migrate examinations to generic model (and start adding mangament)

anatomy/admin.py

@@ -6,7 +6,7 @@ from .models import (
     Answer,
     UserAnswer,
     Exam,
-    Modality,
+    #Modality,
     Region,
     BodyPart,
     Structure,
@@ -56,7 +56,6 @@ admin.site.register(AnatomyQuestion, AnatomyAdmin)
 admin.site.register(QuestionType)
 admin.site.register(UserAnswer)
 admin.site.register(Exam, ExamAdmin)
-admin.site.register(Modality)
 admin.site.register(Region)
 admin.site.register(BodyPart)
 admin.site.register(Structure)

anatomy/migrations/0003_alter_anatomyquestion_modality_delete_modality.py

@@ -0,0 +1,47 @@
+# Generated by Django 4.1.4 on 2023-06-19 10:51
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("longs", "0002_alter_longseries_modality"),
+        ("atlas", "0003_alter_series_modality"),
+        ("generic", "0002_modality_examination_modality"),
+        ("anatomy", "0002_initial"),
+    ]
+
+    operations = [
+        # migrations.DeleteModel(
+        #    name='Modality',
+        # ),
+        migrations.SeparateDatabaseAndState(
+            state_operations=[
+                migrations.DeleteModel(
+                    name="Modality",
+                ),
+            ],
+            database_operations=[
+                migrations.AlterModelTable(
+                    name="Modality",
+                    table="generic_modality",
+                ),
+            ],
+        ),
+        migrations.SeparateDatabaseAndState(
+            state_operations=[
+                migrations.AlterField(
+                    model_name="anatomyquestion",
+                    name="modality",
+                    field=models.ForeignKey(
+                        help_text="Modality of the image",
+                        null=True,
+                        on_delete=django.db.models.deletion.SET_NULL,
+                        to="generic.modality",
+                    ),
+                ),
+            ],
+            database_operations=[],
+        ),
+    ]

anatomy/models.py

@@ -16,7 +16,7 @@ from sortedm2m.fields import SortedManyToManyField
 
 import string
 
-from generic.models import CidUser, CidUserGroup, ExamUserStatus, Examination, ExamBase, QuestionBase, QuestionNote, UserAnswerBase, UserUserGroup
+from generic.models import CidUser, CidUserGroup, ExamUserStatus, Examination, ExamBase, QuestionBase, QuestionNote, UserAnswerBase, UserUserGroup, Modality
 
 from collections import defaultdict
 from helpers.images import image_as_base64
@@ -57,11 +57,12 @@ class Region(models.Model):
         return self.region
 
 
-class Modality(models.Model):
+## TODO: ??? Move to generic app
-    modality = models.CharField(max_length=200)
+#class Modality(models.Model):
-
+#    modality = models.CharField(max_length=200)
-    def __str__(self):
+#
-        return self.modality
+#    def __str__(self):
+#        return self.modality
 
 
 class QuestionType(models.Model):

atlas/migrations/0003_alter_series_modality.py

@@ -0,0 +1,29 @@
+# Generated by Django 4.1.4 on 2023-06-19 10:51
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("generic", "0002_modality_examination_modality"),
+        ("atlas", "0002_initial"),
+    ]
+
+    operations = [
+        migrations.SeparateDatabaseAndState(
+            state_operations=[
+                migrations.AlterField(
+                    model_name="series",
+                    name="modality",
+                    field=models.ForeignKey(
+                        null=True,
+                        on_delete=django.db.models.deletion.SET_NULL,
+                        related_name="atlas_series_modality",
+                        to="generic.modality",
+                    ),
+                ),
+            ],
+            database_operations=[],
+        )
+    ]

atlas/models.py

@@ -29,7 +29,6 @@ import string
 from collections import defaultdict
 from helpers.images import image_as_base64, pretty_print_dicom
 
-from anatomy.models import Modality
 
 from generic.models import (
     CidUser,
@@ -44,6 +43,7 @@ from generic.models import (
     QuestionNote,
     SeriesBase,
     SeriesImageBase,
+    Modality,
 )
 
