clinicedc 2.0.15__py3-none-any.whl → 2.0.16__py3-none-any.whl

{clinicedc-2.0.15.dist-info → clinicedc-2.0.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: clinicedc
-Version: 2.0.15
+Version: 2.0.16
 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-2.0.15.dist-info → clinicedc-2.0.16.dist-info}/RECORD

@@ -1087,13 +1087,13 @@ edc_fieldsets/models.py,sha256=sAQOBRo_PM7Uu3Hvxx2j5CLDDpuei8-vAYdkOUSuYkg,32
 edc_fieldsets/urls.py,sha256=_SQMjzRQvSHqalE_zviNqzpbcwJgLdjAgOh3-Eprb58,749
 edc_form_describer/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 edc_form_describer/apps.py,sha256=unr6UihcCOaoVtj56Q6DRQq9WDjivoE1zZjyy2HTBqU,121
-edc_form_describer/form_describer.py,sha256=w94XyAabCOGhuSE6sGedvoPEkTBxpNp6skxR_tsNkvQ,8204
-edc_form_describer/forms_reference.py,sha256=U9P0rRq5fDmUoplXnou6VqyusHVpC9u1wu-kW2jyFgc,4684
-edc_form_describer/make_forms_reference.py,sha256=JdeR1lMo4A2NTvgschdSR-TPpHXvmCO_hlPcK7zKo4U,1371
+edc_form_describer/form_describer.py,sha256=0F7eu2rLpThwv9lU7taSZFr6mJed1Gpv6hUeMYEWlGA,8435
+edc_form_describer/forms_reference.py,sha256=TYofCReEipIceNXSddL29jcApYUrgU8LNq5UElJtSz0,4709
+edc_form_describer/make_forms_reference.py,sha256=wQY39EFscPWTszj8gzpLhf0WKktL91uIVBdx1cMh_gU,1327
 edc_form_describer/management/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 edc_form_describer/management/commands/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-edc_form_describer/management/commands/make_forms_reference.py,sha256=KOUOCN27YvAsBjSQ-0gDk98wnltNoVnrt8k4JJyBWBk,3123
-edc_form_describer/markdown_writer.py,sha256=KILzp0HAY2omaw3SnLTjW9KcjpvJkzjAvyaZ_on7bkI,1799
+edc_form_describer/management/commands/make_forms_reference.py,sha256=Pni3ZPpGM5Ds7-GYXPvl_m2zxHOE2_rFvmdlXre0FnM,3168
+edc_form_describer/markdown_writer.py,sha256=UFjVvz5cUHyJnlUDNm6RIPBGc675HL-IsoUS6TDrKJg,1809
 edc_form_describer/migrations/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 edc_form_describer/models.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 edc_form_describer/urls.py,sha256=_FX1x4JJH8wKclMUbJI847xPbjxqHJazbRZYj30wW7g,113
@@ -3287,7 +3287,7 @@ edc_visit_schedule/navbars.py,sha256=RWx57OD-KxpPh0ihRyangGGiOOR7vfxRFjPCj8C5uF4
 edc_visit_schedule/ordered_collection.py,sha256=7A5YqG0qGx6jAE0z6bd3BijlW9oYxiQrF-5fzB3hvok,1699
 edc_visit_schedule/post_migrate_signals.py,sha256=7vFfx7ifMwmvrf7MCzpk9q4g1pbM4n44uM4TrH1hPGQ,748
 edc_visit_schedule/schedule/__init__.py,sha256=bzyYW9y3pPCFTjwjvkUVgkW3d1g1D2SCNfgE9bnLjII,101
-edc_visit_schedule/schedule/schedule.py,sha256=daKuzIx0sa9c4RjedXQtFFzx79bqdEvAJEDNmzZ8R-s,14874
+edc_visit_schedule/schedule/schedule.py,sha256=RhUc5UPKZacqYmdxI8-tkEkERZFfq0TAN-wDF8dBMEU,14881
 edc_visit_schedule/schedule/visit_collection.py,sha256=9OJKrLtx-H0eL9oo0dsRqYGPICiAMqEF4xIhhlinx0A,2033
 edc_visit_schedule/schedule/window.py,sha256=P_hNhAXBmRxED_0UrlpQoYHF5r_nTEpTK7U2JSAnpCs,5222
 edc_visit_schedule/simple_model_validator.py,sha256=pE2QCSI1VhSr9Dd-NGd-72u6e479_vzbS8iL17eg4Yc,771
@@ -3406,7 +3406,7 @@ 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-2.0.15.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-clinicedc-2.0.15.dist-info/WHEEL,sha256=-neZj6nU9KAMg2CnCY6T3w8J53nx1kFGw_9HfoSzM60,79
-clinicedc-2.0.15.dist-info/METADATA,sha256=OYiw0Dnv4nYU6PEi6gKTj-xbM-7sc6meDbengt5P2zY,15899
-clinicedc-2.0.15.dist-info/RECORD,,
+clinicedc-2.0.16.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
+clinicedc-2.0.16.dist-info/WHEEL,sha256=-neZj6nU9KAMg2CnCY6T3w8J53nx1kFGw_9HfoSzM60,79
+clinicedc-2.0.16.dist-info/METADATA,sha256=yACQMEfCdkmBMoz9yz7R4jaTs-ToDfcahB4QqGBUqII,15899
+clinicedc-2.0.16.dist-info/RECORD,,

