start integrating cimar

atlas/forms.py

@@ -67,6 +67,9 @@ from atlas.helpers import get_cases_available_to_user
 
 from typing import Any
 
+from helpers.cimar import CimarAPI, NotFoundError
+from rad.settings import CIMAR_USERNAME, CIMAR_PASSWORD
+
 class CaseSelect(Select):
     template_name = "atlas/case_select_widget.html"
 
@@ -363,6 +366,7 @@ class CaseForm(ModelForm):
                 "open_access",
                 "previous_case",
                 "diagnostic_certainty",
+                "cimar_uuid"
             ),
 
         )
@@ -396,6 +400,7 @@ class CaseForm(ModelForm):
             "open_access",
             "previous_case",
             "diagnostic_certainty",
+            "cimar_uuid"
         ]
         # fields = ['question', 'findings', 'subspecialty', 'references']
         widgets = {
@@ -418,6 +423,18 @@ class CaseForm(ModelForm):
             "previous_case": CaseSelect(),
         }
     
+    def clean_cimar_uuid(self):
+        cimar_uuid = self.cleaned_data["cimar_uuid"]
+        if cimar_uuid:
+            with CimarAPI(username=CIMAR_USERNAME, password=CIMAR_PASSWORD) as api:
+                try:
+                    study = api.get_study_by_uuid(cimar_uuid)
+
+                except NotFoundError:
+                    raise ValidationError("Study not found in CIMAR")
+
+        return cimar_uuid
+
     def save(self, commit=True):
         # Get the unsaved Case instance
         instance = ModelForm.save(self, False)

atlas/migrations/0067_case_cimar_uuid.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.1.4 on 2025-02-10 13:07
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('atlas', '0066_case_total_images_series_size'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='case',
+            name='cimar_uuid',
+            field=models.CharField(blank=True, max_length=255, null=True),
+        ),
+    ]

atlas/models.py

@@ -46,6 +46,7 @@ from generic.models import (
     CidUser,
     CidUserExam,
     CidUserGroup,
+    CimarCase,
     ExamOrCollectionGenericBase,
     ExamUserStatus,
     Examination,
@@ -392,6 +393,8 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
 
     total_images_series_size = models.BigIntegerField(null=True, blank=True)
 
+    cimar_uuid = models.CharField(max_length=255, null=True, blank=True)
+
     def get_app_name(self):
         return "atlas"
 
@@ -404,6 +407,14 @@ 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_cimar_case(self):
+        return get_object_or_404(CimarCase, uuid=self.cimar_uuid)
+
+    def get_cimar_case_details(self):
+        cimar_case = self.get_cimar_case()
+        return cimar_case.study_details
+
+
     # def get_base_template(self):
 
     # def get_edit_template_links(self):
@@ -427,6 +438,7 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
 
     def get_case_dicom_json(self, case_title_as_patient_name=True, priors=None):
         series_json = []
+        series: Series
         for series in self.series.all():
             series_json.append(series.get_series_dicom_json())
 
@@ -509,6 +521,8 @@ class Case(models.Model, AuthorMixin, QuestionMixin):
     
 
 
+
+
 def extract_image_dicom_json_from_ds(ds, url, image_index):
     to_keep = [
         "Columns",