 # from generic.models import Examination, Site, Condition, Sign

atlas/templates/atlas/case_display_block.html

@@ -34,8 +34,8 @@
                     </a>
                     <br>
                     <span class="series-block-popup-link">
-                    <a href="#"
+                        <a href="#"
-                        onclick="return window.create_popup_window('/atlas/series/{{series.pk}}', 'Series')">Popup</a>
+                           onclick="return window.create_popup_window('/atlas/series/{{series.pk}}', 'Series')">Popup</a>
                     </span>
                 </span>
             </span>
@@ -53,51 +53,53 @@
                     <li>{{con.get_link}}</li>
                 {% endfor %}
             </ul>
-            <details>
+            <div>
-                <summary><b>Findings</b></summary>
+                <details>
-                {% if case.series.all %}
+                    <summary><b>Findings</b></summary>
-                    See individual series for more details.<br/>
+                    {% if case.series.all %}
-                    {% for series in case.series.all %}
+                        {% for series in case.series.all %}
-                        {% for finding in series.findings.all %}
+                            {% for finding in series.findings.all %}
-                            <div class="finding-box">
+                                <div class="finding-box">
-                                <span>
-                                    <a href="{{series.get_absolute_url}}">Series {{series.pk}}</a>: {{series.get_examination_full}} |&nbsp;
-                                </span>
-                                {% if finding.findings.all %}
                                     <span>
-                                        Findings: {% for f in finding.findings.all %}
+                                        <a href="{{series.get_absolute_url}}">Series {{series.pk}}</a>: {{series.get_examination_full}} |&nbsp;
-                                            {{f.get_link}},&nbsp;
-                                        {% endfor %}
                                     </span>
-                                {% endif %}
+                                    {% if finding.findings.all %}
-                                {% if finding.structures.all %}
+                                        <span>
-                                    <span>
+                                            Findings: {% for f in finding.findings.all %}
-                                        Structure: {% for s in finding.structures.all %}
+                                                {{f.get_link}},&nbsp;
-                                            {{s.get_link}},&nbsp;
+                                            {% endfor %}
-                                        {% endfor %}
+                                        </span>
-                                    </span>
+                                    {% endif %}
-                                {% endif %}
+                                    {% if finding.structures.all %}
-                                {% if finding.description %}
+                                        <span>
-                                    <span>
+                                            Structure: {% for s in finding.structures.all %}
-                                        Description: {{finding.description}}
+                                                {{s.get_link}},&nbsp;
-                                    </span>
+                                            {% endfor %}
-                                {% endif %}
+                                        </span>
-                            </div>
+                                    {% endif %}
-
+                                    {% if finding.description %}
+                                        <span>
+                                            Description: {{finding.description}}
+                                        </span>
+                                    {% endif %}
+                                </div>
+                            {% endfor %}
                         {% endfor %}
-                    {% endfor %}
+                    {% else %}
-                {% else %}
+                        No series associated with case.
-                    No findings associated with case.
+                    {% endif %}
-                {% endif %}
+                </details>
-            </details>
+            </div>
-            <details open>
+            <div>
-                <summary><b>Differentials</b></summary>
+                <details open>
-                <ul>
+                    <summary><b>Differentials</b></summary>
-                    {% for diff in case.differentialcase.all %}
+                    <ul>
-                        <li>{{diff.condition.get_link}} - {{diff.text}}</li>
+                        {% for diff in case.differentialcase.all %}
-                    {% endfor %}
+                            <li>{{diff.condition.get_link}} - {{diff.text}}</li>
-                </ul>
+                        {% endfor %}
-            </details>
+                    </ul>
+                </details>
+            </div>
         </p>
     </div>
     Subspecialty:
@@ -114,9 +116,9 @@
     </ul>
     <b>Collections:</b>
     <button
-    hx-get="{% url 'atlas:case_collection_form' case.pk %}" 
+        hx-get="{% url 'atlas:case_collection_form' case.pk %}"
-    hx-target="#collection-form">
+        hx-target="#collection-form">
-    Add collection</button>
+        Add collection</button>
     <div id="collection-form"></div>
     <ul>
         {% for collection in case.casecollection_set.all %}

