more rapid merging/fixing

anatomy/migrations/0019_auto_20210118_1339.py

@@ -0,0 +1,20 @@
+# Generated by Django 3.1.2 on 2021-01-18 13:39
+
+import anatomy.models
+import django.core.files.storage
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('anatomy', '0018_auto_20210112_1726'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='anatomyquestion',
+            name='image',
+            field=models.ImageField(storage=django.core.files.storage.FileSystemStorage(base_url='/media/anatomy/', location='/home/ross/sites/rad/media//anatomy/'), upload_to=anatomy.models.image_directory_path),
+        ),
+    ]

rad/settings.py

@@ -32,6 +32,7 @@ ALLOWED_HOSTS = ["localhost", "127.0.0.1", "161.35.163.87", "penracourses.org.uk
 INSTALLED_APPS = [
     'anatomy',
     'physics',
+    'rapids',
     "reversion",
     "django_tables2",
     "django_filters",

rapids/admin.py

@@ -1,6 +1,6 @@
 from django.contrib import admin
 from .models import Rapid, RapidImage, Examination, Site, Abnormality, Region, Note, RapidCreationDefault
-import tagulous.admin
+#import tagulous.admin
 
 from django.forms import ModelForm
 
@@ -30,7 +30,7 @@ class RapidAdminForm(ModelForm):
 
         fields = [
             "normal", "abnormality", "region", "laterality", "examination",
-            "condition", "sign", "site", "feedback", "author"
+            "site", "feedback", "author"
         ]
 
         widgets = {

rapids/forms.py

@@ -82,7 +82,7 @@ class RapidForm(ModelForm):
         #fields = '__all__'
         fields = [
             "normal", "abnormality", "region", "laterality", "examination",
-            "condition", "sign", "site", "feedback"
+            "site", "feedback"
         ]
         #fields = ['question', 'feedback', 'subspecialty', 'references']
         widgets = {

rapids/migrations/0001_initial.py

@@ -0,0 +1,122 @@
+# Generated by Django 3.1.2 on 2021-01-18 13:39
+
+from django.conf import settings
+import django.core.files.storage
+from django.db import migrations, models
+import django.db.models.deletion
+import django.utils.timezone
+import rapids.models
+
+
+class Migration(migrations.Migration):
+
+    initial = True
+
+    dependencies = [
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='Abnormality',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(help_text='Primary abnormality on the film(s)', max_length=200, unique=True)),
+            ],
+            options={
+                'ordering': ('name',),
+            },
+        ),
+        migrations.CreateModel(
+            name='Examination',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('examination', models.CharField(max_length=200)),
+            ],
+            options={
+                'ordering': ('examination',),
+            },
+        ),
+        migrations.CreateModel(
+            name='Rapid',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('question', models.TextField(blank=True, null=True)),
+                ('feedback', models.TextField(blank=True, null=True)),
+                ('normal', models.BooleanField(default=False, help_text='Tick if true')),
+                ('laterality', models.CharField(choices=[('NONE', 'None'), ('LEFT', 'Left'), ('RIGHT', 'Right'), ('BILAT', 'Bilateral')], default='NONE', help_text='Applies to the answer, not the examination', max_length=20)),
+                ('verified', models.BooleanField(default=False)),
+                ('created_date', models.DateTimeField(default=django.utils.timezone.now)),
+                ('published_date', models.DateTimeField(blank=True, null=True)),
+                ('scrapped', models.BooleanField(default=False, help_text='Question has been scrapped and will not be shown')),
+                ('abnormality', models.ManyToManyField(blank=True, help_text='The abnormality (laterality and region independent)', to='rapids.Abnormality')),
+                ('author', models.ManyToManyField(blank=True, help_text='Author of question', related_name='rapid_authored_questions', to=settings.AUTH_USER_MODEL)),
+                ('examination', models.ManyToManyField(help_text='Name of the (primary) examination', to='rapids.Examination')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Region',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('name', models.CharField(blank=True, help_text='Region of the abnormality (not including lateralitiy)', max_length=200, unique=True)),
+            ],
+            options={
+                'ordering': ('name',),
+            },
+        ),
+        migrations.CreateModel(
+            name='Site',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('site', models.CharField(max_length=200)),
+                ('initials', models.CharField(max_length=200)),
+            ],
+        ),
+        migrations.CreateModel(
+            name='RapidImage',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('image', models.ImageField(storage=django.core.files.storage.FileSystemStorage(base_url='/media/rapids/', location='/home/ross/sites/rad/media//rapids/'), upload_to=rapids.models.image_directory_path)),
+                ('feedback_image', models.BooleanField(default=False)),
+                ('rapid', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='images', to='rapids.rapid')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='RapidCreationDefault',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('author', models.OneToOneField(on_delete=django.db.models.deletion.CASCADE, related_name='rapid_default', to=settings.AUTH_USER_MODEL)),
+                ('site', models.ManyToManyField(blank=True, default=1, help_text='Default site to use when creating a new rapid', to='rapids.Site')),
+            ],
+        ),
+        migrations.AddField(
+            model_name='rapid',
+            name='region',
+            field=models.ManyToManyField(blank=True, help_text='Region of the abnormality (laterality independent)', to='rapids.Region'),
+        ),
+        migrations.AddField(
+            model_name='rapid',
+            name='site',
+            field=models.ManyToManyField(blank=True, default=1, help_text='If we know the source of the image (should possibly be removed?)', to='rapids.Site'),
+        ),
+        migrations.CreateModel(
+            name='Note',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('note', models.TextField()),
+                ('created_on', models.DateTimeField(auto_now_add=True)),
+                ('author', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='rapid_notes', to=settings.AUTH_USER_MODEL)),
+                ('rapid', models.ForeignKey(null=True, on_delete=django.db.models.deletion.CASCADE, related_name='rapid_notes', to='rapids.rapid')),
+            ],
+        ),
+        migrations.CreateModel(
+            name='Answer',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('answer', models.TextField(max_length=500)),
+                ('answer_compare', models.TextField(max_length=500)),
+                ('status', models.CharField(choices=[('', 'Unmarked'), ('0', 'Incorrect'), ('1', 'Half mark'), ('2', 'Correct')], default='', max_length=1)),
+                ('question', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='answers', to='rapids.rapid')),
+            ],
+        ),
+    ]