atlas/templates/atlas/case_display_block.html

@@ -19,7 +19,65 @@
             </div>
         </div>
     {% endif %}
-    <div><a href="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:case_dicom_json' case.pk %}">View case in OHIF</a> <a target="_blank" href="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:case_dicom_json' case.pk %}">(new tab)</a>
+    <div>
+        
+        {% if case.cimar_uuid %}
+
+        <details><summary>Details</summary>
+            <br/>
+            Case uuid: {{case.cimar_uuid}}
+            <br/>
+            {{case.get_cimar_case.viewer_link}}?{{cimar_sid}}
+
+<button
+    hx-get='{% url "cimar_study_viewer_embed" case.cimar_uuid %}'
+    hx-target="#modals-here"
+    hx-trigger="click"
+    data-bs-toggle="modal"
+    data-bs-target="#modals-here"
+    class="btn primary">Open Modal</button>
+
+<div id="modals-here"
+    class="modal modal-blur fade"
+    style="display: none"
+    aria-hidden="false"
+    tabindex="-1">
+    <div class="modal-dialog modal-lg modal-dialog-centered" role="document">
+        <div class="modal-content"></div>
+    </div>
+</div>
+
+            <a href='{% url "cimar_study_viewer" case.cimar_uuid %}'>Viewer</a>
+
+
+            <details>
+                <summary>Study details</summary>
+                {{ case.get_cimar_case.get_pretty_study_details }}
+            </details>
+            <details>
+                <summary>Study schema</summary>
+                {{ case.get_cimar_case.get_pretty_study_schema }}
+            </details>
+            <details>
+                <summary>Study series</summary>
+<button
+  id='load-series'
+  hx-get='{% url "cimar_study_series_block" case.cimar_uuid %}'
+  hx-trigger='load'
+  hx-swap='outerHTML'>
+  Load Series
+</button>
+            </details>
+            <a href='{% url "generic:cimar_case_refresh" case.cimar_uuid %}'>Refresh</a>
+
+        </details>
+
+
+            
+        {% else %}
+        <a href="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:case_dicom_json' case.pk %}">View case in OHIF</a> <a target="_blank" href="/ohif/viewer/dicomjson?url=https://www.penracourses.org.uk{% url 'atlas:case_dicom_json' case.pk %}">(new tab)</a>
+        {% endif %}
+            
 
         <div class="date">
             {{ case.created_date|date:"d/m/Y" }}

atlas/urls.py

@@ -378,6 +378,7 @@ urlpatterns = [
     # path("all_questions/", views.all_questions, name="all_questions"),
     path("case/<int:pk>/scrap", views.atlas_scrap, name="case_scrap"),
     path("case/<int:pk>/delete", views.CaseDelete.as_view(), name="case_delete"),
+    path("case/<int:case_id>/push_to_cimar", views.push_case_to_cimar, name="push_case_to_cimar"),
     path("case/create/", views.AtlasCreate.as_view(), name="case_create"),
     path(
         "case/collection/<int:pk>/create",

atlas/views.py

@@ -22,6 +22,7 @@ from django.contrib.auth.mixins import LoginRequiredMixin, PermissionRequiredMix
 from django.views.generic import View
 from django.views.generic.detail import DetailView
 import pydicom
+from pydicom.uid import generate_uid
 from generic.mixins import SuperuserRequiredMixin
 
 from django.views.generic.edit import CreateView, UpdateView, DeleteView, FormView
@@ -33,8 +34,9 @@ from django.urls import reverse_lazy, reverse
 from django.http import Http404, JsonResponse
 from django.http import HttpResponseRedirect, HttpResponse
 
-from generic.models import CidUser, CidUserExam
+from generic.models import CidUser, CidUserExam, CimarCase
 from atlas.helpers import get_cases_available_to_user
+from rad.settings import REMOTE_URL, CIMAR_USERNAME, CIMAR_PASSWORD
 
 from .forms import (
     AddCollectionToCaseForm,
@@ -159,6 +161,8 @@ import reversion
 import os
 import difflib
 
+from helpers.cimar import CimarAPI
+
 logger = logging.getLogger(__name__)
 
 
@@ -195,7 +199,7 @@ def case_detail(request, pk):
     #    raise PermissionDenied
 
     # logging.debug(atlas.subspecialty.first().name.all())
-    return render(request, "atlas/case_detail.html", {"case": case})
+    return render(request, "atlas/case_detail.html", {"case": case, "cimar_sid":request.user.userprofile.cimar_sid})
 
 @login_required
 @user_is_author_or_atlas_series_checker_or_atlas_marker_or_open_access
@@ -955,6 +959,9 @@ class AtlasCreateBase(RevisionMixin, LoginRequiredMixin):
 
         form.instance.author.add(self.request.user.id)
 
+        # Check Cimar Case
+        #CimarAPI().get_study_by_uuid(self.object.cimar_uuid)
+
         context = self.get_context_data(form=form)
         series_formset = context["series_formset"]
         casedifferential_formset = context["casedifferential_formset"]
@@ -2390,6 +2397,7 @@ def collection_case_view(request, pk, case_number):
             "previous": previous,
             "next": next,
             "answer": answer,
+            "cimar_sid":request.user.userprofile.cimar_sid
         },
     )
 
@@ -2419,6 +2427,7 @@ def collection_case_dicom_json(request, exam_id, case_id):
     return JsonResponse(case_detail.case.get_case_dicom_json(priors=priors))
 
 
+
 def case_dicom_json(request, pk):
     case = get_object_or_404(Case, pk=pk)
 
