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This commit is contained in:
Ross
+10
-181
@@ -10,8 +10,6 @@ from django.utils import timezone
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import pydicom
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import dicognito.anonymizer
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from django.core.files.storage import FileSystemStorage
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from django.conf import settings
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@@ -43,13 +41,11 @@ from generic.models import (
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Plane,
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Contrast,
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QuestionNote,
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SeriesBase,
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)
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# from generic.models import Examination, Site, Condition, Sign
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from easy_thumbnails.files import get_thumbnailer
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from easy_thumbnails.exceptions import InvalidImageFormatError
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import pydicom.errors
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import datetime
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from django.utils import timezone
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@@ -343,7 +339,6 @@ class SeriesImage(models.Model):
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class SeriesFinding(models.Model):
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series = models.ForeignKey(
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"Series", related_name="findings", on_delete=models.SET_NULL, null=True
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)
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@@ -364,7 +359,7 @@ class SeriesFinding(models.Model):
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@reversion.register
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class Series(models.Model):
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class Series(SeriesBase):
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modality = models.ForeignKey(
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Modality,
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related_name="atlas_series_modality",
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@@ -394,10 +389,6 @@ class Series(models.Model):
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null=True,
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blank=True,
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)
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description = models.TextField(
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blank=True,
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help_text="Description of stack",
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)
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author = models.ManyToManyField(
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settings.AUTH_USER_MODEL,
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@@ -407,13 +398,6 @@ class Series(models.Model):
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# findings = models.TextField(null=True, blank=True, help_text="Findings on the series / stack")
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open_access = models.BooleanField(
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help_text="If a series should be freely available to browse", default=True
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)
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def __str__(self):
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return f"{self.pk}:{self.description}"
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def get_full_str(self):
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if self.case:
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case_id = ", ".format([case.pk for case in self.case.all()])
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@@ -424,167 +408,10 @@ class Series(models.Model):
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self.pk, self.get_examination_full(), self.description, case_id
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)
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def get_absolute_url(self):
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return reverse("series:question_detail", kwargs={"pk": self.pk})
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# def get_string(self):
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# examination = self.get_examination_full()
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# return
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def get_author_objects(self):
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"""Returns a comma seperated text list of authors"""
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if self.author:
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return self.author.all()
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else:
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return ["None"]
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def get_author_display(self):
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return ", ".join([i.username for i in self.get_author_objects()])
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def get_examination(self):
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"""Returns a comma seperated text list of regions"""
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return str(self.examination)
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def get_examination_full(self):
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examination = ""
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plane = ""
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contrast = ""
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if self.examination:
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examination = self.examination
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if self.plane:
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plane = " {}".format(self.plane)
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if self.contrast:
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contrast = " {}".format(self.contrast)
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return "{}{}{}".format(examination, plane, contrast)
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def get_absolute_url(self):
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return reverse("atlas:series_detail", kwargs={"pk": self.pk})
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def get_image_urls(self, findings=False):
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images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
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return ",".join(images)
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def get_image_url_array_not_json(self):
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return self.get_image_url_array(json_output=False)
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def get_image_url_array(self, findings=False, json_output=True):
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images = [f"{REMOTE_URL}{i.image.url}" for i in self.images.all()]
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if json_output:
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return json.dumps(images)
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else:
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# This is a mess...
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return format_html('", "'.join(images))
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def get_thumbnail(self):
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images = self.images.all()
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if len(images) < 1:
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return "No images", 0
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img = findMiddle(images).image
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try:
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thumbnailer = get_thumbnailer(img)
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thumbnail = thumbnailer["exam-list"]
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except InvalidImageFormatError:
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return format_html('<span title="{}">Invalid image url<span>', img), len(
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images
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)
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return format_html('<img src="/media/{}" />', thumbnail), len(images)
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def get_thumbnail_link(self):
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return format_html(
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"<a href='{}'>{}<a/>", self.get_absolute_url(), self.get_thumbnail()[0]
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)
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def get_block(self):
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examination = self.get_examination_full()
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thumb, image_number = self.get_thumbnail()
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return format_html(
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"<div>{}<br/>{}<br/>Images: {}</div>", examination, thumb, image_number
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)
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def order_by_upload_filename(self):
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images = self.images.all()
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filenames = []
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map = {}
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for i in images:
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filenames.append(i.upload_filename)
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map[i.upload_filename] = i
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filenames = sorted(filenames)
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n = 1
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for f in filenames:
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i = map[f]
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i.position = n
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i.save()
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n = n + 1
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def order_by_dicom(self, field="SliceLocation"):
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images = self.images.all()
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files = []
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for i in images:
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files.append((i, pydicom.dcmread(i.image.path)))
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# print("file count: {}".format(len(files)))
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# skip files with no SliceLocation (eg scout views)
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slices = []
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map = {}
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skipcount = 0
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for i, f in files:
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if hasattr(f, field):
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slices.append(f)
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# map[f.SliceLocation] = i
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map[f[field].value] = i
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else:
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skipcount = skipcount + 1
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print("skipped, no {}: {}".format(field, skipcount))
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# ensure they are in the correct order
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slices = sorted(slices, key=lambda s: s[field].value)
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# print(slices)
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n = 1
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for f in slices:
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i = map[f[field].value]
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i.position = n
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i.save()
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n = n + 1
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def get_total_image_size(self):
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images = self.images.all()
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size = 0
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for i in images:
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size += i.image.size
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return size
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def anonymise_images(self):
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# NOTE: this will not maintain the correct hashed filename
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# but that doesn't matter as we will never get the same anonymisation
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# even with the same dicom...
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anonymizer = dicognito.anonymizer.Anonymizer()
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for series_image in self.images.all():
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file_path = os.path.join(settings.MEDIA_ROOT, series_image.image.name)
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try:
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with pydicom.dcmread(file_path) as dataset:
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anonymizer.anonymize(dataset)
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dataset.save_as(file_path)
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except pydicom.errors.InvalidDicomError:
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pass
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class CaseCollection(models.Model):
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@@ -647,8 +474,11 @@ class CaseCollection(models.Model):
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CidUser, blank=True, related_name="casecollection_exams"
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)
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cid_user_groups = models.ManyToManyField(CidUserGroup, blank=True, help_text="These groups define which candidates are able to be added to the exams/collection.")
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cid_user_groups = models.ManyToManyField(
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CidUserGroup,
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blank=True,
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help_text="These groups define which candidates are able to be added to the exams/collection.",
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)
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archive = models.BooleanField(default=False)
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exam_mode = models.BooleanField(default=False)
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@@ -693,7 +523,6 @@ class CaseCollection(models.Model):
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return True
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if self.valid_cid_users.exists():
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user = self.valid_cid_users.filter(cid=cid).first()
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if not user or user.passcode != passcode:
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@@ -771,13 +600,13 @@ class BaseReportAnswer(models.Model):
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class Meta:
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abstract = True
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class CidReportAnswer(BaseReportAnswer):
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cid = models.BigIntegerField(
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blank=False,
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help_text="Candidate ID",
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)
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class UserReportAnswer(BaseReportAnswer):
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user = models.ForeignKey(
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settings.AUTH_USER_MODEL, on_delete=models.CASCADE
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)
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user = models.ForeignKey(settings.AUTH_USER_MODEL, on_delete=models.CASCADE)
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