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jupyterhealth-exchange/apis.md

@@ -8,7 +8,7 @@ title: Working with APIs
 - The Patient authorization code is generated by the server and then shared out-of-band as a secret link with the user.
 - OAuth is configured from the Django Admin page (See Getting Started above).
 - Endpoints and configuration details can be discovered from the OIDC metadata endpoint:
-    `/o/.well-known/openid-configuration`
+  `/o/.well-known/openid-configuration`
 - The returned Access Token should be included in the `Authorization` header for all API requests with the prefix `Bearer `.
 - Because the Patient authorization code is generated by the server, the PKCE code challenge and code verifier must be static values and set by the env vars (example below). The client then sends this `code_verifier` along with the authorization code to obtain tokens.
 
@@ -123,7 +123,7 @@ code=4AWKhgaaomTSf9PfwxN4ExnXjdSEqh&grant_type=authorization_code&redirect_uri=h
     }
   ]
 }
-  
+
 ```
 
 - A `PATCH` request can be sent with the same payload to update an existing Consent
@@ -135,10 +135,10 @@ code=4AWKhgaaomTSf9PfwxN4ExnXjdSEqh&grant_type=authorization_code&redirect_uri=h
 
 - The `FHIR Patient` endpoint returns a list of Patients as a FHIR Bundle for a given Study ID passed as query parameter`_has:Group:member:_id` or alternatively a single Patient matching the query parameter `identifier=<system>|<value>`
 
-| Query Parameter         | Example                         | Description                                                  |
-| ----------------------- | ------------------------------- | ------------------------------------------------------------ |
-| `_has:Group:member:_id` | `30001`                         | Filter by Patients that are in the Study with ID 30001       |
-| `identifier`            | `http://ehr.example.com|abc123` | Filter by single Patient with Identifier System `http://ehr.example.com` and Value `abc123` |
+| Query Parameter         | Example                  | Description                                            |
+| ----------------------- | ------------------------ | ------------------------------------------------------ |
+| `_has:Group:member:_id` | `30001`                  | Filter by Patients that are in the Study with ID 30001 |
+| `identifier`            | \`http://ehr.example.com | abc123\`                                               |
 
 ```json
 // GET /fhir/r5/Patient?_has:Group:member:_id=30001
@@ -191,14 +191,12 @@ code=4AWKhgaaomTSf9PfwxN4ExnXjdSEqh&grant_type=authorization_code&redirect_uri=h
 - `device.reference` references a Data Source ID
 - `valueAttachment` is Base 64 Encoded Binary JSON
 
