from django.db.models.signals import pre_save
+import contextlib
+
+from django.db.models.signals import post_save, pre_save
 from django.dispatch import receiver
 
 from edc_sites import site_sites
+from edc_visit_schedule.exceptions import NotOnScheduleError
+from edc_visit_schedule.site_visit_schedules import site_visit_schedules
+from edc_visit_schedule.subject_schedule import SubjectSchedule
 
-from ..model_mixins import RequiresConsentFieldsModelMixin
+from ..model_mixins import ConsentExtensionModelMixin, RequiresConsentFieldsModelMixin
 from ..site_consents import site_consents
 
 
@@ -50,27 +55,28 @@ def requires_consent_on_pre_save(instance, raw, using, update_fields, **kwargs):
         instance.consent_model = consent_definition.model
 
 
-# @receiver(
-#     post_save,
-#     weak=False,
-#     dispatch_uid="update_appointment_from_consentext_post_save",
-# )
-# def update_appointment_from_consentext_post_save(
-#     sender, instance, raw, created, using, **kwargs
-# ):
-#     if (
-#         not raw
-#         and not kwargs.get("update_fields")
-#         and isinstance(instance, (ConsentExtensionModelMixin,))
-#     ):
-#         cdef = site_consents.get_consent_definition(
-#             model=instance.subject_consent._meta.label_lower,
-#             version=instance.subject_consent.version,
-#         )
-#         visit_schedule, schedule = site_visit_schedules.get_by_consent_definition(cdef)
-#         subject_schedule = SubjectSchedule(
-#             instance.subject_consent.subject_identifier,
-#             visit_schedule=visit_schedule,
-#             schedule=schedule,
-#         )
-#         subject_schedule.refresh_appointments()
+@receiver(
+    post_save,
+    weak=False,
+    dispatch_uid="update_appointment_from_consentext_post_save",
+)
+def update_appointment_from_consentext_post_save(
+    sender, instance, raw, created, using, **kwargs
+):
+    if (
+        not raw
+        and not kwargs.get("update_fields")
+        and isinstance(instance, (ConsentExtensionModelMixin,))
+    ):
+        cdef = site_consents.get_consent_definition(
+            model=instance.subject_consent._meta.label_lower,
+            version=instance.subject_consent.version,
+        )
+        for visit_schedule, schedule in site_visit_schedules.get_by_consent_definition(cdef):
+            subject_schedule = SubjectSchedule(
+                instance.subject_consent.subject_identifier,
+                visit_schedule=visit_schedule,
+                schedule=schedule,
+            )
+            with contextlib.suppress(NotOnScheduleError):
+                subject_schedule.refresh_appointments()

edc_constants/choices.py

@@ -4,6 +4,7 @@ from .constants import (
     ABNORMAL,
     ABSENT,
     AFTERNOON,
+    AGREE,
     ALIVE,
     ALWAYS,
     ANYTIME,
@@ -11,8 +12,11 @@ from .constants import (
     COMPLETE,
     DEAD,
     DECLINED,
+    DIFFICULT,
+    DISAGREE,
     DONT_KNOW,
     DWTA,
+    EASY,
     EVENING,
     FALSE,
     FASTING,
@@ -26,6 +30,7 @@ from .constants import (
     MORNING,
     NAIVE,
     NEG,
+    NEUTRAL,
     NEVER,
     NO,
     NON_FASTING,
@@ -51,9 +56,13 @@ from .constants import (
     REFUSED,
     SMOKER,
     SOMETIMES,
+    STRONGLY_AGREE,
+    STRONGLY_DISAGREE,
     TBD,
     TRUE,
     UNKNOWN,
+    VERY_DIFFICULT,
+    VERY_EASY,
     VERY_OFTEN,
     WEEKDAYS,
     WEEKENDS,
@@ -833,3 +842,20 @@ WHYNOPARTICIPATE_CHOICE = (
     ("OTHER", _("Other, specify:")),
     ("not_answering", _("Don't want to answer")),
 )
+
+
+DISAGREE_TO_AGREE_CHOICE = (
+    (STRONGLY_DISAGREE, _("Strongly disagree")),
+    (DISAGREE, _("disagree")),
+    (NEUTRAL, _("Neutral")),
+    (AGREE, _("Agree")),
+    (STRONGLY_AGREE, _("Strongly agree")),
+)
+
+DIFFICULT_TO_EASY_CHOICE = (
+    (VERY_DIFFICULT, _("Very difficult")),
+    (DIFFICULT, _("Difficult")),
+    (NEUTRAL, _("Neutral")),
+    (EASY, _("Easy")),
+    (VERY_EASY, _("Very easy")),
+)

edc_constants/constants.py

@@ -8,6 +8,7 @@ ABNORMAL = "ABNORMAL"
 ABSENT = "absent"
 ADDITIONAL = True
 AFTERNOON = "afternoon"
+AGREE = "agree"
 ALIVE = "alive"
 ALWAYS = "always"
 ANONYMOUS = "anonymous"
@@ -40,6 +41,7 @@ DEFAULTER = "defaulter"
 DELETE = "DELETE"
 DELIVERY = "delivery"
 DIABETES = "diabetes"
+DISAGREE = "disagree"
 DIVORCED = "divorced"
 DM = "dm"
 DONE = "done"
@@ -109,6 +111,7 @@ MULTI_MORBIDITY = "multi"
 NAIVE = "NAIVE"
 NCD = "NCD"
 NEG = "NEG"
+NEUTRAL = "neutral"
 NEVER = "NEVER"
 NEW = "New"
 NEW_FIELD = "new_field"
@@ -192,6 +195,8 @@ SMOKER = "smoker"
 SOMETIMES = "sometimes"
 STEROIDS = "steroids"
 STOPPED = "stopped"
+STRONGLY_AGREE = "strongly_agree"
+STRONGLY_DISAGREE = "strongly_disagree"
 STUDY_DEFINED_TIMEPOINT = "study_defined_timepoint"
 SUBJECT = "subject"
 SYSTEMATIC = "systematic"
@@ -238,3 +243,8 @@ THURSDAY = "thursday"
 FRIDAY = "friday"
 SATURDAY = "saturday"
 SUNDAY = "sunday"
+
+VERY_DIFFICULT = "very_difficult"
+DIFFICULT = "difficult"
+EASY = "easy"
+VERY_EASY = "very_easy"