@@ -2971,3 +2980,29 @@ def collection_reset_answers(request, exam_id: int):
 
     else:
         raise Http404("Invalid request")
+
+def push_case_to_cimar(request, case_id):
+    case = get_object_or_404(Case, pk=case_id)
+
+    api = CimarAPI()
+    api.login(username=CIMAR_USERNAME, password=CIMAR_PASSWORD)
+
+    # We use the same study_uid for all images in a case
+    study_uid = generate_uid()
+
+    for series in case.get_series():
+        for image in series.images.all():
+            data = api.upload_dicom(image.image.path, study_uid=study_uid)
+
+    
+    cimar_uuid = api.get_study_by_study_uid(data["study_uid"])["uuid"]
+
+    case.cimar_uuid = cimar_uuid
+
+    case.save()
+
+    cimar_case, created = CimarCase.objects.get_or_create(uuid=cimar_uuid)
+
+    cimar_case.refresh_study()
+
+    return HttpResponse("Success")

generic/migrations/0021_userprofile_cimar_sid.py

@@ -0,0 +1,18 @@
+# Generated by Django 5.1.4 on 2025-02-10 12:47
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('generic', '0020_remove_examuserstatus_share_with_supervisor_and_more'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='userprofile',
+            name='cimar_sid',
+            field=models.CharField(blank=True, max_length=100),
+        ),
+    ]

generic/migrations/0022_cimarcase.py

@@ -0,0 +1,22 @@
+# Generated by Django 5.1.4 on 2025-02-10 13:46
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('generic', '0021_userprofile_cimar_sid'),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name='CimarCase',
+            fields=[
+                ('id', models.AutoField(auto_created=True, primary_key=True, serialize=False, verbose_name='ID')),
+                ('uuid', models.CharField(max_length=255, unique=True)),
+                ('viewer_link', models.URLField(blank=True)),
+                ('study_details', models.JSONField(blank=True)),
+            ],
+        ),
+    ]

generic/migrations/0023_cimarcase_valid_uuid_alter_cimarcase_study_details.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.1.4 on 2025-02-17 10:26
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('generic', '0022_cimarcase'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='cimarcase',
+            name='valid_uuid',
+            field=models.BooleanField(default=False),
+        ),
+        migrations.AlterField(
+            model_name='cimarcase',
+            name='study_details',
+            field=models.JSONField(blank=True, default=dict),
+        ),
+    ]

generic/migrations/0024_cimarcase_series_data_cimarcase_study_schema.py

@@ -0,0 +1,23 @@
+# Generated by Django 5.1.4 on 2025-02-17 11:49
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('generic', '0023_cimarcase_valid_uuid_alter_cimarcase_study_details'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='cimarcase',
+            name='series_data',
+            field=models.JSONField(blank=True, default=dict),
+        ),
+        migrations.AddField(
+            model_name='cimarcase',
+            name='study_schema',
+            field=models.JSONField(blank=True, default=dict),
+        ),
+    ]

generic/models.py

@@ -7,6 +7,7 @@ from django.contrib.auth.mixins import LoginRequiredMixin
 from django.db import models
 from django.forms import ValidationError
 from django.http import Http404, HttpRequest
+from django.shortcuts import render
 from django.utils import timezone
 from django.core.validators import MaxValueValidator, MinValueValidator
 from smtplib import SMTPException
@@ -29,7 +30,8 @@ from django.db.models.signals import post_save
 from django.dispatch import receiver
 from generic.mixins import AuthorMixin, QuestionMixin
 from helpers.images import get_image_hash, pretty_print_dicom
-from rad.settings import REMOTE_URL
+from helpers.cimar import CimarAPI, STORAGE_API_URL
+from rad.settings import REMOTE_URL, CIMAR_USERNAME, CIMAR_PASSWORD
 from django.utils.html import format_html
 
 from easy_thumbnails.files import get_thumbnailer
@@ -45,6 +47,34 @@ from django.forms.utils import from_current_timezone, to_current_timezone
 