generic/admin.py

@@ -6,7 +6,7 @@ from .models import (
     CidUserGroup,
     Examination,
     #Sign,
-    #Condition,
+    Modality,
     Plane,
     Contrast,
     QuestionNote,
@@ -35,3 +35,4 @@ admin.site.register(CidUserGroup)
 admin.site.register(UserProfile)
 admin.site.register(UserGrades)
 admin.site.register(Supervisor)
+admin.site.register(Modality)

generic/filters.py

@@ -3,7 +3,7 @@ import django_filters
 
 from django.contrib.auth.models import User
 
-from generic.models import CidUser, Supervisor, UserGrades
+from generic.models import CidUser, Examination, Supervisor, UserGrades
 
 
 class CidUserFilter(django_filters.FilterSet):
@@ -61,3 +61,22 @@ class UserUserFilter(django_filters.FilterSet):
         #    return parent.filter(active=True)
 
         return parent
+
+class ExaminationFilter(django_filters.FilterSet):
+    class Meta:
+        model = Examination
+        fields = {"examination": ["icontains"], "modality": ["exact"]}
+
+    def __init__(
+        self,
+        data=None,
+        queryset=None,
+        prefix=None,
+        strict=None,
+        user=None,
+        request=None,
+    ):
+        super(ExaminationFilter, self).__init__(
+            data=data, queryset=queryset, prefix=prefix, request=request
+        )
+        pass

generic/forms.py

@@ -115,9 +115,17 @@ class ExamAuthorFormMixin(ModelForm):
 
 
 class ExaminationForm(ModelForm):
+    def __init__(self, *args, **kwargs):
+        # Where is this coming from?
+        if "user" in kwargs:
+            user = kwargs.pop("user")
+
+        ModelForm.__init__(self, *args, **kwargs)
+        super(ExaminationForm, self).__init__(*args, **kwargs)
+
     class Meta:
         model = Examination
-        fields = ["examination"]
+        fields = ["examination", "modality"]
 
 
 class QuestionNoteForm(ModelForm):

generic/migrations/0002_modality_examination_modality.py

@@ -0,0 +1,47 @@
+# Generated by Django 4.1.4 on 2023-06-19 10:51
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("generic", "0001_initial"),
+    ]
+
+    operations = [
+        migrations.SeparateDatabaseAndState(
+            state_operations=[
+                migrations.CreateModel(
+                    name="Modality",
+                    fields=[
+                        (
+                            "id",
+                            models.AutoField(
+                                auto_created=True,
+                                primary_key=True,
+                                serialize=False,
+                                verbose_name="ID",
+                            ),
+                        ),
+                        ("modality", models.CharField(max_length=200)),
+                    ],
+                ),
+            ],
+            database_operations=[],
+        ),
+        migrations.SeparateDatabaseAndState(
+            state_operations=[
+                migrations.AddField(
+                    model_name="examination",
+                    name="modality",
+                    field=models.ForeignKey(
+                        null=True,
+                        on_delete=django.db.models.deletion.SET_NULL,
+                        to="generic.modality",
+                    ),
+                ),
+            ],
+            database_operations=[],
+        ),
+    ]

generic/migrations/0003_remove_examination_modality.py

@@ -0,0 +1,21 @@
+# Generated by Django 4.1.4 on 2023-06-19 11:13
+
+from django.db import migrations
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("generic", "0002_modality_examination_modality"),
+    ]
+
+    operations = [
+        migrations.SeparateDatabaseAndState(
+            state_operations=[
+                migrations.RemoveField(
+                    model_name="examination",
+                    name="modality",
+                ),
+            ],
+            database_operations=[],
+        ),
+    ]

generic/migrations/0004_examination_modality.py

@@ -0,0 +1,19 @@
+# Generated by Django 4.1.4 on 2023-06-19 11:13
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('generic', '0003_remove_examination_modality'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='examination',
+            name='modality',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, to='generic.modality'),
+        ),
+    ]

generic/models.py

@@ -1,5 +1,6 @@
 from collections import defaultdict
 import json
+import os
 from typing import Tuple
 from django.contrib.auth.mixins import LoginRequiredMixin
 from django.db import models
@@ -42,6 +43,11 @@ def findMiddle(input_list):
     else:
         return input_list[int(middle)]
 