edc_form_describer/form_describer.py

@@ -1,12 +1,13 @@
 from __future__ import annotations
 
+import contextlib
 import re
 import string
 import sys
-from datetime import datetime
 from math import floor
 
 from django.core.management.color import color_style
+from django.utils import timezone
 
 from edc_fieldsets.fieldsets import Fieldsets
 from edc_model.constants import DEFAULT_BASE_FIELDS
@@ -57,14 +58,20 @@ class FormDescriber:
         self.markdown: list[str] = []
         add_timestamp = True if add_timestamp is None else add_timestamp
         self.anchor_prefix = anchor_prefix or self.anchor_prefix
-        timestamp = datetime.today().strftime("%Y-%m-%d %H:%M")
+        timestamp = timezone.now().strftime("%Y-%m-%d %H:%M")
         self.level = level or self.level
         self.conditional_fieldset = None
         self.admin_cls = admin_cls
         try:
             self.model_cls = admin_cls.model
         except AttributeError:
-            self.model_cls = admin_cls.form._meta.model
+            try:
+                self.model_cls = admin_cls.form._meta.model
+            except AttributeError as e:
+                raise FormDescriberError(
+                    f"Unable to determine admin class model. Got {admin_cls}"
+                ) from e
+
         self.visit_code = visit_code
         self.models_fields = {fld.name: fld for fld in self.model_cls._meta.get_fields()}
 
@@ -115,7 +122,7 @@ class FormDescriber:
     def anchor(self):
         allow = string.ascii_letters + string.digits + "-"
         slug = self.verbose_name.lower().replace(" ", "-")
-        slug = re.sub("[^%s]" % allow, "", slug)
+        slug = re.sub(f"[^{allow}]", "", slug)
         return f"{self.anchor_prefix}-{slug}"
 
     def describe(self):
@@ -135,7 +142,7 @@ class FormDescriber:
 
         for fieldset_name, fieldset in self.fieldsets:
             if fieldset_name not in ["Audit"]:
-                fieldset_name = fieldset_name or "Main"
+                fieldset_name = fieldset_name or "Main"  # noqa: PLW2901
                 self.markdown.append(f"\n**Section: {fieldset_name}**")
                 if fieldset.get("classes") != "collapse":
                     for fname in fieldset.get("fields"):
@@ -172,10 +179,8 @@ class FormDescriber:
             self.markdown.append(f"* custom_prompt: *{self.custom_form_labels.get(fname)}*")
         self.markdown.append(f"- db_table: {self.model_cls._meta.db_table}")
         self.markdown.append(f"- column: {field_cls.name}")
-        try:
+        with contextlib.suppress(AttributeError):
             self.markdown.append(f"- metadata: {field_cls.metadata}")
-        except AttributeError:
-            pass
         self.markdown.append(f"- type: {field_cls.get_internal_type()}")
         if field_cls.max_length:
             self.markdown.append(f"- length: {field_cls.max_length}")

edc_form_describer/forms_reference.py

@@ -1,8 +1,9 @@
-from datetime import datetime
 from importlib.metadata import version
+from pathlib import Path
 
 from django.apps import apps as django_apps
 from django.conf import settings
+from django.utils import timezone
 
 from .form_describer import FormDescriber
 from .markdown_writer import MarkdownWriter
@@ -36,24 +37,20 @@ class FormsReference:
         self.add_per_form_timestamp = (
             True if add_per_form_timestamp is None else add_per_form_timestamp
         )
-        self.timestamp = datetime.today().strftime("%Y-%m-%d %H:%M")
+        self.timestamp = timezone.now().strftime("%Y-%m-%d %H:%M")
         for visit_schedule in self.visit_schedules:
             self.plans.update({visit_schedule.name: {}})
             for schedule in visit_schedule.schedules.values():
                 for visit_code, visit in schedule.visits.items():
-                    crfs = []
-                    requisitions = []
-                    for c in visit.crfs:
-                        crfs.append(c.model)
-                    for r in visit.requisitions:
-                        requisitions.append(r.panel.name)
+                    crfs = [c.model for c in visit.crfs]
+                    requisitions = [r.panel.name for r in visit.requisitions]
                     self.plans[visit_schedule.name].update(
                         {visit_code: {"crfs": crfs, "requisitions": requisitions}}
                     )
 