rapids/models.py

@@ -24,12 +24,6 @@ def image_directory_path(instance, filename):
     return u"picture/{0}".format(filename)
 
 
-class AnswerStrings(models.Model):
-    text = models.CharField(max_length=255, unique=True)
-
-    def __str__(self):
-        return self.text
-
 
 class Abnormality(models.Model):
     name = models.CharField(max_length=200,
@@ -80,7 +74,7 @@ class Site(models.Model):
 
 class Answer(models.Model):
     question = models.ForeignKey(
-        Rapid, related_name="answers", on_delete=models.CASCADE
+        "Rapid", related_name="answers", on_delete=models.CASCADE
     )
     answer = models.TextField(max_length=500)
     answer_compare = models.TextField(max_length=500)
@@ -148,15 +142,15 @@ class Rapid(models.Model):
         choices=LATERALITY_CHOICES,
         default=NONE,
         help_text="Applies to the answer, not the examination")
-    condition = tagulous.models.TagField(
+#    condition = tagulous.models.TagField(
-        to=Condition,
+#        to=Condition,
-        blank=True,
+#        blank=True,
-        help_text=
+#        help_text=
-        "Associated condition. Will allow searching / filtering and tips / hints to be displayed. Conditions with spaces must be enclosed in quotes \"...\""
+#        "Associated condition. Will allow searching / filtering and tips / hints to be displayed. Conditions with spaces must be enclosed in quotes \"...\""
-    )
+#    )
-
+#
-    sign = tagulous.models.TagField(
+#    sign = tagulous.models.TagField(
-        to=Sign, blank=True, help_text='Radiological signs in the question')
+#        to=Sign, blank=True, help_text='Radiological signs in the question')
 
     DEFAULT_SITE_ID = 1
     site = models.ManyToManyField(
@@ -206,134 +200,6 @@ class Rapid(models.Model):
             lat = self.laterality
         return "{} / {} {}".format(exams, lat, n)
 
