Merge pull request #48 from minrk/npm

minrk · web-flow · commit e2e937c7e7f4 · 2025-10-09T10:17:33.000-07:00
freeze mystmd version with package-lock.json
diff --git a/.github/dependabot.yaml b/.github/dependabot.yaml
@@ -4,6 +4,8 @@ updates:
   - package-ecosystem: github-actions
     directory: /
     schedule:
-      interval: monthly
-      time: "05:00"
-      timezone: Etc/UTC
+      interval: daily
+  - package-ecosystem: npm
+    directory: /
+    schedule:
+      interval: weekly
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -33,11 +33,11 @@ jobs:
         uses: actions/configure-pages@v5
       - uses: actions/setup-node@v5
         with:
-          node-version: 18.x
+          node-version: 24.x
       - name: Install MyST Markdown
-        run: npm install -g mystmd
+        run: npm ci
       - name: Build HTML Assets
-        run: myst build --html
+        run: npm run myst build --html
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v4
         with:
diff --git a/.github/workflows/test-docs.yaml b/.github/workflows/test-docs.yaml
@@ -0,0 +1,27 @@
+name: test docs
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  test-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - uses: actions/setup-node@v5
+        with:
+          node-version: 24.x
+      - name: Install
+        run: npm ci
+      - name: Check links
+        run: npm test
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: './_build/html'
diff --git a/.gitignore b/.gitignore
@@ -161,3 +161,5 @@ cython_debug/
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
 .DS_Store
+
+node_modules
diff --git a/contributing/developer-setup.md b/contributing/developer-setup.md
@@ -77,9 +77,9 @@ On Windows systems (particularly when running Django via Visual Studio Code or G
 #### Examples of Incorrectly Set Values
 
 - `OIDC_CLIENT_REDIRECT_URI`:
-  http://localhost:8000C:/Program Files/Git/auth/callback
+  `http://localhost:8000C:/Program Files/Git/auth/callback`
 - `OIDC_CLIENT_AUTHORITY`:
-  http://localhost:8000O://
+  `http://localhost:8000O://`
 
 #### Solution
 
diff --git a/explanation/cloud-storage-reference-app.md b/explanation/cloud-storage-reference-app.md
@@ -318,9 +318,6 @@ Information on the previous CHCS service utilized for the Preliminary Blood Pres
 
 - [Tech Design Doc](https://docs.google.com/document/d/1jyS6A78BfAVTRzmwBRAim5MyQUOUHa_T7rm9tbzWLaE/edit?usp=sharing)
 - [Example Requests and Responses](https://docs.google.com/document/d/1Q9cFnwGLdWdcwGE8p6O9TS7LwKzYeseY0UAuZxJ2xw0/edit?usp=sharing)
-- [CommonHealth-CloudStorage README](https://github.com/the-commons-project/CommonHealth-CloudStorage/tree/main)
-- [chcs-partner-client README](https://github.com/the-commons-project/chcs-partner-client)
-- [chcs-partner-client-docker README](https://github.com/the-commons-project/chcs-partner-client-docker)
 
 ## Previous CHCS Flow
 
diff --git a/explanation/exchange-overview.md b/explanation/exchange-overview.md
@@ -2,7 +2,7 @@
 title: Overview
 ---
 
-JupyterHealth Exchange is a Django web application that facilitates the sharing of user-consented medical data with authorized consumers through a [web UI](web-ui), [REST, and FHIR APIs](apis).
+JupyterHealth Exchange is a Django web application that facilitates the sharing of user-consented medical data with authorized consumers through a web UI, REST, and FHIR APIs.
 
 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*).
 
diff --git a/explanation/index.md b/explanation/index.md
@@ -1,6 +1,6 @@
 # Explanations
 
-Here we will have [explanations](https://diataxis.fr/explanations/) for learning about JupyterHealth.
+Here we will have [explanations](https://diataxis.fr/explanation/) for learning about JupyterHealth.
 