 from loguru import logger
 
+from pygments import highlight
+from pygments.lexers import JsonLexer
+from pygments.formatters import HtmlFormatter
+
+from django.contrib import admin
+from django.utils.safestring import mark_safe
+from django.template.loader import render_to_string
+
+
+def get_pretty_json(data):
+    """Function to display pretty version of our data"""
+    if not data:
+        return "No data"
+
+    # Convert the data to sorted, indented JSON
+    response = json.dumps(data, sort_keys=True, indent=2)
+
+    # Get the Pygments formatter
+    formatter = HtmlFormatter(style='colorful')
+
+    # Highlight the data
+    response = highlight(response, JsonLexer(), formatter)
+
+    # Get the stylesheet
+    style = "<style>" + formatter.get_style_defs() + "</style><br>"
+
+    # Safe the output
+    return mark_safe(style + response)
 
 def findMiddle(input_list):
     """Returns the middle element of a list"""
@@ -1690,6 +1720,8 @@ class UserProfile(models.Model):
 
     username = property(getusername)
 
+    cimar_sid = models.CharField(max_length=100, blank=True)
+
     def get_exams(self):
         available_exams = defaultdict(list)
 
@@ -1827,3 +1859,88 @@ class ExamCollection(models.Model, AuthorMixin):
 #        blank=True,
 #        help_text="Author/Manager(s) of the exam collection",
 #    )
+
+class CimarCase(models.Model):
+    uuid = models.CharField(max_length=255, unique=True)
+
+    viewer_link = models.URLField(blank=True)
+
+    study_details = models.JSONField(blank=True, default=dict)
+
+    study_schema = models.JSONField(blank=True, default=dict)
+
+    series_data = models.JSONField(blank=True, default=dict)
+
+    valid_uuid = models.BooleanField(default=False)
+
+    def load_series_data(self, api=None):
+        if api is None:
+            api = CimarAPI()
+            api.login(username=CIMAR_USERNAME, password=CIMAR_PASSWORD)
+        
+
+
+
+    def refresh_study(self):
+        api = CimarAPI()
+        api.login(username=CIMAR_USERNAME, password=CIMAR_PASSWORD)
+
+        self.study_details = api.get_study_by_uuid(self.uuid)
+        self.study_schema = api.get_study_schema_by_uuid(self.uuid)
+
+        self.viewer_link = api.get_study_viewer_url_by_uuid(self.uuid)
+
+        series_data = []
+
+        for series in self.study_schema["series"]:
+            series_data.append({
+                "series_id" : series["id"],
+                "series_description" : series["description"],
+                "image_count": len(series["images"]),
+                "thumbnail": self.get_series_image_thumbnail_link(series)
+
+            }
+            )
+
+        self.series_data = {}
+        self.series_data["series"] = series_data
+
+        self.valid_uuid = True
+        self.save()
+
+    def __str__(self):
+        return f"{self.uuid} ({self.valid_uuid})"
+
+    def get_user_viewer_link(self, user):
+        return self.viewer_link +  f"?sid={user.userprofile.cimar_sid}"
+
+
+    def get_pretty_study_details(self):
+        """Function to display pretty version of our data"""
+        return get_pretty_json(self.study_details)
+
+    def get_pretty_study_schema(self):
+        """Function to display pretty version of our data"""
+        return get_pretty_json(self.study_schema)
+
+    def get_pretty_study_series(self):
+        """Function to display pretty version of our data"""
+        return get_pretty_json(self.series_data)
+
+    #def get_series_details_block(self, cimar_sid=None):
+    #    if "series" in self.series_data:
+    #        return render_to_string("cimar_series.html", {"series_data": self.series_data["series"], cimar_sid: cimar_sid})
+    #    
+    #    return "No series data available"
+
+    #    return render_to_string("cimar_series.html", {"series_data": self.series_data["series"]})
+
+
+
+    def get_series_image_thumbnail_link(self,series):
+
+        middle_point = len(series["images"]) // 2
+
+        image = series["images"][middle_point]
+
+        return STORAGE_API_URL + f"/study/{self.study_details["storage_namespace"]}/{self.study_details["study_uid"]}/image/{image["id"]}/version/{image["version"]}/frame/0/thumbnail"

generic/urls.py

@@ -243,6 +243,13 @@ urlpatterns = [
         views.toggle_share_with_supervisor,
         name="toggle_share_with_supervisor",
     ),
+    path(
+        "cimar_case/<str:uuid>/refresh",
+        views.cimar_case_refresh,
+        name="cimar_case_refresh"
+    ),
+
+
 ]
 
