i should break these commits up

atlas/models.py

@@ -311,20 +311,32 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
     # findings = models.TextField(null=True, blank=True)
 
     # subspecialty = models.CharField(max_length=2, choices=SubspecialtyChoices.choices)
-    subspecialty = models.ManyToManyField(Subspecialty, blank=True)
+    subspecialty = models.ManyToManyField(
+        Subspecialty,
+        blank=True,
+        help_text="The subspecialties the case is associated with. Multiple subspecialties can be selected.",
+    )
 
-    condition = models.ManyToManyField(Condition, blank=True)
+    condition = models.ManyToManyField(
+        Condition, blank=True, help_text="The condition(s) the case demonstrates."
+    )
 
-    presentation = models.ManyToManyField(Presentation, blank=True)
+    presentation = models.ManyToManyField(
+        Presentation,
+        blank=True,
+        help_text="The presentation(s) the case is associated with.",
+    )
 
     pathological_process = models.ManyToManyField(PathologicalProcess, blank=True)
 
     differential = models.ManyToManyField(
-        Condition, through=Differential, related_name="casedifferential"
+        Condition, through=Differential, related_name="casedifferential",
+        help_text="The differential diagnosis for the case.",
     )
 
     diagnostic_certainty = models.IntegerField(
-        choices=CertaintyChoices.choices, default=CertaintyChoices.NONE
+        choices=CertaintyChoices.choices, default=CertaintyChoices.NONE,
+        help_text="The diagnostic certainty of the case.",
     )
 
     verified = models.BooleanField(default=False)
@@ -352,7 +364,9 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
         help_text="If a case should be freely available to browse", default=True
     )
 
-    series = models.ManyToManyField("Series", through="SeriesDetail", related_name="case")
+    series = models.ManyToManyField(
+        "Series", through="SeriesDetail", related_name="case"
+    )
 
     notes = GenericRelation(QuestionNote)
 
@@ -362,6 +376,7 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
         null=True,
         related_name="next_case",
         blank=True,
+        help_text="If this case is related to another case on the system (e.g. follow up), link them here.",
     )
 
     resource = models.ManyToManyField("Resource", through="CaseResource")
@@ -378,12 +393,15 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
         # return f"{self.pk}: {self.title}"
         return format_html("<a href='{}'>{}</a>", self.get_absolute_url(), str(self))
 
-    #def get_base_template(self):
+    # def get_base_template(self):
 
-    #def get_edit_template_links(self):
+    # def get_edit_template_links(self):
 
     def __str__(self):
-        return f"{self.pk}: {self.title}"
+        if self.open_access:
+            return f"{self.pk}: {self.title} [OA]"
+        else:
+            return f"{self.pk}: {self.title}"
 
     def get_series_blocks(self):
         html = ""
@@ -396,7 +414,7 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
         examinations = [series.get_examination() for series in self.series.all()]
         return f"{self.pk}:{self.title} {'/'.join([str(c) for c in self.condition.all()])} [{', '.join(examinations)}]"
 
-    def get_case_dicom_json(self, case_title_as_patient_name = True):
+    def get_case_dicom_json(self, case_title_as_patient_name=True):
         series_json = []
         for series in self.series.all():
             series_json.append(series.get_series_dicom_json())
@@ -435,7 +453,6 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
         return json.dumps(self.get_viva_details())
 
 
-
 def extract_image_dicom_json_from_ds(ds, url, image_index):
     to_keep = [
         "Columns",
@@ -597,7 +614,7 @@ class Series(SeriesBase):
             "<a href='{}'>{}</a>", self.get_absolute_url(), self.get_full_str()
         )
 
-    #@lru_cache(maxsize=128)
+    # @lru_cache(maxsize=128)
     def get_series_dicom_json(self):
         instances = []
 
@@ -662,12 +679,13 @@ class Series(SeriesBase):
         image = self.images.first()
 
         with pydicom.dcmread(image.image) as ds:
-            date =  ds.get("StudyDate", "No date")
+            date = ds.get("StudyDate", "No date")
 
         self.description = f"{date[:4]}-{date[4:6]}-{date[6:]}"
 
         self.save()
 
+
 class CaseCollection(ExamOrCollectionGenericBase):
     app_name = "atlas"
 
@@ -806,9 +824,13 @@ class CaseCollection(ExamOrCollectionGenericBase):
             self.VIEWER_MODE_CHOICES.BUILT_IN_WITH_OHIF,
         )
 
-    def show_ohif_viewer_link(self) -> bool:
+    def show_ohif_viewer(self) -> bool:
         return self.viewer_mode in (
             self.VIEWER_MODE_CHOICES.OHIF,
+        )
+
+    def show_ohif_viewer_link(self) -> bool:
+        return self.viewer_mode in (
             self.VIEWER_MODE_CHOICES.BUILT_IN_WITH_OHIF,
         )
 
