add list methods to formscollection, pep8, build

.github/workflows/build.yml

@@ -13,24 +13,12 @@ jobs:
         python-version: ['3.9']
         django-version: ['3.2']
 
-    services:
-
-      mysql:
-        image: mysql:latest
-        env:
-          MYSQL_DATABASE: mysql
-          MYSQL_ROOT_PASSWORD: mysql
-        ports:
-          - 3306:3306
-        options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
-
     steps:
     - name: Install pycups and words dependency
       run: |
         sudo apt-get install libcups2-dev wamerican
 
     - uses: actions/checkout@v2
-
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:
@@ -62,7 +50,7 @@ jobs:
       env:
         DJANGO: ${{ matrix.django-version }}
 
-    - name: Upload coverage
-      uses: codecov/codecov-action@v1
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v2
       with:
         name: Python ${{ matrix.python-version }}

.gitignore

@@ -1,3 +1,4 @@
+_version.py
 django_crypto_fields
 .env
 

MANIFEST.in

@@ -3,4 +3,3 @@ include MANIFEST.in
 include *.rst
 include *.txt
 recursive-include edc_visit_schedule/templates *
-recursive-include edc_visit_schedule/static *

edc_visit_schedule/admin/subject_schedule_history_admin.py

@@ -95,7 +95,10 @@ def dashboard(self, obj=None, label=None):
 
     def review(self, obj=None):
         try:
-            url = f"{reverse('edc_review_dashboard:subject_review_listboard_url')}?q={obj.subject_identifier}"
+            url = (
+                f"{reverse('edc_review_dashboard:subject_review_listboard_url')}?"
+                f"q={obj.subject_identifier}"
+            )
         except NoReverseMatch:
             context = {}
         else:

edc_visit_schedule/forms.py

@@ -5,11 +5,9 @@
 
 class SubjectScheduleHistoryForm(forms.ModelForm):
     def clean(self):
-        cleaned_data = super().clean()
         raise forms.ValidationError(
             "This is not a user form. This form may only be edited by the system."
         )
-        return cleaned_data
 
     class Meta:
         model = SubjectScheduleHistory

edc_visit_schedule/ordered_collection.py

@@ -41,7 +41,7 @@ def _iter_keys(self, key=None, reverse=None):
             seq = reversed(self.keys())
         else:
             seq = iter(self.keys())
-        keys = itertools.dropwhile(lambda k: k != key, seq)
+        keys = itertools.dropwhile(lambda x: x != key, seq)
         try:
             k = next(keys)
         except StopIteration:

edc_visit_schedule/schedule/window.py

@@ -78,7 +78,7 @@ def raise_for_scheduled_not_in_window(self):
 
     def raise_for_unscheduled_not_in_window(self):
         """Returns the datetime if it falls within the
-        window period for a unscheduled `visit` otherwise
+        window period for an unscheduled `visit` otherwise
         raises an exception.
 
         Window period for an unscheduled date is anytime

edc_visit_schedule/tests/tests/test_forms_collection.py

@@ -1,4 +1,4 @@
-from django.test import TestCase, tag
+from django.test import TestCase
 from django.test.utils import override_settings
 
 from edc_visit_schedule.visit import Crf, FormsCollection, FormsCollectionError
@@ -59,3 +59,20 @@ def test_forms_collection_excludes_by_site_id3(self):
             crfs.append(Crf(show_order=i, model=f"x.{i}"))
         forms = FormsCollection(*crfs)
         self.assertEqual(len(forms.forms), 10)
+
+    @override_settings(SITE_ID=40)
+    def test_forms_collection_list_like_behaviour(self):
+        forms = FormsCollection()
+        for i in range(0, 5):
+            forms.append(Crf(show_order=i, model=f"x.{i}"))
+        for i in range(6, 11):
+            forms.append(Crf(show_order=i, model=f"x.{i}"))
+        self.assertEqual(len(forms), 10)
+        forms.remove(Crf(show_order=1, model="x.1"))
+        self.assertEqual(len(forms), 9)
+        max_show_order = max([item.show_order for item in forms])
+        forms.insert_last(Crf(show_order=1, model="x.1"))
+        self.assertGreater(max([item.show_order for item in forms]), max_show_order)
+        self.assertRaises(
+            FormsCollectionError, forms.insert_last, Crf(show_order=1, model="x.1")
+        )

edc_visit_schedule/tests/tests/test_schedules_collection.py

@@ -1,4 +1,4 @@
-from django.test import TestCase, tag
+from django.test import TestCase
 
 from edc_visit_schedule.visit_schedule import (
     SchedulesCollection,

edc_visit_schedule/tests/tests/test_site_visit_schedule.py

@@ -1,4 +1,4 @@
-from django.test import TestCase, tag
+from django.test import TestCase
 
 from edc_visit_schedule.schedule import Schedule
 from edc_visit_schedule.site_visit_schedules import (