edc_randomization/randomization_list_importer.py

@@ -2,6 +2,7 @@ from __future__ import annotations
 
 import csv
 import sys
+from itertools import islice
 from pathlib import Path
 from pprint import pprint
 from uuid import uuid4
@@ -72,6 +73,7 @@ class RandomizationListImporter:
         username: str | None = None,
         revision: str | None = None,
         sid_count_for_tests: int | None = None,
+        skip_verify: bool | None = None,
         extra_csv_fieldnames: tuple[str] | None = None,
         **kwargs,  # noqa: ARG002
     ):
@@ -84,6 +86,7 @@ class RandomizationListImporter:
         self.revision = revision
         self.user = username
         self.sid_count_for_tests = sid_count_for_tests
+        self.skip_verify = skip_verify
         self.randomizer_model_cls = randomizer_model_cls
         self.randomizer_name = randomizer_name
         self.assignment_map = assignment_map
@@ -120,8 +123,9 @@ class RandomizationListImporter:
                 )
             )
         rec_count = self._import_csv_to_model()
-        self.verify_messages = self._verify_data(**kwargs)
-        self._summarize_results()
+        if not self.skip_verify:
+            self.verify_messages = self._verify_data(**kwargs)
+            self._summarize_results()
         if self.verbose:
             sys.stdout.write(
                 style.SUCCESS("\nDone.------------------------------------------------\n")
@@ -221,13 +225,15 @@ class RandomizationListImporter:
             sid_count = len(self.get_sid_list())
         with self.randomizationlist_path.open(mode="r") as f:
             reader = csv.DictReader(f)
+            if self.sid_count_for_tests:
+                reader = islice(reader, self.sid_count_for_tests)
             all_rows = [{k: v.strip() for k, v in row.items() if k} for row in reader]
             sorted_rows = sorted(
                 all_rows, key=lambda row: (row.get("site_name", ""), row.get("sid", ""))
             )
             for row in tqdm(sorted_rows, total=sid_count):
-                if self.sid_count_for_tests and len(objs) == self.sid_count_for_tests:
-                    break
+                # if self.sid_count_for_tests and len(objs) == self.sid_count_for_tests:
+                #     break
                 try:
                     self.randomizer_model_cls.objects.get(sid=row["sid"])
                 except ObjectDoesNotExist:

edc_randomization/randomization_list_verifier.py

@@ -1,5 +1,6 @@
 import csv
 import sys
+from itertools import islice
 from pathlib import Path
 
 from django.core.exceptions import ObjectDoesNotExist
@@ -72,15 +73,16 @@ class RandomizationListVerifier:
 
     def verify(self) -> str | None:
         message = None
-
         # read and sort from CSV file
         with self.randomizationlist_path.open(mode="r") as f:
             reader = csv.DictReader(f)
+            if self.sid_count_for_tests:
+                reader = islice(reader, self.sid_count_for_tests)
             all_rows = [{k: v.strip() for k, v in row.items() if k} for row in reader]
             sorted_rows = sorted(
-                all_rows, key=lambda row: (row.get("site_name", ""), int(row.get("sid", 0)))
+                all_rows,
+                key=lambda row: (row.get("site_name", ""), int(row.get("sid", 0))),
             )
-
         # compare sorted CSV length with DB
         if len(sorted_rows) != self.randomizer_model_cls.objects.all().count():
             expected_cnt = len(sorted_rows)

edc_visit_schedule/site_visit_schedules.py

@@ -95,9 +95,11 @@ class SiteVisitSchedules:
     def get_by_consent_definition(
         self,
         cdef: ConsentDefinition,
-    ) -> tuple[VisitSchedule, Schedule]:
-        """Returns a visit schedule instance or raises."""
-        ret = []
+    ) -> tuple[tuple[VisitSchedule, Schedule], ...]:
+        """Returns a tuple of (visit schedule, schedule instances) that
+        match this cdef or raises.
+        """
+        visit_schedules = []
         attr = "consent_definitions"
         for visit_schedule in self.visit_schedules.values():
             for schedule in visit_schedule.schedules.values():
@@ -109,18 +111,12 @@ class SiteVisitSchedules:
                     ) from e
                 for _cdef in consent_definitions:
                     if _cdef == cdef:
-                        ret.append([visit_schedule, schedule])  # noqa: PERF401
-        if not ret:
+                        visit_schedules.append((visit_schedule, schedule))  # noqa: PERF401
+        if not visit_schedules:
             raise SiteVisitScheduleError(
                 f"Schedule not found. No schedule exists for {attr}={cdef}."
             )
-        if len(ret) > 1:
-            raise SiteVisitScheduleError(
-                f"Schedule is ambiguous. More than one schedule exists for "
-                f"{attr}={cdef}. Got {ret}"
-            )
-        visit_schedule, schedule = ret[0]
-        return visit_schedule, schedule
+        return tuple(visit_schedules)
 
     def get_by_onschedule_model(self, onschedule_model: str) -> tuple[VisitSchedule, Schedule]:
         """Returns a tuple of (visit_schedule, schedule)