penracourses/anatomy/models.py

from django.contrib.contenttypes.fields import GenericRelation
from django.db import models
from django.utils import timezone

from django.core.files.storage import FileSystemStorage
from django.conf import settings
from django.utils.html import format_html

from django.urls import reverse

from django.utils.translation import ugettext_lazy as _

from sortedm2m.fields import SortedManyToManyField

import string

from generic.models import Examination, ExamBase, QuestionNote

from collections import defaultdict
from helpers.images import image_as_base64

import reversion

image_storage = FileSystemStorage(
    # Physical file location ROOT
    location=u"{0}/".format(settings.MEDIA_ROOT),
    # Url for file
    base_url=u"{0}/".format(settings.MEDIA_URL),
)


def image_directory_path(instance, filename):
    # file will be uploaded to MEDIA_ROOT/anatomy/picture/<filename>
    return u"picture/anatomy/{0}".format(filename)


class BodyPart(models.Model):
    bodypart = models.CharField(max_length=200)

    def __str__(self):
        return self.bodypart


class Structure(models.Model):
    structure = models.CharField(max_length=200)

    def __str__(self):
        return self.structure


class Region(models.Model):
    region = models.CharField(max_length=200)

    def __str__(self):
        return self.region


class Modality(models.Model):
    modality = models.CharField(max_length=200)

    def __str__(self):
        return self.modality


class QuestionType(models.Model):
    text = models.CharField(max_length=400)

    def __str__(self):
        return self.text


@reversion.register
class AnatomyQuestion(models.Model):
    # author = models.ForeignKey('auth.User', on_delete=models.CASCADE)
    # image = models.ImageField()
    # feedback = models.TextField(null=True)
    question_type = models.ForeignKey(
        QuestionType, on_delete=models.SET_NULL, null=True, default=1
    )

    image = models.ImageField(upload_to=image_directory_path)

    image_annotations = models.TextField(
        blank=True,
        help_text="Stores a JSON representation of annotations to be applied by cornerstonetools",
    )

    description = models.CharField(
        max_length=400,
        help_text="Short description of the image e.g. 'Sagittal CT Chest, Abdomen & Pelvis', will be displayed as the title.",
    )

    examination = models.ForeignKey(
        Examination, on_delete=models.SET_NULL, null=True, blank=True
    )
    modality = models.ForeignKey(
        Modality,
        on_delete=models.SET_NULL,
        null=True,
        help_text="Modality of the image",
    )
    region = models.ForeignKey(
        Region,
        on_delete=models.SET_NULL,
        null=True,
        blank=True,
        help_text="Region the image covers",
    )
    body_part = models.ForeignKey(
        BodyPart, on_delete=models.SET_NULL, null=True, blank=True
    )
    structure = models.ForeignKey(
        Structure, on_delete=models.SET_NULL, null=True, blank=True
    )
    created_date = models.DateTimeField(default=timezone.now)

    open_access = models.BooleanField(
        help_text="If a question should be freely available to browse", default=True
    )

    author = models.ManyToManyField(
        settings.AUTH_USER_MODEL,
        blank=True,
        help_text="Author(s) of question",
        related_name="anatomy_authored_questions",
    )

    notes = GenericRelation(QuestionNote)

    class Meta:
        permissions = ()

    def __str__(self):
        # Get first answer
        return "{}/{}: {} [{}, {}]".format(
            self.pk, self.question_type, self.get_primary_answer(), self.modality, self.structure
        )
        # Get associated exams
        e = self.exams.all().values_list("name", flat=True)
        exams = ", ".join(e)

        if a is None:
            return "({})".format(exams)
        else:
            return "{} ({}) [{}, {}]".format(
                a.answer, exams, self.modality, self.structure
            )

    def get_absolute_url(self):
        return reverse("anatomy:question_detail", kwargs={"pk": self.pk})

    def get_primary_answer(self):
        if len(self.answers.filter(proposed=False)) > 0:
            return self.answers.filter(proposed=False).first().answer
        else:
            return "None yet..."