edc_visit_schedule/tests/tests/test_subject_schedule.py

@@ -1,5 +1,5 @@
 from django.core.exceptions import ObjectDoesNotExist
-from django.test import TestCase, tag
+from django.test import TestCase
 from edc_consent import site_consents
 from edc_consent.consent import Consent
 from edc_constants.constants import FEMALE, MALE

edc_visit_schedule/tests/tests/test_system_checks.py

@@ -1,6 +1,6 @@
 from dateutil.relativedelta import relativedelta
 from django.apps import apps as django_apps
-from django.test import TestCase, tag
+from django.test import TestCase
 
 from edc_visit_schedule.schedule import Schedule
 from edc_visit_schedule.site_visit_schedules import site_visit_schedules

edc_visit_schedule/tests/tests/test_utils.py

@@ -1,7 +1,7 @@
 from datetime import date
 
 from dateutil.relativedelta import relativedelta
-from django.test import TestCase, override_settings, tag
+from django.test import TestCase, override_settings
 from edc_appointment.models import Appointment
 from edc_consent import site_consents
 from edc_consent.consent import Consent

edc_visit_schedule/tests/tests/test_visit.py

@@ -126,7 +126,7 @@ def test_good_codes(self):
                 rupper=relativedelta(days=6),
                 timepoint=1,
             )
-        except (VisitCodeError) as e:
+        except VisitCodeError as e:
             self.fail(f"VisitError unexpectedly raised. Got {e}")
         try:
             Visit(

edc_visit_schedule/tests/tests/test_visit_schedule.py

@@ -2,7 +2,7 @@
 
 from dateutil.relativedelta import relativedelta
 from dateutil.tz import tzutc
-from django.test import TestCase, override_settings, tag
+from django.test import TestCase, override_settings
 from edc_appointment.models import Appointment
 from edc_consent import site_consents
 from edc_consent.consent import Consent

edc_visit_schedule/views/home_view.py

@@ -3,27 +3,9 @@
 from edc_dashboard.view_mixins import EdcViewMixin
 from edc_navbar.view_mixin import NavbarViewMixin
 
-from ..site_visit_schedules import SiteVisitScheduleError, site_visit_schedules
-
 
 class HomeView(EdcViewMixin, NavbarViewMixin, TemplateView):
 
     template_name = f"edc_visit_schedule/bootstrap{settings.EDC_BOOTSTRAP}/home.html"
     navbar_name = "edc_visit_schedule"
     navbar_selected_item = "visit_schedule"
-
-    # def get_context_data(self, **kwargs):
-    #     context_data = super().get_context_data(**kwargs)
-    #     try:
-    #         selected_visit_schedule = site_visit_schedules.get_visit_schedule(
-    #             visit_schedule_name=self.kwargs.get("visit_schedule")
-    #         )
-    #     except SiteVisitScheduleError:
-    #         selected_visit_schedule = None
-    #     context_data.update(
-    #         {
-    #             "visit_schedules": site_visit_schedules.registry,
-    #             "selected_visit_schedule": selected_visit_schedule,
-    #         }
-    #     )
-    #     return context_data

edc_visit_schedule/visit/crf.py

@@ -32,6 +32,10 @@ def __str__(self):
         required = "Required" if self.required else ""
         return f"{self.model} {required}"
 
+    @property
+    def name(self) -> str:
+        return f"{self.model}.{'required' if self.required else 'not_required'}"
+
     def validate(self):
         """Raises an exception if the model class lookup fails."""
         try:

edc_visit_schedule/visit/forms_collection.py

@@ -1,14 +1,20 @@
+from typing import Optional, Tuple, Union
+from uuid import uuid4
+
 from django.conf import settings
 
+from .crf import Crf
+from .requisition import Requisition
+
 
 class FormsCollectionError(Exception):
     pass
 
 
 class FormsCollection:
-    def __init__(self, *forms, name=None, **kwargs):
-        self._forms = None
-        self.name = name
+    def __init__(self, *forms: Union[Crf, Requisition], name: Optional[str] = None, **kwargs):
+        self._forms: Optional[Tuple[Union[Crf, Requisition]]] = None
+        self.name = name or uuid4().hex
         forms = [] if not forms or forms == (None,) else list(forms)
 
         # exclude any flagged for a site that is not the current
@@ -37,6 +43,62 @@ def __repr__(self):
     def __iter__(self):
         return iter(self._forms)
 