     def to_file(
         self,
-        path: str | None = None,
+        path: Path | str | None = None,
         overwrite: bool | None = None,
         pad: int | None = None,
     ):
@@ -95,23 +92,25 @@ class FormsReference:
                     for index, model in enumerate(documents.get("crfs")):
                         model_cls = django_apps.get_model(model)
                         admin_cls = self.admin_site._registry.get(model_cls)
-                        describer = self.describer_cls(
-                            admin_cls=admin_cls,
-                            include_hidden_fields=self.include_hidden_fields,
-                            visit_code=visit_code,
-                            level=self.h4,
-                            anchor_prefix=self.anchor_prefix,
-                            add_timestamp=self.add_per_form_timestamp,
-                        )
-                        describer.markdown.append("\n")
-                        anchor = f"{self.get_anchor(describer.anchor)}"
-                        toc.append(
-                            f'{index + 1}. <a href="#{anchor}">{describer.verbose_name}</a>'
-                        )
-                        markdown.extend(describer.markdown)
+                        if admin_cls:
+                            describer = self.describer_cls(
+                                admin_cls=admin_cls,
+                                include_hidden_fields=self.include_hidden_fields,
+                                visit_code=visit_code,
+                                level=self.h4,
+                                anchor_prefix=self.anchor_prefix,
+                                add_timestamp=self.add_per_form_timestamp,
+                            )
+                            describer.markdown.append("\n")
+                            anchor = f"{self.get_anchor(describer.anchor)}"
+                            toc.append(
+                                f'{index + 1}. <a href="#{anchor}">{describer.verbose_name}</a>'
+                            )
+                            markdown.extend(describer.markdown)
                     markdown.append(f"{self.h4} Requisitions\n")
-                    for panel_name in documents.get("requisitions"):
-                        markdown.append(f"* {panel_name}\n")
+                    markdown.extend(
+                        [f"* {panel_name}\n" for panel_name in documents.get("requisitions")]
+                    )
             markdown = self.insert_toc(toc, markdown)
             markdown.insert(0, f"{self.h1} {self.title}")
             markdown.append(

edc_form_describer/make_forms_reference.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import os
 import sys
 from importlib import import_module
 
@@ -16,11 +15,10 @@ style = color_style()
 
 
 def make_forms_reference(
-    app_label: str = None,
-    admin_site_name: str = None,
-    visit_schedule_name: str = None,
-    title: str = None,
-    path: str | None = None,
+    app_label: str,
+    admin_site_name: str,
+    visit_schedule_name: str,
+    title: str | None = None,
 ):
     module = import_module(app_label)
     admin_site = getattr(module.admin_site, admin_site_name)
@@ -29,9 +27,9 @@ def make_forms_reference(
     sys.stdout.write(
         style.MIGRATE_HEADING(f"Refreshing CRF reference document for {app_label}\n")
     )
-    doc_folder = os.path.join(settings.BASE_DIR, "docs")
-    if not os.path.exists(doc_folder):
-        os.mkdir(doc_folder)
+    doc_folder = settings.BASE_DIR / "docs"
+    if not doc_folder.exists():
+        doc_folder.mkdir()
 
     forms = FormsReference(
         visit_schedules=[visit_schedule],
@@ -40,8 +38,8 @@ def make_forms_reference(
         add_per_form_timestamp=False,
     )
 
-    path = os.path.join(doc_folder, "forms_reference.md")
+    path = doc_folder / f"forms_reference_{app_label}.md"
     forms.to_file(path=path, overwrite=True)
 
-    print(path)
-    print("Done.")
+    sys.stdout.write(f"{path}\n")
+    sys.stdout.write("Done.\n")

edc_form_describer/management/commands/make_forms_reference.py

@@ -17,16 +17,16 @@ style = color_style()
 
 
 def update_forms_reference(
-    app_label: str = None,
-    admin_site_name: str = None,
-    visit_schedule_name: str = None,
-    title: str = None,
+    app_label: str,
+    admin_site_name: str,
+    visit_schedule_name: str,
+    title: str | None = None,
     filename: str | None = None,
     doc_folder: str | None = None,
 ):
     module = import_module(app_label)
     default_doc_folder = Path(settings.BASE_DIR / "docs")
-    filename = filename or "forms_reference.md"
+    filename = filename or f"forms_reference_{app_label}.md"
     admin_site = getattr(module.admin_site, admin_site_name)
     visit_schedule = site_visit_schedules.get_visit_schedule(visit_schedule_name)
     title = title or _("%(title_app)s Forms Reference") % dict(title_app=app_label.upper())
@@ -47,8 +47,8 @@ def update_forms_reference(
     path = doc_folder / filename
     forms.to_file(path=path, overwrite=True)
 