    def get_exams(self):
        e = self.exams.all().values_list("name", flat=True)
        exams = ", ".join(e)
        return exams

    def get_unmarked_answer_string(self, exam_pk=None):
        unmarked_answers = self.get_unmarked_answers(exam_pk)

        if not unmarked_answers:
            return "No answers to mark"
        return format_html(
            "<span class='warn'>{} answer unmarked:</span> {}".format(
                len(unmarked_answers), ", ".join(unmarked_answers)
            )
        )

    def get_unmarked_answers(self, exam_pk=None):
        if exam_pk is None:
            user_answers = set([i.answer_compare for i in self.cid_user_answers.all()])
        else:
            user_answers = set(
                [
                    i.answer_compare
                    for i in self.cid_user_answers.filter(exam__id=exam_pk)
                ]
            )

        unmarked_answers = user_answers - self.get_marked_answers()

        return unmarked_answers

    def get_unmarked_answer_count(self, exam_pk=None):
        return len(self.get_unmarked_answers(exam_pk))

    def get_marked_answers(self):
        return set(
            [
                i.answer_compare
                for i in self.answers.filter(proposed=False)
                if i.status != i.MarkOptions.UNMARKED
            ]
        )
        # correct_answers = set(
        #    [i.answer.get_compare_string() for i in self.answers.all()]
        # )
        # half_mark_answers = set(
        #    [i.answer.get_compare_string() for i in self.half_mark_answers.all()]
        # )
        # incorrect_answers = set(
        #    [i.answer.get_compare_string() for i in self.incorrect_answers.all()]
        # )

        # marked_answers = correct_answers | half_mark_answers | incorrect_answers
        # return marked_answers

    def get_annotations(self):
        return self.image_annotations

    def get_title(self):
        return "{}".format(self.description)

    def get_correct_unstripped_answers(self):
        return set(
            [
                str(i)
                for i in self.answers.filter(proposed=False)
                if i.status == i.MarkOptions.CORRECT
            ]
        )

    def get_question_json(self, based=True):
        """Returns a json representation of the question"""

        # Loop through rapidimage associations
        images = []
        annotations = []
        feedback_images = []

        if based:
            images.append(image_as_base64(self.image))
        else:
            images.append("{}/{}".format(settings.REMOTE_URL, self.image.url))

        if self.image_annotations:
            annotations.append(str(self.image_annotations))



        json = {
            "images": images,
            #"feedback_image": [],
            "annotations": annotations,
            "type": "anatomy",
            "title": self.get_title(),
            "question": str(self.question_type),
        }

        json["answers"] = list(self.get_correct_unstripped_answers())

        return json


@reversion.register
class Answer(models.Model):
    question = models.ForeignKey(
        AnatomyQuestion, related_name="answers", on_delete=models.CASCADE
    )
    answer = models.TextField(max_length=500)
    answer_compare = models.TextField(max_length=500)

    class MarkOptions(models.TextChoices):
        UNMARKED = "", _("Unmarked")
        INCORRECT = "0", _("Incorrect")
        HALF_MARK = "1", _("Half mark")
        CORRECT = "2", _("Correct")

    status = models.CharField(
        max_length=1, choices=MarkOptions.choices, default=MarkOptions.UNMARKED
    )

    proposed = models.BooleanField(default=False)

    def __str__(self):
        return self.answer

    def save(self, *args, **kwargs):
        self.clean()
        return super(Answer, self).save(*args, **kwargs)

    def clean(self):
        if self.answer:
            self.answer = self.answer.strip()

            s = self.answer.lower()
            s = s.translate(str.maketrans("", "", string.punctuation))

            self.answer_compare = s

    # def get_compare_string(self):
    #     s = self.answer.lower().strip()
    #     s = s.translate(str.maketrans('', '', string.punctuation))
    #     return s


# class HalfMarkAnswers(models.Model):
#    question = models.ForeignKey(AnatomyQuestion,
#                                 related_name="half_mark_answers",
#                                 on_delete=models.CASCADE)
#    answer = models.CharField(max_length=500)
#
#    def __str__(self):
#        return self.answer
#
#    def clean(self):
#        if self.answer:
#            self.answer.strip()
#
#
# class IncorrectAnswers(models.Model):
#    question = models.ForeignKey(AnatomyQuestion,
#                                 related_name="incorrect_answers",
#                                 on_delete=models.CASCADE)
#    answer = models.CharField(max_length=500)
#
#    def __str__(self):
#        return self.answer
#
#    def clean(self):
#        if self.answer:
#            self.answer.strip()