+    def __len__(self):
+        return len(self._forms)
+
+    def append(self, value):
+        if value:
+            forms = list(self._forms)
+            for item in forms:
+                if item.name == value.name:
+                    raise FormsCollectionError(
+                        f"Append failed. Item is not unique. Got {value.name}"
+                    )
+            forms.append(value)
+            forms.sort(key=lambda x: x.show_order)
+            self._forms = forms
+
+    def extend(self, value: Union[tuple, list]):
+        if value:
+            for v in value:
+                self.append(v)
+            forms = list(self._forms)
+            forms.sort(key=lambda x: x.show_order)
+            self._forms = tuple(forms)
+
+    def insert(self, index, value):
+        if value:
+            forms = list(self._forms)
+            for index, item in forms:
+                if item.name == value.name:
+                    raise FormsCollectionError(
+                        f"Insert failed. Item is not unique. Got {value.name}"
+                    )
+            forms.insert(index, value)
+            forms.sort(key=lambda x: x.show_order)
+            self._forms = tuple(forms)
+
+    def remove(self, value):
+        if value:
+            forms = list(self._forms)
+            for index, item in enumerate(forms):
+                if item.name == value.name:
+                    forms.pop(index)
+                    self._forms = tuple(forms)
+                    break
+            else:
+                raise FormsCollectionError("Remove failed. Item not found")
+
+    def pop(self, index):
+        forms = list(self._forms)
+        forms.pop(index)
+        self._forms = tuple(forms)
+
+    def insert_last(self, value):
+        forms = list(self._forms)
+        value.show_order = 100 + max([item.show_order for item in forms or []])
+        self.append(value)
+
     @property
     def forms(self):
         return self._forms

edc_visit_schedule/visit/visit.py

@@ -1,10 +1,13 @@
 import re
 from decimal import Decimal
+from typing import Optional
 
 import arrow
+from dateutil.relativedelta import relativedelta
 from django.apps import apps as django_apps
 from django.conf import settings
 
+from .forms_collection import FormsCollection
 from .window_period import WindowPeriod
 
 
@@ -49,34 +52,41 @@ class Visit:
 
     def __init__(
         self,
-        code=None,
-        timepoint=None,
-        rbase=None,
-        rlower=None,
-        rupper=None,
-        crfs=None,
-        requisitions=None,
-        crfs_unscheduled=None,
-        crfs_missed=None,
-        requisitions_unscheduled=None,
-        crfs_prn=None,
-        requisitions_prn=None,
-        title=None,
+        code: Optional[str] = None,
+        timepoint: Optional[int] = None,
+        rbase: Optional[relativedelta] = None,
+        rlower: Optional[relativedelta] = None,
+        rupper: Optional[relativedelta] = None,
+        crfs: Optional[FormsCollection] = None,
+        requisitions: Optional[FormsCollection] = None,
+        crfs_unscheduled: Optional[FormsCollection] = None,
+        crfs_missed: Optional[FormsCollection] = None,
+        requisitions_unscheduled: Optional[FormsCollection] = None,
+        crfs_prn: Optional[FormsCollection] = None,
+        requisitions_prn: Optional[FormsCollection] = None,
+        title: Optional[str] = None,
+        allow_unscheduled: Optional[bool] = None,
+        facility_name: Optional[str] = None,
         instructions=None,
         grouping=None,
-        allow_unscheduled=None,
-        facility_name=None,
     ):
 
-        self.crfs = crfs.forms if crfs else ()
+        self.crfs = crfs.forms if crfs else tuple()
         self.crfs_unscheduled = crfs_unscheduled.forms if crfs_unscheduled else ()
         self.crfs_missed = crfs_missed.forms if crfs_missed else ()
         self.crfs_prn = crfs_prn.forms if crfs_prn else ()
+        for prn in self.crfs_prn:
+            prn.required = False
+
         self.requisitions = requisitions.forms if requisitions else ()
         self.requisitions_unscheduled = (
             requisitions_unscheduled.forms if requisitions_unscheduled else ()
         )
         self.requisitions_prn = requisitions_prn.forms if requisitions_prn else ()
+        for prn in self.requisitions_prn:
+            prn.required = False
+        # self.requisitions = self.requisitions + self.requisitions_prn
+
         self.instructions = instructions
         self.timepoint = Decimal(str(timepoint))
         self.rbase = rbase
@@ -186,6 +196,7 @@ def timepoint_datetime(self, dt=None):
 
     def check(self):
         warnings = []
+        crf = None
         try:
             for crf in self.crfs:
                 django_apps.get_model(crf.model)

edc_visit_schedule/visit_schedule/visit_schedule.py

@@ -111,10 +111,14 @@ def check(self):
 
     @property
     def all_post_consent_models(self):
-        """Returns a dictionary of models and the needed consent model.
+        """Returns a dictionary of models and the needed consent
+        model.
+
         These models may only be complete after the consent model.
 
-        {model_name1: consent_model_name, model_name2: consent_model_name, ...}
+        {model_name1:
+            consent_model_name, model_name2:
+                consent_model_name, ...}
         """
         if not self._all_post_consent_models:
             models = {}
@@ -131,7 +135,7 @@ def all_post_consent_models(self):
                         models.update({crf.model: schedule.consent_model})
             if None in (list(models.keys())):
                 raise VisitScheduleError(
-                    f"One or more required models has not been defined. "
+                    "One or more required models has not been defined. "
                     f"Check the declaration for visit schedule '{self}'. "
                     f"Got {models}."
                 )