+class Modality(models.Model):
+    modality = models.CharField(max_length=200)
+
+    def __str__(self):
+        return self.modality
 
 class Plane(models.Model):
     plane = models.CharField(max_length=200, unique=True)
@@ -66,6 +72,8 @@ class Contrast(models.Model):
 class Examination(models.Model):
     examination = models.CharField(max_length=200, unique=True)
 
+    modality = models.ForeignKey(Modality, on_delete=models.SET_NULL, null=True)
+
     def __str__(self):
         return self.examination
 

generic/tables.py

@@ -7,7 +7,7 @@ from easy_thumbnails.files import get_thumbnailer
 
 from easy_thumbnails.exceptions import InvalidImageFormatError
 
-from generic.models import CidUser
+from generic.models import CidUser, Examination
 
 from django.contrib.auth.models import User
 
@@ -259,3 +259,27 @@ class UserUserTable(tables.Table):
             record.username,
             record.email,
         )
+
+class ExaminationTable(tables.Table):
+    examination = tables.Column(
+        linkify=("generic:examination_detail", {"pk": tables.A("pk")}),
+        verbose_name="Condition",
+    )
+
+    #edit = tables.LinkColumn(
+    #    "generic:examination_update", text="Edit", args=[A("pk")], orderable=False
+    #)
+    delete = tables.LinkColumn(
+        "generic:examination_delete", text="Delete", args=[A("pk")], orderable=False
+    )
+    selection = tables.CheckBoxColumn(accessor="pk", orderable=False)
+
+    # synonym = tables.ManyToManyColumn(verbose_name="Synonyms")
+    #synonym = tables.Column(empty_values=())
+    #parent = tables.ManyToManyColumn(verbose_name="Parents")
+
+    class Meta:
+        model = Examination
+        template_name = "django_tables2/bootstrap4.html"
+        #fields = ("primary", "subspecialty")
+        sequence = ("examination",)

generic/templates/generic/examination_detail.html

@@ -0,0 +1,44 @@
+{% extends 'generic/base.html' %}
+
+{% block content %}
+
+
+
+    <div class="floating-header">
+        <a href="{% url 'generic:examination_update' pk=examination.pk %}" title="Edit the Examination">Edit</a>
+        <a href="{% url 'generic:examination_delete' pk=examination.pk %}" title="Delete the Examination">Delete</a>
+        {% if request.user.is_superuser %}
+            <a href="{% url 'admin:generic_examination_change' examination.id %}"
+                title="Edit the Examination using the admin interface">Admin Edit</a>
+        {% endif %}
+    </div>
+    <div>
+        <h3>Name: {{examination.examination}}</h3>
+        Modality: {{examination.modality}}
+    </div>
+    {% if examination.atlas_series_examination_set.all %}
+        <h4>Associated Atlas Cases</h4>
+        <ul>
+
+            {% for case in examination.atlas_series_examination_set.all %}
+                <li>{{case}}</li>
+            {% endfor %}
+
+        </ul>
+    {% endif %}
+    {% if examination.longs_series_examination_set.all %}
+        <h4>Associated Longs Cases</h4>
+        <ul>
+
+            {% for case in examination.longs_series_examination_set.all %}
+                <li>{{case}}</li>
+            {% endfor %}
+
+        </ul>
+    {% endif %}
+
+{% endblock %}
+
+{% block js %}
+
+{% endblock %}

generic/templates/generic/examination_form.html

@@ -0,0 +1,26 @@
+{% extends "atlas/base.html" %}
+<!-- {% load static from static %} -->
+
+{% block css %}
+{% endblock %}
+{% block js %}
+    <!--<script type="text/javascript" src="/admin/jsi18n/"></script>-->
+    {{form.media}}
+
+    <script type="text/javascript">
+    </script>
+
+    <!-- {{ form.media }} -->
+{% endblock %}
+{% block content %}
+    <h2>Add/Edit Examination</h2>
+    Use this form to create or edit a examination.
+    <form action="" method="post" enctype="multipart/form-data" id="examination-form">
+        {% csrf_token %}
+
+        <table>
+            {{ form.as_table }}
+        </table>
+        <input type="submit" class="submit-button" value="Submit" name="submit">
+    </form>
+{% endblock %}

generic/urls.py

@@ -9,6 +9,10 @@ app_name = "generic"
 