 

generic/views.py

@@ -84,6 +84,7 @@ from .models import (
     CidUser,
     CidUserExam,
     CidUserGroup,
+    CimarCase,
     ExamBase,
     ExamCollection,
     ExamUserStatus,
@@ -4085,3 +4086,16 @@ def exam_collection_add_marker(request, collection_id, exam_type):
     collection.add_marker_to_exams(users, exam_types=(exam_type,))
 
     return HttpResponse("Marker added to exams")
+
+
+def cimar_case_refresh(request, uuid):
+    try:
+        CimarCase.objects.get(uuid=uuid).refresh_study()
+    except CimarCase.DoesNotExist:
+        CimarCase(uuid=uuid).save()
+
+
+
+    return HttpResponse("Case refreshed")
+
+    

helpers/cimar.py

@@ -0,0 +1,284 @@
+import json
+import requests
+from PIL import Image
+import io
+
+#def fetch_and_print_articles(api_url):
+#    response = requests.get(api_url)
+#    
+#    if response.status_code == 200:
+#        articles = response.json().get('articles', [])
+#        
+#        for index, article in enumerate(articles[:3], start=1):
+#            print(f"Article {index}:\n{json.dumps(article, sort_keys=True, indent=4)}\n")
+#    else:
+#        print(f"Error: {response.status_code}")
+
+#API_KEY = '3805f6bbabcb42b3a0c08a489baf603d'
+#api_endpoint = f"https://newsapi.org/v2/top-headlines?country=us&category=business&apiKey={API_KEY}"
+
+
+
+
+API_URL = "https://cloud.cimar.co.uk/api/v3"
+STORAGE_API_URL = 'https://storelpu.cimar.co.uk' + "/api/v3/storage"
+
+class CimarAPI:
+
+    def __init__(self, sid=None, username=None, password=None):
+        self.sid = sid
+        self.context = False
+        self.username = username
+        self.password = password
+
+        # Default namespace to save studies to
+        self.namespace = "eff0ca95-6ce6-443c-80dd-1136c8a58e4d" 
+
+    def get_storage(self, endpoint ):
+        pass
+
+    def post(self, endpoint, data=None, add_sid=True):
+        if data is None:
+            data = {}
+        if add_sid:
+            if self.sid is None:
+                raise NoSession("No session ID")
+            data["sid"] = self.sid
+
+        print(f"{data=}")
+
+        r = requests.post(API_URL + endpoint, data=data)
+
+
+        if r.status_code == 412:
+            match r.json():
+                case {"status": "ERROR", "error_type": "NOT_FOUND"}:
+                    raise NotFoundError("Study not found")
+                case {"status": "ERROR", "error_type": error}:
+                    raise APIError(error)
+        if r.status_code == 401:
+            raise InvalidCredentials("Invalid credentials")
+
+        print(r.status_code)
+        print(r.content)
+        
+        return r.json()
+
+    
+    def login(self, username=None, password=None):
+        if username is None:
+            username = self.username
+        if password is None:
+            password = self.password
+
+        data={"login": username, "password": password}
+        r = requests.post(API_URL + "/session/login", data=data)
+
+        if r.status_code == 412:
+            raise InvalidCredentials()
+        
+        self.sid = r.json()["sid"]
+        
+        return self.sid
+
+    def check_login_status(self):
+        try:
+            data = self.post("/session/user")
+        except InvalidCredentials:
+            return False
+
+        return data["status"] == "OK"
+
+    def logout(self):
+        data = self.post("/session/logout")
+
+
+    def __enter__(self):
+        if self.sid is None:
+            self.login()
+
+        self.context = True
+
+        return self
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        if self.context:
+            self.logout()
+            self.sid = None
+
+    def list_studies(self):
+        return self.post("/study/list")
+
+    def get_study_image_thumbnail(self, study_json):
+        schema = self.get_study_schema(study_json)
+
+        image = schema["series"][0]["images"][0]
+
+        r = requests.get(STORAGE_API_URL + f"/study/{study_json["storage_namespace"]}/{study_json["study_uid"]}/image/{image["id"]}/version/{image["version"]}/frame/0/thumbnail", params={"sid": self.sid})
+
+        print(r.status_code)
+
+        img = Image.open(io.BytesIO(r.content))
+
+        print(r.json())
+
+#    def get_series_image_thumbnail_link(self, study_json, series):
+#
+#        middle_point = len(series["images"]) // 2
+#
+#        image = series["images"][middle_point]
+#
+#        return requests.Request("GET",STORAGE_API_URL + f"/study/{study_json["storage_namespace"]}/{study_json["study_uid"]}/image/{image["id"]}/version/{image["version"]}/frame/0/thumbnail").prepare()
+#
+
+    def get_diagnostic_image(self, study_json, image_id, version, frame):
+        r = requests.get(STORAGE_API_URL + f"/study/{study_json["storage_namespace"]}/{study_json["study_uid"]}/image/{image_id}/version/{version}/frame/{frame}/diagnostic", params={"sid": self.sid})