-| Query Parameter                 | Example                                               | Description                                                  |
-| ------------------------------- | ----------------------------------------------------- | ------------------------------------------------------------ |
-| `patient._has:Group:member:_id` | `30001`                                               | Filter by Patients that are in the Study with ID 30001       |
-| `patient`                       | `40001`                                               | Filter by single Patient with ID 40001                       |
-| `patient.identifier`            | `http://ehr.example.com|abc123`                       | Filter by single Patient with Identifier System `http://ehr.example.com` and Value `abc123` |
-| `code`                          | `https://w3id.org/openmhealth|omh:blood-pressure:4.0` | Filter by Type/Scope with System `https://w3id.org/openmhealth` and Code `omh:blood-pressure:4.0` |
-
-
+| Query Parameter                 | Example                        | Description                                            |
+| ------------------------------- | ------------------------------ | ------------------------------------------------------ |
+| `patient._has:Group:member:_id` | `30001`                        | Filter by Patients that are in the Study with ID 30001 |
+| `patient`                       | `40001`                        | Filter by single Patient with ID 40001                 |
+| `patient.identifier`            | \`http://ehr.example.com       | abc123\`                                               |
+| `code`                          | \`https://w3id.org/openmhealth | omh:blood-pressure:4.0\`                               |
 
 ```json
 // GET /fhir/r5/Observation?patient._has:Group:member:_id=30001&patient=40001&code=https://w3id.org/openmhealth|omh:blood-pressure:4.0
@@ -286,4 +284,4 @@ code=4AWKhgaaomTSf9PfwxN4ExnXjdSEqh&grant_type=authorization_code&redirect_uri=h
       }
     },
     ...
-```
+```

jupyterhealth-exchange/architecture.md

@@ -14,7 +14,9 @@ Django is a mature and well-supported web framework but was specifically chosen
 ### DRF Serializers and Pydantic
 
 - The Django Rest Framework uses the concept of Serializers to validate schemas, whereas the FHIR validator uses Pydantic.
+
 - It is not reasonable to re-write the entire validation in the Serializer, so instead a combination of the two are used:
+
   - Top-level fields (most importantly the `id` of a record) are managed by the Serializer.
   - Nested fields (for example `code{}.coding[].system` above) are configured as a JSON field in the Serializer (so the top level field is this example is `code`) and then Pydantic is used to validate the whole schema including nested JSON.
 
@@ -111,7 +113,7 @@ erDiagram
         int study_id
         int user_id
     }
-    
+
     "observations (FHIR Observation)" ||--|| "codeable_concepts (FHIR CodeableConcept)": ""
     "observations (FHIR Observation)" ||--|{ "observation_identifiers": ""
     "observations (FHIR Observation)" ||--|| "data_sources": ""
@@ -129,7 +131,7 @@ erDiagram
         varchar system
         varchar value
     }
-    
+
     "studies (FHIR Group)" ||--|{ "study_patients": ""
     "codeable_concepts (FHIR CodeableConcept)" {
         int id
@@ -144,7 +146,7 @@ erDiagram
         enum scope_action
         int scope_code_id
         bool consented
-        timestamp consented_time       
+        timestamp consented_time
     }
     "data_sources" ||--|{ "data_source_supported_scopes": ""
     "data_sources" ||--|{ "study_data_sources": ""

jupyterhealth-exchange/developer-setup.md

@@ -6,7 +6,7 @@ This guide provides a comprehensive walkthrough for setting up your development
 
 ## Step by Step
 
-1. Set up your Python environment. This project uses Django **version 5.2** which requires python  **3.10, 3.11, 3.12 or 3.13**.
+1. Set up your Python environment. This project uses Django **version 5.2** which requires python **3.10, 3.11, 3.12 or 3.13**.
    ```{note}
    If using pipenv it is recommended to run `pipenv sync` against the lock file to match package versions.
    ```
@@ -41,18 +41,20 @@ This guide provides a comprehensive walkthrough for setting up your development
    import random
    import string
 
+
    def generate_pkce_verifier(length=44):
        characters = string.ascii_letters + string.digits
-       return ''.join(random.choices(characters, k=length))
+       return "".join(random.choices(characters, k=length))
+
 
    print(generate_pkce_verifier())
    ```
 1. Use the PKCE verifier to generate the [PKCE code challenge](https://tonyxu-io.github.io/pkce-generator).
 1. Return to the `.env` file
-    - Update `OIDC_CLIENT_ID` with the newly created app Client ID
-    - Update the `OIDC_RSA_PRIVATE_KEY` with the newly created Private Key
-    - Update `PATIENT_AUTHORIZATION_CODE_CHALLENGE` and `PATIENT_AUTHORIZATION_CODE_VERIFIER` with PKCE static values generated above
-    - Restart the python environment and Django server
+   - Update `OIDC_CLIENT_ID` with the newly created app Client ID
+   - Update the `OIDC_RSA_PRIVATE_KEY` with the newly created Private Key
+   - Update `PATIENT_AUTHORIZATION_CODE_CHALLENGE` and `PATIENT_AUTHORIZATION_CODE_VERIFIER` with PKCE static values generated above
+   - Restart the python environment and Django server
 1. Browse to http://localhost:8000/ and log in with the credentials `[email protected]` `Jhe1234!`and you should be directed to the `/portal/organizations` path with some example Organizations is the dropdown.
 
 ```{note} Static PKCE Values
@@ -69,19 +71,21 @@ It is understood this runs against best practices; however, this is only used fo
 After logging in on Windows, users are redirected to the portal, but a blank screen persists. This issue seems related to the `oidc-client-ts` library but is actually due to incorrectly set environment variables on Windows.
 