-
-class RapidImage(models.Model):
-    rapid = models.ForeignKey(Rapid,
-                              related_name="images",
-                              on_delete=models.CASCADE)
-    image = models.ImageField(upload_to=image_directory_path, storage=image_storage)
-
-    feedback_image = models.BooleanField(default=False)
-
-    def image_tag(self):
-        if self.image:
-            return mark_safe(
-                '<img src="{}{}" class="admin-rapid-image" /><span class="admin-rapid-image-info">Click and hold to zoom<span>'
-                .format(settings.MEDIA_URL, self.image))
-        else:
-            return ""
-
-    image_tag.short_description = 'Image'
-
-
-class Note(models.Model):
-    rapid = models.ForeignKey(Rapid,
-                              related_name="rapid_notes",
-                              on_delete=models.CASCADE,
-                              null=True)
-    author = models.ForeignKey(User,
-                               related_name="rapid_notes",
-                               on_delete=models.CASCADE)
-    note = models.TextField()
-    created_on = models.DateTimeField(auto_now_add=True)
-
-    def get_absolute_url(self):
-        self.pk = self.rapid_id
-        return reverse('rapids:rapid_detail', kwargs={'pk': self.pk})
-
-    def __str__(self):
-        return "{} [{}] {}".format(self.rapid, self.author, self.created_on)
-
-
-class RapidCreationDefault(models.Model):
-    author = models.OneToOneField(User,
-                                  related_name="rapid_default",
-                                  on_delete=models.CASCADE)
-
-    site = models.ManyToManyField(
-        Site,
-        blank=True,
-        default=1,
-        help_text="Default site to use when creating a new rapid")
-
-    def get_absolute_url(self):
-        return reverse('rapids:rapid_create')
-
-
-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
-    )
-
-    image = models.ImageField(upload_to=image_directory_path, storage=image_storage)
-
-    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 an 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",
-    )
-
-    def __str__(self):
-        # Get first answer
-        return "{} [{}, {}]".format(
-            self.GetPrimaryAnswer(), 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 GetPrimaryAnswer(self):
         if len(self.answers.all()) > 0:
             return self.answers.all().first().answer
@@ -387,3 +253,60 @@ class AnatomyQuestion(models.Model):
 
         marked_answers = correct_answers | half_mark_answers | incorrect_answers
         return marked_answers
+
+
+class RapidImage(models.Model):
+    rapid = models.ForeignKey(Rapid,
+                              related_name="images",
+                              on_delete=models.CASCADE)
+    image = models.ImageField(upload_to=image_directory_path, storage=image_storage)
+
+    feedback_image = models.BooleanField(default=False)
+
+    def image_tag(self):
+        if self.image:
+            return mark_safe(
+                '<img src="{}{}" class="admin-rapid-image" /><span class="admin-rapid-image-info">Click and hold to zoom<span>'
+                .format(settings.MEDIA_URL, self.image))
+        else:
+            return ""
+
+    image_tag.short_description = 'Image'
+
+
+class Note(models.Model):
+    rapid = models.ForeignKey(Rapid,
+                              related_name="rapid_notes",
+                              on_delete=models.CASCADE,
+                              null=True)
+    #author = models.ForeignKey(User,
+    author = models.ForeignKey( settings.AUTH_USER_MODEL,
+                               related_name="rapid_notes",
+                               on_delete=models.CASCADE)
+    note = models.TextField()
+    created_on = models.DateTimeField(auto_now_add=True)
+
+    def get_absolute_url(self):
+        self.pk = self.rapid_id
+        return reverse('rapids:rapid_detail', kwargs={'pk': self.pk})
+
+    def __str__(self):
+        return "{} [{}] {}".format(self.rapid, self.author, self.created_on)
+
+
+class RapidCreationDefault(models.Model):
+    #author = models.OneToOneField(User,
+    author = models.OneToOneField(
+        settings.AUTH_USER_MODEL,
+                                  related_name="rapid_default",
+                                  on_delete=models.CASCADE)
+
+    site = models.ManyToManyField(
+        Site,
+        blank=True,
+        default=1,
+        help_text="Default site to use when creating a new rapid")
+
+    def get_absolute_url(self):
+        return reverse('rapids:rapid_create')
+

rapids/templates/rapids/base.html

@@ -9,10 +9,10 @@
     <link rel="stylesheet" href="{% static 'tagulous/lib/select2-3/select2.css' %}">
     <link rel="stylesheet" href="{% static 'css/sbas.css' %}">
 
-    <script src="{% static 'tagulous/lib/jquery.js' %}"></script>
+    {% comment %} <script src="{% static 'tagulous/lib/jquery.js' %}"></script>
     <script src="{% static 'tagulous/lib/select2-3/select2.min.js' %}"></script>
     <script src="{% static 'tagulous/tagulous.js' %}"></script>
-    <script src="{% static 'tagulous/adaptor/select2-3.js' %}"></script>
+    <script src="{% static 'tagulous/adaptor/select2-3.js' %}"></script> {% endcomment %}
     <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
     <script type="text/javascript" src="{% static 'js/dwv/i18next.min.js' %}"></script>
     <script type="text/javascript" src="{% static 'js/dwv/dwv.min.js' %}"></script>