+        print(r.status_code)
+
+        img = Image.open(io.BytesIO(r.content))
+
+        print(r.json())
+
+    def get_study_by_uuid(self, uuid):
+        return self.post("/study/get", data={"uuid": uuid})
+
+    def get_study_viewer_url_by_uuid(self, uuid):
+        return self.get_study_by_uuid(uuid)["viewer_link"]
+
+
+    def get_study_schema_by_uuid(self, uuid):
+        study_json = self.get_study_by_uuid(uuid)
+        return self.get_study_schema(study_json)
+
+    def get_study_by_study_uid(self, study_uid):
+        return self.post("/study/get", data={"study_uid": study_uid, "storage_namespace": self.namespace, "phi_namespace": self.namespace})
+
+    def get_study_schema(self, study_json):
+        r = requests.get(STORAGE_API_URL + f"/study/{study_json["storage_namespace"]}/{study_json["study_uid"]}/schema", params={"sid": self.sid})
+
+        return r.json()
+
+    def get_series_data(self, cimar_study_json):
+        series_json = []
+        for series in cimar_study_json["series"]:
+
+            instances = []
+            for image in series["images"]:
+                p= requests.Request("GET", STORAGE_API_URL + f"/study/{cimar_study_json["namespace"]}/{cimar_study_json["study_uid"]}/image/{image["id"]}/version/{image["version"]}/frame/0/diagnostic", params={"sid": self.sid}).prepare()
+                instances.append({"metadata": {}, "url": f"{p.url}"})
+
+
+
+            new_json = {
+                "SeriesInstanceUID": series["series_uid"],
+                "SeriesDescription": series["description"],
+                "Modality": series["modality"],
+                "instances": instances
+            }
+            
+            series_json.append(new_json)
+        return series_json
+
+    def get_study_dicom_json(self, cimar_study_json):
+
+        series_json = []
+        for series in cimar_study_json["series"]:
+
+            instances = []
+            for image in series["images"]:
+                p= requests.Request("GET", STORAGE_API_URL + f"/study/{cimar_study_json["namespace"]}/{cimar_study_json["study_uid"]}/image/{image["id"]}/version/{image["version"]}/frame/0/diagnostic", params={"sid": self.sid}).prepare()
+                instances.append({"metadata": {}, "url": f"dicomweb:{p.url}"})
+
+
+
+            new_json = {
+                "SeriesInstanceUID": series["series_uid"],
+                "SeriesDescription": series["description"],
+                "Modality": series["modality"],
+                "instances": instances
+            }
+            
+            series_json.append(new_json)
+
+        studies_json = {
+            "studies": [
+                {
+                    "StudyInstanceUID": "1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178",
+                    #"StudyDate": "20000101",
+                    "StudyTime": "",
+                    "PatientName": "Patient^Name",
+                    "PatientID": "LIDC-IDRI-0001",
+                    "AccessionNumber": "",
+                    "PatientAge": "",
+                    "PatientSex": "",
+                    "series": series_json,
+                }
+            ]
+
+        }
+
+        return studies_json
+
+    def get_session_user(self):
+        return self.post("/session/user")
+
+
+    def upload_dicom(self, file, study_uid=""):
+
+        if study_uid:
+            study_uid = f"&study_uid={study_uid}"
+
+        #data = {}
+
+        #data["sid"] = self.sid
+        #data["study_uid"] =  "1.2.840.113773.2.10070.7173.20210208144916.37"
+        #data["image_uid"]= "1.2.840.113773.4.10070.7173.20210208144916.39"
+
+        files = open(file, "rb")
+        #headers = {'content-type': 'application/dicom'}
+        r = requests.post(STORAGE_API_URL + f"/namespace/{self.namespace}/image?sid={self.sid}{study_uid}", data=files)#, headers=headers)
+        print(r)
+        return r.json()
+
+
+#CimarAdminApi = CimarAPI().login("")
+
+
+
+
+if __name__ == "__main__":
+    with CimarAPI(username="ross.kruger@nhs.net", password="") as api:
+        print("***")
+        #data = api.get_session_user()
+        #data = api.upload_dicom()
+
+
+        data = api.get_study_by_study_uid("2.1159655940009962407176401939062805636618")
+        print(data)
+    pass
+    #print(api.sid)
+    ##studies = api.list_studies()
+    ##test_study = studies["studies"][0]
+
+    ##schema = api.get_study_schema(test_study)
+
+    #schema = api.get_study_schema_by_uuid("c9417b53-87aa-4c40-aca0-3fa34c225536")
+
+    #api.get_study_dicom_json(schema)
+
+    #print(schema)
+    ##img = api.get_study_image_thumbnail(test_study)
+    
+
+
+class NoSession(Exception):
+    pass
+
+class InvalidCredentials(Exception):
+    pass
+
+class NotFoundError(Exception):
+    pass
+
+class APIError(Exception):
+    pass