 urlpatterns = [
     # path('', views.question_list, name='question_list'),
+    path("examination/", views.ExaminationView.as_view(), name="examination_view"),
+    path("examination/<int:pk>", views.examination_detail, name="examination_detail"),
+    path("examination/<int:pk>/delete", views.ExaminationDelete.as_view(), name="examination_delete"),
+    path("examination/<int:pk>/update", views.ExaminationUpdate.as_view(), name="examination_update"),
     path("examination/create/", views.create_examination, name="create_examination"),
     path(
         "examination/ajax/get_examination_id",

generic/views.py

@@ -44,9 +44,10 @@ from django_tables2.views import SingleTableMixin
 from reversion.views import RevisionMixin
 from atlas.models import CaseCollection
 from generic.decorators import user_is_cid_user_manager
-from generic.filters import CidUserFilter
+from generic.filters import CidUserFilter, ExaminationFilter
 
-from generic.tables import CidUserExamTable, CidUserTable
+from generic.tables import CidUserExamTable, CidUserTable, ExaminationTable
+from generic.mixins import SuperuserRequiredMixin
 
 from .forms import (
     CidUserForm,
@@ -177,6 +178,21 @@ def create_examination(request):
         request, "rapids/create_simple.html", {"form": form, "name": "Examination"}
     )
 
+@login_required
+@user_passes_test(lambda u: u.is_superuser)
+def examination_detail(request, pk):
+    examination = get_object_or_404(Examination, pk=pk)
+
+    # logging.debug(atlas.subspecialty.first().name.all())
+    return render(
+        request,
+        "generic/examination_detail.html",
+        {
+            "examination": examination,
+        },
+    )
+
+
 
 @csrf_exempt
 def get_examination_id(request):
@@ -2954,3 +2970,21 @@ class SupervisorCreate(CidManagerRequiredMixin, CreateView):
 
 class SupervisorList(CidManagerRequiredMixin, ListView):
     model = Supervisor
+
+class ExaminationView(SuperuserRequiredMixin, SingleTableMixin, FilterView):
+    model = Examination
+    table_class = ExaminationTable
+    template_name = "atlas/view.html"
+
+    filterset_class = ExaminationFilter
+
+
+class ExaminationDelete(RevisionMixin, SuperuserRequiredMixin, DeleteView):
+    model = Examination
+    template_name = "confirm_delete.html"
+    success_url = reverse_lazy("generic:examination_view")
+
+
+class ExaminationUpdate(UpdateView, SuperuserRequiredMixin):
+    model = Examination
+    form_class = ExaminationForm

longs/migrations/0002_alter_longseries_modality.py

@@ -0,0 +1,29 @@
+# Generated by Django 4.1.4 on 2023-06-19 10:51
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("generic", "0002_modality_examination_modality"),
+        ("longs", "0001_initial"),
+    ]
+
+    operations = [
+        migrations.SeparateDatabaseAndState(
+            state_operations=[
+                migrations.AlterField(
+                    model_name="longseries",
+                    name="modality",
+                    field=models.ForeignKey(
+                        null=True,
+                        on_delete=django.db.models.deletion.SET_NULL,
+                        related_name="series_modality",
+                        to="generic.modality",
+                    ),
+                ),
+            ],
+            database_operations=[],
+        )
+    ]

longs/models.py

@@ -25,8 +25,6 @@ import string
 from collections import defaultdict
 from helpers.images import image_as_base64, pretty_print_dicom
 
-from anatomy.models import Modality
-
 from generic.models import (
     CidUser,
     CidUserGroup,
@@ -41,6 +39,7 @@ from generic.models import (
     SeriesImageBase,
     UserAnswerBase,
     UserUserGroup,
+    Modality
 )
 
 # from generic.models import Examination, Site, Condition, Sign

templates/index.html

@@ -31,6 +31,10 @@
     <div>
         {% if request.user.is_staff %}
             Manage users <a href="{% url 'accounts_list'%}">here</a> and candidates <a href="{% url 'generic:manage_cids'%}">here</a>
+
+            <p>Manage <a href="{% url 'generic:examination_view' %}">Examinations</a>
+
+            </p>
         {% endif %}
     </div>
 {% endblock %}