@reversion.register
class Exam(ExamBase):
    app_name = "anatomy"

    exam_questions = SortedManyToManyField(
        AnatomyQuestion, related_name="exams", blank="true"
    )
    time_limit = models.IntegerField(
        help_text="Exam time limit (in seconds)", default=5400
    )

    author = models.ManyToManyField(
        settings.AUTH_USER_MODEL,
        blank=True,
        help_text="Author of exam",
        related_name="anatomy_exam_author",
    )

    def get_exam_json(self):
        questions = self.exam_questions.all()

        exam_questions = defaultdict(dict)

        exam_order = []

        for q in questions:
            exam_order.append(q.id)

            exam_questions[q.id] = {
                "title": q.get_title(),
                "question": str(q.question_type),
                "images": [image_as_base64(q.image)],
                "annotations": [str(q.image_annotations)],
                "type": "anatomy",
            }

        exam_json = {
            "eid": "anatomy/{}".format(self.id),
            "cached": False,
            "exam_type": "anatomy",
            "exam_name": self.name,
            "exam_mode": True,
            "exam_order": exam_order,
            "questions": exam_questions,
        }

        if self.time_limit:
            exam_json["exam_time"] = self.time_limit

        return exam_json


@reversion.register
class CidUserAnswer(models.Model):
    """User answers by candidate"""

    question = models.ForeignKey(
        AnatomyQuestion, related_name="cid_user_answers", on_delete=models.CASCADE
    )
    answer = models.TextField(max_length=500, blank=True)

    answer_compare = models.TextField(max_length=500, blank=True)

    cid = models.BigIntegerField(
        blank=True,
        null=True,
        help_text="Candidate ID (limitied by BigIntegerField size)",
    )

    # Each user answer is associated with a particular exam
    exam = models.ForeignKey(
        Exam, related_name="cid_user_answers", on_delete=models.CASCADE, null=True
    )

    created = models.DateTimeField(auto_now_add=True)
    updated = models.DateTimeField(auto_now=True)

    def __str__(self):
        try:
            exam = self.exam
        except (Exam.DoesNotExist, KeyError) as e:
            exam = "None"
        return "{}/{}/{}: {}".format(
            exam, self.cid, self.question.get_primary_answer(), self.answer
        )

    def save(self, *args, **kwargs):
        self.clean()
        return super(CidUserAnswer, self).save(*args, **kwargs)

    def clean(self):
        if self.answer:
            self.answer = self.answer.strip()

            s = self.answer.lower()
            s = s.translate(str.maketrans("", "", string.punctuation))

            self.answer_compare = s

    def get_absolute_url(self):
        return reverse("anatomy:user_answer_view", kwargs={"pk": self.pk})

    # def get_compare_string(self):
    #     # strip here should be unneccasry (providing clean is now working)
    #     s = self.answer.lower().strip()
    #     s = s.translate(str.maketrans('', '', string.punctuation))
    #     return s

    def get_answer_score(self):
        q = self.question
        ans = self.answer_compare
        marked_ans = q.answers.filter(answer_compare__iexact=ans).first()

        mark = "unmarked"
        if marked_ans is not None:
            if marked_ans.status == Answer.MarkOptions.CORRECT:
                mark = 2
            elif marked_ans.status == Answer.MarkOptions.HALF_MARK:
                mark = 1
            elif marked_ans.status == Answer.MarkOptions.INCORRECT:
                mark = 0

        return mark

        if (
            q.answers.filter(
                answer_compare__iexact=ans, status=Answer.MarkOptions.CORRECT
            ).first()
            is not None
        ):
            mark = 2
        elif (
            q.answers.filter(
                answer_compare__iexact=ans, status=Answer.MarkOptions.HALF_MARK
            ).first()
            is not None
        ):
            mark = 1
        elif q.answers.filter(
            answer_compare__iexact=ans, status=Answer.MarkOptions.INCORRECT
        ).first():
            mark = 0
        else:
            mark = "unmarked"
        return mark