rad/settings.py

@@ -315,6 +315,9 @@ STATICFILES_DIRS = (
     os.path.join(BASE_DIR, "rad", "static"), # That's it!!
 )
 
+CIMAR_USERNAME = ""
+CIMAR_PASSWORD = ""
+
 try:
     from .settings_local import *
 except ImportError as e:

rad/urls.py

@@ -158,6 +158,28 @@ urlpatterns = [
     path("ac/", autocomplete_urls),
     path('psutil/', psutil_urlpatterns(), name='psutil'),
     path("cimar/", views.cimar, name="cimar"),
+    path(
+        "cimar/study/<str:uuid>/dicom_json",
+        views.cimar_study_dicom_json,
+        name="cimar_study_dicom_json",
+    ),
+    path(
+        "cimar/study/<str:uuid>/viewer",
+        views.cimar_study_viewer,
+        name="cimar_study_viewer",
+    ),
+    path(
+        "cimar/study/<str:uuid>/viewer/embed",
+        views.cimar_study_viewer_embed,
+        name="cimar_study_viewer_embed",
+    ),
+    path(
+        "cimar/study/<str:uuid>/series_block",
+        views.cimar_study_series_block,
+        name="cimar_study_series_block",
+    ),
+
+    path("cimar/login/", views.cimar_login, name="cimar_login"),
 
 ]
 

rad/views.py

@@ -48,6 +48,7 @@ from anatomy.models import AnatomyQuestion
 from anatomy.models import Answer as AnatomyAnswer
 from rad.filters import UserListFilter
 
+from helpers.cimar import CimarAPI, InvalidCredentials, NoSession
 from rapids.models import UserAnswer as RapidsUserAnswer
 from rapids.models import Exam as RapidsExam
 from rapids.models import Rapid
@@ -65,7 +66,7 @@ from rapids.views import GenericExamViews as RapidsExamsViews
 from longs.views import GenericExamViews as LongsExamViews
 
 from generic.forms import QuestionNoteForm
-from generic.models import CidUser, ExamCollection, QuestionNote, Supervisor, UserGrades, UserProfile
+from generic.models import CidUser, CimarCase, ExamCollection, QuestionNote, Supervisor, UserGrades, UserProfile
 