 #### Cause
+
 On Windows systems (particularly when running Django via Visual Studio Code or Git Bash), the environment variables related to OIDC in `settings.py` may become incorrectly formatted. This causes URLs to be malformed, preventing proper authentication.
 
 #### Examples of Incorrectly Set Values
-- `OIDC_CLIENT_REDIRECT_URI`:  
+
+- `OIDC_CLIENT_REDIRECT_URI`:
   http://localhost:8000C:/Program Files/Git/auth/callback
-- `OIDC_CLIENT_AUTHORITY`:  
+- `OIDC_CLIENT_AUTHORITY`:
   http://localhost:8000O://
 
 #### Solution
 
 The solution is to explicitly hardcode the correct values to OIDC variables in your `settings.py`. This will prevent incorrect path injections and ensure proper URL formation, resolving the blank screen issue after login on Windows machines.
 
 ```python
-OIDC_CLIENT_REDIRECT_URI = 'http://localhost:8000/auth/callback'
-OIDC_CLIENT_AUTHORITY = 'http://localhost:8000/o/'
-```
+OIDC_CLIENT_REDIRECT_URI = "http://localhost:8000/auth/callback"
+OIDC_CLIENT_AUTHORITY = "http://localhost:8000/o/"
+```

jupyterhealth-exchange/overview.md

@@ -7,8 +7,10 @@ JupyterHealth Exchange is a Django web application that facilitates the sharing
 In the context of JupyterHealth, data producers are typically study participants (FHIR *Patients*) using the [CommonHealth Android App](https://play.google.com/store/apps/details?id=org.thecommonsproject.android.phr) linked to personal devices (e.g., Glucose Monitors), and data consumers are typically researchers (FHIR *Practitioners*).
 
 ```{image} ../assets/images/jupyterhealth-exchange-overview.jpg
-:alt: Diagram of application components
-:width: 800px
+---
+alt: Diagram of application components
+width: 800px
+---
 ```
 
 ## Features
@@ -20,4 +22,4 @@ In the context of JupyterHealth, data producers are typically study participants
 
 ## Status
 
-This project is currently in a Proof of Concept stage. You can monitor progress in our [GitHub Project](https://github.com/orgs/the-commons-project/projects/8).
+This project is currently in a Proof of Concept stage. You can monitor progress in our [GitHub Project](https://github.com/orgs/the-commons-project/projects/8).

jupyterhealth-exchange/security.md

@@ -81,5 +81,7 @@ This will allow per-user access control, registered and enforced by SMART-on-FHI
 ## Data Flow Diagram
 
 ```{image} ../assets/images/CHCS-Architecture.png
-:alt: CHCS Architecture
-```
+---
+alt: CHCS Architecture
+---
+```

jupyterhealth-exchange/web-ui.md

@@ -38,12 +38,12 @@ title: Web User Interface
 ## Use Case Example
 
 1. Sign up as a new user from the web UI.
-2. Create a new Organization.
-3. Add yourself to the Organization (View Organization > Users+).
-4. Create a new Study for the Organization (View Organization > Studies+).
-5. Create a new Patient for the Organization using a different email than (1) (Patients > Add Patient).
-6. Add Data Sources and Scopes to the Study (View Study > Data Sources+, Scope Requests+).
-7. Add the Patient to the Study (Patients > check box > Add Patient(s) to Study).
-8. Create an Invitation Link for the Patient (View Patient > Generate Invitation Link).
-9. Use the code in the invitation link with the Auth API to swap it for tokens.
-10. Upload Observations using the FHIR API.
+1. Create a new Organization.
+1. Add yourself to the Organization (View Organization > Users+).
+1. Create a new Study for the Organization (View Organization > Studies+).
+1. Create a new Patient for the Organization using a different email than (1) (Patients > Add Patient).
+1. Add Data Sources and Scopes to the Study (View Study > Data Sources+, Scope Requests+).
+1. Add the Patient to the Study (Patients > check box > Add Patient(s) to Study).
+1. Create an Invitation Link for the Patient (View Patient > Generate Invitation Link).
+1. Use the code in the invitation link with the Auth API to swap it for tokens.
+1. Upload Observations using the FHIR API.