@@ -843,9 +865,7 @@ class CaseCollection(ExamOrCollectionGenericBase):
     ) -> Case | Tuple[Case, int]:
         # Seems to be a bug when case_number is 0 or 1 the same (first) object gets returned
         # forces a list fixes (but is likely inefficient)
-        cases = list(
-            self.get_cases().prefetch_related()
-        )
+        cases = list(self.get_cases().prefetch_related())
 
         try:
             case = cases[case_index]
@@ -859,16 +879,14 @@ class CaseCollection(ExamOrCollectionGenericBase):
             return case
 
     def get_case_take_url(self, case):
-        cases = list(
-            self.get_cases().prefetch_related()
-        )
+        cases = list(self.get_cases().prefetch_related())
 
         return reverse(
             "atlas:collection_case_view_take_user",
             kwargs={"pk": self.pk, "case_number": cases.index(case)},
         )
 
-    def get_ohif_dicom_json(self, case_title_as_patient_name = True):
+    def get_ohif_dicom_json(self, case_title_as_patient_name=True):
         studies = []
         for n, case in enumerate(self.cases.all()):
             series_json = []
@@ -880,7 +898,6 @@ class CaseCollection(ExamOrCollectionGenericBase):
                 patient_name = case.title
 
             studies.append(
-
                 {
                     "StudyInstanceUID": f"1.3.6.1.4.1.14519.5.2.1.6279.6001.{n}",
                     "StudyDate": "20000101",
@@ -894,21 +911,16 @@ class CaseCollection(ExamOrCollectionGenericBase):
                 }
             )
 
-            
-
-        return {
-            "studies": studies
-        }
+        return {"studies": studies}
 
     def add_case(self, case):
         """Adds a case to the collection and makes sure order is maintained"""
         # We might be better off adding via the case detail model direct
-        #CaseDetail.objects.create(case=case, collection=self)
+        # CaseDetail.objects.create(case=case, collection=self)
         self.cases.add(case)
         self.order_cases()
 
-
-    def order_cases(self): 
+    def order_cases(self):
         """Modifies the casedetail sort_order to sequentially order the cases"""
         for n, c in enumerate(self.casedetail_set.all().order_by("sort_order")):
             c.sort_order = n
@@ -921,11 +933,15 @@ class SeriesDetail(models.Model):
 
     sort_order = models.IntegerField(default=1000)
 
-    feedback = models.BooleanField(default=False, help_text="Set to true if the series should only be shown for feedback purposes.")
+    feedback = models.BooleanField(
+        default=False,
+        help_text="Set to true if the series should only be shown for feedback purposes.",
+    )
 
     class Meta:
         ordering = ("sort_order",)
 
+
 class CaseDetail(models.Model):
     case = models.ForeignKey(Case, on_delete=models.CASCADE)
     collection = models.ForeignKey(CaseCollection, on_delete=models.CASCADE)
@@ -950,6 +966,8 @@ class BaseReportAnswer(models.Model):
         blank=True, null=True, validators=[MaxValueValidator(10), MinValueValidator(0)]
     )
 
+    completed = models.BooleanField(default=False)
+
     def save(self, *args, **kwargs):
         self.clean()
         return super(BaseReportAnswer, self).save(*args, **kwargs)
@@ -1145,6 +1163,7 @@ class UncategorisedDicom(models.Model):
 class DuplicateDicom(Exception):
     pass
 
+
 class Resource(models.Model, AuthorMixin):
     name = models.CharField(max_length=255)
     description = models.TextField(blank=True, null=True)
@@ -1166,11 +1185,26 @@ class Resource(models.Model, AuthorMixin):
     def get_link(self):
         return format_html("<a href='{}'>{}</a>", self.get_absolute_url(), self.name)
 
+    def get_display(self) -> str:
+        if self.url:
+            html =  f"<a target='_blank' href='{self.url}'>{self.name}</a>"
+        elif self.file:
+            html =  f"<a target='_blank' href='{self.file.url}'>{self.name}</a>"
+        else:
+            html =  self.name
+
+        return format_html(html)
+
+
+
 class CaseResource(models.Model):
     resource = models.ForeignKey(Resource, on_delete=models.CASCADE)
     case = models.ForeignKey(Case, on_delete=models.CASCADE)
 
-    pre_review = models.BooleanField(default=False)
+    pre_review = models.BooleanField(
+        default=False,
+        help_text="Defines if the resource should be shown pre review (i.e. for pre reading before the case is taken)",
+    )
 
     def __str__(self) -> str:
-        return f"{self.resource} - {self.case}"
+        return f"{self.resource} - {self.case} (Pre: {self.pre_review})"