 from django_filters.views import FilterView
 
@@ -919,3 +920,65 @@ def request_cid_details(request):
     return HttpResponse(
         f"Candidate details will be sent to the requested email (if it is found in the system). If you have not received an email after a few minutes you may need to contact <a href='mailto:{settings.CONTACT_EMAIL}'>{settings.CONTACT_EMAIL}</a>"
     )
+
+
+def cimar_study_dicom_json(request, uuid="c9417b53-87aa-4c40-aca0-3fa34c225536"):
+    with CimarAPI(request.user.userprofile.cimar_sid) as api:
+        print(api.sid)
+        #studies = api.list_studies()
+        #test_study = studies["studies"][0]
+
+        #schema = api.get_study_schema(test_study)
+
+        schema = api.get_study_schema_by_uuid("c9417b53-87aa-4c40-aca0-3fa34c225536")
+
+        return JsonResponse(api.get_study_dicom_json(schema))
+
+def cimar_study_viewer(request, uuid="c9417b53-87aa-4c40-aca0-3fa34c225536"):
+
+        case = get_object_or_404(CimarCase, uuid=uuid)
+            
+        viewer_link = case.viewer_link + f"?sid={request.user.userprofile.cimar_sid}"
+        return render(request, "cimar_embed.html", {"viewer_link": viewer_link})
+
+def cimar_study_viewer_embed(request, uuid="c9417b53-87aa-4c40-aca0-3fa34c225536"):
+
+        case = get_object_or_404(CimarCase, uuid=uuid)
+            
+        viewer_link = case.viewer_link + f"?sid={request.user.userprofile.cimar_sid}"
+        return render(request, "cimar_embed.html#embed", {"viewer_link": viewer_link})
+
+def cimar_study_series_block(request, uuid):
+
+        case = get_object_or_404(CimarCase, uuid=uuid)
+            
+        return render(request, "cimar_series.html", {"series_data": case.series_data["series"], "cimar_sid": request.user.userprofile.cimar_sid})
+
+def cimar_login(request):
+
+    if request.htmx:
+        username = request.POST.get("username")
+        password = request.POST.get("password")
+
+
+
+        if not username and not password:
+            return HttpResponse("Please fill in login details")
+
+        try:
+            sid = CimarAPI().login(username, password)
+
+            request.user.userprofile.cimar_sid = sid
+            request.user.userprofile.save()
+        except InvalidCredentials:
+            return HttpResponse("Invalid login details")
+
+
+        return HttpResponse("Logged in")
+
+    else:
+        try:
+            login_status = CimarAPI(request.user.userprofile.cimar_sid).check_login_status()
+        except NoSession:
+            login_status = False
+        return render(request, "cimar_login.html", {"login_status": login_status, "cimar_sid": request.user.userprofile.cimar_sid})

requirements.txt

@@ -54,3 +54,5 @@ psutil
 django-psutil-dash
 django-template-partials
 easy_thumbnails
+requests
+pygments

templates/cimar_embed.html

@@ -0,0 +1,39 @@
+{% extends 'base.html' %}
+{% load partials %}
+
+{% partialdef viewer %}
+    <div style="height: 100vh; width: 95%, mangin: 0; padding: 0; overflow: hidden;">
+
+        
+        <iframe  class="embedded-viewer" src="{{viewer_link}}" width="100%" height="95%" style="border:none;"></iframe>
+
+    </div>
+
+<style>
+    .embedded-viewer {
+        border: none;
+        pointer-events: auto;
+        margin: 0; height: 100%; overflow: hidden
+    }
+</style>
+    
+{% endpartialdef %}
+
+{% partialdef embed %}
+Close
+
+{% partial viewer %}
+    
+{% endpartialdef %}
+
+
+{% block content %}
+{% partial viewer %}
+    
+{% endblock content %}
+    
+
+{% block css %}
+    
+{% endblock css %}
+    

templates/cimar_login.html

@@ -0,0 +1,23 @@
+{% extends 'base.html' %}
+
+{% block content %}
+    <div class="anatomy">
+
+        
+ <h2>CIMAR login</h2>
+Login status: {{ login_status }} ({{cimar_sid}})<br/> 
+
+ Logging in here allows your account to be linked with CIMAR. You may periodically need to re-login to keep the link active.
+ <form method="POST" class="post-form">
+ Username: <input type="text" id="username" name="username" value=""/> <br/>
+Password: <input type="password" id="password" name="password" value=""/> <br/>
+<button hx-post='{% url "cimar_login" %}'
+hx-target="#results">Login</button>
+ </form>
+
+ <div id="results"></div>
+        
+
+
+    </div>
+{% endblock %}

templates/cimar_series.html

@@ -0,0 +1,15 @@
+<h3>Series</h3>
+        <div class="pre-whitespace multi-image-block"><b>Series:</b>
+                {% for series in series_data %}
+     <span class="series-block">
+                        <span>
+                            <span class="series-block-series-number">Series {{ forloop.counter }}:</span><br>
+                                            <span>
+            <span class='series-block-examination'>{{series|get_item:"series_description"}}</span><br/>
+            <span class='series-block-thumbnail'><img src='{{series|get_item:"thumbnail"}}?{{cimar_sid}}' /></span><br/>
+            <span class='series-block-image-number'>Images: <span class='series-block-image-number-count'>{{series|get_item:"image_count"}}</span></span>
+            </span>
+                        </span>
+                    </span>
+                {% endfor %}
+</div>