-    print(path)
-    print("Done.")
+    sys.stdout.write(f"{path}\n")
+    sys.stdout.write("Done\n")
 
 
 class Command(BaseCommand):
@@ -85,7 +85,7 @@ class Command(BaseCommand):
             default=None,
         )
 
-    def handle(self, *args, **options):
+    def handle(self, *args, **options):  # noqa: ARG002
         app_label = options["app_label"]
         admin_site_name = options["admin_site_name"]
         visit_schedule_name = options["visit_schedule_name"]

edc_form_describer/markdown_writer.py

@@ -1,7 +1,8 @@
 from __future__ import annotations
 
-import os
-from datetime import datetime
+from pathlib import Path
+
+from django.utils import timezone
 
 
 class MarkdownWriter:
@@ -11,23 +12,23 @@ class MarkdownWriter:
     @staticmethod
     def get_path(path: str | None = None, overwrite: bool | None = None) -> str:
         if not path:
-            timestamp = datetime.today().strftime("%Y%m%d%H%M")
+            timestamp = timezone.now().strftime("%Y%m%d%H%M")
             path = f"forms_{timestamp}.md"
-        if os.path.exists(path):
+        if Path(path).exists():
             if overwrite:
-                os.remove(path)
+                Path(path).unlink()
             else:
                 raise FileExistsError(f"File exists. Got '{path}'")
         return path
 
     @staticmethod
-    def to_markdown(markdown: list[str] = None) -> str:
+    def to_markdown(markdown: list[str]) -> str:
         """Returns the markdown as a text string."""
         return "\n".join(markdown)
 
     def to_file(
         self,
-        markdown: list[str] = None,
+        markdown: list[str],
         pad: int | None = None,
         append: bool | None = None,
         prepend: bool | None = None,
@@ -42,9 +43,9 @@ class MarkdownWriter:
         else:
             self._write(markdown)
 
-    def _write(self, markdown: str = None, mode: str | None = None) -> None:
+    def _write(self, markdown: str, mode: str | None = None) -> None:
         mode = mode or "w"
-        with open(self.path, mode) as f:
+        with Path(self.path).open(mode) as f:
             f.write(markdown)
 
     def _append(self, markdown) -> None:
@@ -53,7 +54,7 @@ class MarkdownWriter:
 
     def _prepend(self, markdown=None) -> None:
         mode = "r+"
-        with open(self.path, mode) as f:
+        with Path(self.path).open(mode) as f:
             content = f.read()
             f.seek(0, 0)
             f.write(markdown + "\n" + content)

edc_visit_schedule/schedule/schedule.py

@@ -45,7 +45,7 @@ class ScheduleNameError(Exception):
     pass
 
 
-class AlreadyRegisteredVisit(Exception):
+class AlreadyRegisteredVisit(Exception):  # noqa: N818
     pass
 
 
@@ -69,15 +69,15 @@ class Schedule:
 
     def __init__(
         self,
-        name=None,
-        verbose_name: str = None,
-        onschedule_model: str = None,
-        offschedule_model: str = None,
-        loss_to_followup_model: str = None,
-        appointment_model: str | None = None,
-        history_model: str | None = None,
+        name: str,
+        onschedule_model: str,
+        offschedule_model: str,
         consent_definitions: list[ConsentDefinition] | ConsentDefinition = None,
+        loss_to_followup_model: str | None = None,
+        appointment_model: str | None = None,
         offstudymedication_model: str | None = None,
+        history_model: str | None = None,
+        verbose_name: str | None = None,
         sequence: str | None = None,
         base_timepoint: float | Decimal | None = None,
     ):
@@ -146,10 +146,10 @@ class Schedule:
 
     def visits_for_subject(
         self,
-        subject_identifier: str = None,
-        report_datetime: datetime = None,
-        site_id: int = None,
-        consent_definition: ConsentDefinition = None,
+        subject_identifier: str,
+        report_datetime: datetime,
+        site_id: int | None = None,
+        consent_definition: ConsentDefinition | None = None,
     ) -> VisitCollection:
         """Returns a deep copy of visits collection filtered for a
         given consented subject.
@@ -352,7 +352,7 @@ class Schedule:
 
     def get_consent_definition(
         self,
-        report_datetime: datetime = None,
+        report_datetime: datetime,
         site: SingleSite = None,
         consent_definition: ConsentDefinition = None,
     ) -> ConsentDefinition: