hms-dbmi · b32147 · Jul 1, 2024 · Feb 7, 2024 · Mar 25, 2024 · Jun 28, 2024
diff --git a/app/api/urls.py b/app/api/urls.py
@@ -9,7 +9,7 @@
 # Wire up our API using automatic URL routing.
 # Additionally, we include login URLs for the browsable API.
 urlpatterns = [
-    re_path(r'^consent/(?P<study>[\w\d-]+)/(?P<ppm_id>[\d]+)/?$', views.ConsentView.as_view(), name='consent'),
+    re_path(r'^consent/(?P<study>[\w\d-]+)/(?P<ppm_id>[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}|[\d]+)/?$', views.ConsentView.as_view(), name='consent'),
     re_path(r'^consent/(?P<study>[\w\d-]+)/?$', views.ConsentsView.as_view(), name='consents'),
     re_path(r'^questionnaire/?$', views.QuestionnaireView.as_view(), name='questionnaire'),
     re_path(r'^questionnaire/(?P<questionnaire_id>[\w\d-]+)/?$', views.QuestionnaireView.as_view(), name='questionnaire'),

diff --git a/app/api/views.py b/app/api/views.py
@@ -49,7 +49,7 @@ def get(self, request, study, ppm_id, format=None):
 
         try:
             # Check patient
-            if not FHIR.query_patient(patient=ppm_id):
+            if not FHIR.get_patient(patient=ppm_id):
                 return Response(f'Participant {ppm_id} does not exist', status=status.HTTP_404_NOT_FOUND)
 
             # Check FHIR
@@ -82,7 +82,7 @@ def post(self, request, study, ppm_id=None, format=None):
 
         try:
             # Check patient
-            if not FHIR.query_patient(patient=ppm_id):
+            if not FHIR.get_patient(patient=ppm_id):
                 return Response(f'Participant {ppm_id} does not exist', status=status.HTTP_404_NOT_FOUND)
 
             # Check if we should overwrite
@@ -140,18 +140,8 @@ def delete_consent_document_reference(request, study, ppm_id, document_reference
             # Get their consent composition
             composition = FHIR.get_consent_composition(patient=ppm_id, study=study)
             if not composition:
-                compositions = FHIR.query_consent_compositions(patient=ppm_id)
-                if not compositions:
-                    logger.error(f'PPM/{study}/{ppm_id}: No consent compositions')
-                    return False
-
-                elif len(compositions) > 1:
-                    logger.error(f'PPM/{study}/{ppm_id}: Too many generic consent '
-                                 f'compositions: {[r["resource"]["id"] for r in compositions]}')
-                    return False
-
-                else:
-                    composition = compositions[0]
+                logger.error(f'PPM/{study}/{ppm_id}: No consent compositions')
+                return False
 
             # Update it
             if FHIR.update_consent_composition(patient=ppm_id, study=study, composition=composition):
@@ -189,7 +179,7 @@ def create_consent_document_reference(request, study, ppm_id=None):
             ppm_id = FHIR.query_patient_id(get_jwt_email(request=request, verify=False))
 
         # Pull their record
-        bundle = FHIR.query_participant(patient=ppm_id, flatten_return=True)
+        participant = FHIR.get_participant(patient=ppm_id, flatten_return=True)
 
         # Get study title
         study_title = PPM.Study.title(study)
@@ -204,7 +194,7 @@ def create_consent_document_reference(request, study, ppm_id=None):
         # Submit consent PDF
         logger.debug(f"PPM/{study}: Rendering consent with template: {template_name}")
         response = render_pdf(f'People-Powered Medicine {study_title} Consent', request, template_name,
-                              context=bundle.get('composition'), options={})
+                              context=participant.get('composition'), options={})
 
         # Hash the content
         hash = hashlib.md5(response.content).hexdigest()
@@ -409,9 +399,9 @@ def get(self, request, questionnaire_id=None, format=None):
         if questionnaire_id:
 
             # Try to fetch it
-            questionnaire = FHIR.get_questionnaire(
-                questionnaire_id=questionnaire_id,
-                flatten_return=False
+            questionnaire = FHIR.fhir_read(
+                resource_type="Questionnaire",
+                resource_id=questionnaire_id,
             )
 
             # Return it or 404

diff --git a/app/consent/fhir/example-signature.json b/app/consent/fhir/example-signature.json
@@ -6,6 +6,33 @@
   "subjectType": [
     "patient"
   ],
+  "useContext": [
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "program",
+        "display": "Program"
+      },
+       "valueReference": {"reference": "ResearchStudy/ppm-example"}
+    },
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "task",
+        "display": "Workflow Task"
+      },
+       "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://peoplepoweredmedicine.org/fhir/questionnaire/context",
+            "code": "ppm-example",
+            "display": "ppm-example"
+          }
+        ],
+        "text": "ppm-example"
+      }
+    }
+  ],
   "item": [
     {
       "linkId": "display-1",

diff --git a/app/consent/fhir/guardian-signature-part-1.json b/app/consent/fhir/guardian-signature-part-1.json
@@ -14,6 +14,33 @@
   "subjectType": [
     "patient"
   ],
+  "useContext": [
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "program",
+        "display": "Program"
+      },
+       "valueReference": {"reference": "ResearchStudy/ppm-asd"}
+    },
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "task",
+        "display": "Workflow Task"
+      },
+       "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://peoplepoweredmedicine.org/fhir/questionnaire/context",
+            "code": "ppm-asd",
+            "display": "ppm-asd"
+          }
+        ],
+        "text": "ppm-asd"
+      }
+    }
+  ],
   "item": [
     {
       "linkId": "display-1",

diff --git a/app/consent/fhir/guardian-signature-part-2.json b/app/consent/fhir/guardian-signature-part-2.json
@@ -14,6 +14,33 @@
   "subjectType": [
     "patient"
   ],
+  "useContext": [
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "program",
+        "display": "Program"
+      },
+       "valueReference": {"reference": "ResearchStudy/ppm-asd"}
+    },
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "task",
+        "display": "Workflow Task"
+      },
+       "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://peoplepoweredmedicine.org/fhir/questionnaire/context",
+            "code": "ppm-asd",
+            "display": "ppm-asd"
+          }
+        ],
+        "text": "ppm-asd"
+      }
+    }
+  ],
   "item": [
     {
       "linkId": "display-1",
@@ -23,9 +50,9 @@
     {
       "linkId": "question-1",
       "text": "I acknowledge that I have explained this study to my child or individual in my care who will be participating.",
-      "type": "question",
+      "type": "choice",
       "required": true,
-      "option": [
+      "answerOption": [
         {
           "valueString": "yes"
         },
@@ -41,7 +68,8 @@
           "enableWhen": [
             {
               "question": "question-1",
-              "answerString": "no"
+              "answerString": "no",
+              "operator": "="
             }
           ],
           "required": true

diff --git a/app/consent/fhir/guardian-signature-part-3.json b/app/consent/fhir/guardian-signature-part-3.json
@@ -6,6 +6,33 @@
   "subjectType": [
     "patient"
   ],
+  "useContext": [
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "program",
+        "display": "Program"
+      },
+       "valueReference": {"reference": "ResearchStudy/ppm-asd"}
+    },
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "task",
+        "display": "Workflow Task"
+      },
+       "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://peoplepoweredmedicine.org/fhir/questionnaire/context",
+            "code": "ppm-asd",
+            "display": "ppm-asd"
+          }
+        ],
+        "text": "ppm-asd"
+      }
+    }
+  ],
   "item": [
     {
       "linkId": "display-1",

diff --git a/app/consent/fhir/individual-signature-part-1.json b/app/consent/fhir/individual-signature-part-1.json
@@ -14,6 +14,33 @@
   "subjectType": [
     "patient"
   ],
+  "useContext": [
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "program",
+        "display": "Program"
+      },
+       "valueReference": {"reference": "ResearchStudy/ppm-asd"}
+    },
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "task",
+        "display": "Workflow Task"
+      },
+       "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://peoplepoweredmedicine.org/fhir/questionnaire/context",
+            "code": "ppm-asd",
+            "display": "ppm-asd"
+          }
+        ],
+        "text": "ppm-asd"
+      }
+    }
+  ],
   "item": [
     {
       "linkId": "display-1",

diff --git a/app/consent/fhir/neer-signature-v2.json b/app/consent/fhir/neer-signature-v2.json
@@ -14,6 +14,33 @@
   "subjectType": [
     "patient"
   ],
+  "useContext": [
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "program",
+        "display": "Program"
+      },
+       "valueReference": {"reference": "ResearchStudy/ppm-neer"}
+    },
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "task",
+        "display": "Workflow Task"
+      },
+       "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://peoplepoweredmedicine.org/fhir/questionnaire/context",
+            "code": "ppm-neer",
+            "display": "ppm-neer"
+          }
+        ],
+        "text": "ppm-neer"
+      }
+    }
+  ],
   "item": [
     {
       "linkId": "display-1",

diff --git a/app/consent/fhir/neer-signature-v3.json b/app/consent/fhir/neer-signature-v3.json
@@ -14,6 +14,33 @@
   "subjectType": [
     "patient"
   ],
+  "useContext": [
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "program",
+        "display": "Program"
+      },
+       "valueReference": {"reference": "ResearchStudy/ppm-neer"}
+    },
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "task",
+        "display": "Workflow Task"
+      },
+       "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://peoplepoweredmedicine.org/fhir/questionnaire/context",
+            "code": "ppm-neer",
+            "display": "ppm-neer"
+          }
+        ],
+        "text": "ppm-neer"
+      }
+    }
+  ],
   "item": [
     {
       "linkId": "display-1",

diff --git a/app/consent/fhir/neer-signature.json b/app/consent/fhir/neer-signature.json
@@ -14,6 +14,33 @@
   "subjectType": [
     "patient"
   ],
+  "useContext": [
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "program",
+        "display": "Program"
+      },
+       "valueReference": {"reference": "ResearchStudy/ppm-neer"}
+    },
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "task",
+        "display": "Workflow Task"
+      },
+       "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://peoplepoweredmedicine.org/fhir/questionnaire/context",
+            "code": "ppm-neer",
+            "display": "ppm-neer"
+          }
+        ],
+        "text": "ppm-neer"
+      }
+    }
+  ],
   "item": [
     {
       "linkId": "display-1",