 > Explanation is a discursive treatment of a subject, that permits reflection. Explanation is understanding-oriented.
 
diff --git a/myst.yml b/myst.yml
@@ -28,7 +28,13 @@ project:
     - title: Contributing
       children:
         - pattern: contributing/*
-
+  error_rules:
+    # check-links error ignores
+    - rule: link-resolves
+      severity: ignore
+      keys:
+        - "http://localhost:8000/"
+        - "http://localhost:8000/admin"
 site:
   template: book-theme
   title: JupyterHealth Software
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -0,0 +1,11 @@
+{
+  "name": "jupyter-health-software-documentation",
+  "version": "0.0.0",
+  "scripts": {
+    "myst": "myst",
+    "test": "myst build --html --check-links --strict"
+  },
+  "dependencies": {
+    "mystmd": "^1.6.2"
+  }
+}
diff --git a/reference/security.md b/reference/security.md
@@ -48,7 +48,7 @@ In the demonstration, all JupyterHealth Exchange users are equivalent permission
 Users are authenticated as themselves and only have access to patient data associated with studies run by their Organization.
 However, currently all JHE users have full permission to manage Organizations, so effectively **all authenticated users have full access to all data in Exchange**.
 
-Following the pre-MVP, appropriate access controls will be [implemented](https://github.com/the-commons-project/jupyterhealth-exchange/issues/7) in the Exchange.
+Following the pre-MVP, appropriate access controls will be [implemented](https://github.com/jupyterhealth/jupyterhealth-exchange/issues/7) in the Exchange.
 
 ## Data Flow Diagram
 
diff --git a/tutorial/exchange-on-kubernetes.md b/tutorial/exchange-on-kubernetes.md
@@ -5,7 +5,7 @@ downloads:
     title: Example kubernetes resources
 ---
 
-This page documents how to deploy the [jupyterhealth-exchange](https://github.com/the-commons-project/jupyterhealth-exchange) application onto a kubernetes cluster running on AWS. In this case, the associated JupyterHub happened to also be running on AWS, but in a different AWS account.
+This page documents how to deploy the [jupyterhealth-exchange](https://github.com/jupyterhealth/jupyterhealth-exchange) application onto a kubernetes cluster running on AWS. In this case, the associated JupyterHub happened to also be running on AWS, but in a different AWS account.
 
 ## Create the Kubernetes Cluster
 
@@ -97,7 +97,7 @@ helm install \
 
 ### Install the Application
 
-Finally, install the application into the cluster. [jhe-example.yml](examples/jhe-example.yml) is provided as example kubernetes configuration, although you will need to substitute values appropriate for your deployment.
+Finally, install the application into the cluster. [jhe-example.yaml](./examples/jhe-example.yaml) is provided as example kubernetes configuration, although you will need to substitute values appropriate for your deployment.
 
 ```shell-session
 kubectl apply -f jhe-example.yml
@@ -227,9 +227,9 @@ kubectl apply -f job-manage-migrate.yml
 
 ### Seed the Database
 
-This requires the [seed.sql](https://github.com/the-commons-project/jupyterhealth-exchange/blob/main/db/seed.sql) file from the [jupyterhealth-exchange repository](https://github.com/the-commons-project/jupyterhealth-exchange), and a new python script, `jhe/scripts/seed.py` to import it. `seed.py` is currently available in a [pull request to jupyterhealth-exchange](https://github.com/the-commons-project/jupyterhealth-exchange/pull/37/files).
+**((OUTDATED))**
 
-Injest them as ConfigMaps by running the following commands from within the working directory of [jupyterhealth-exchange](https://github.com/the-commons-project/jupyterhealth-exchange).
+Seed the database (needs update):
 
 ```shell-session
 kubectl -n jhe create configmap db-seed-sql --from-file=db/seed.sql
@@ -282,19 +282,19 @@ kubectl apply -f job-import-seed.yml
 
 ## Administering JHE
 
-1. Login to your JupyterHealth Exchange app, https://jhe.example.org/admin/
+1. Login to your JupyterHealth Exchange app, `https://jhe.example.org/admin/`
 
 1. Under Django OAuth Toolkit, add application
 
    a. Save the value of `Client id` into the `jhe-config` ConfigMap in `jhe-example.yml` under `OIDC_CLIENT_ID`.
 
    b. Add space-separated redirect uris for hubs
 
-   - http://localhost:8000/auth/callback
-   - https://jupyterhub.example.org/hub/oauth_callback
-   - https://jupyterhub.example.org/services/smart/oauth_callback
-   - https://jupyterhub.example.org/user-redirect/smart/oauth_callback
-   - https://jhe.example.org/auth/callback
+   - `http://localhost:8000/auth/callback`
+   - `https://jupyterhub.example.org/hub/oauth_callback`
+   - `https://jupyterhub.example.org/services/smart/oauth_callback`
+   - `https://jupyterhub.example.org/user-redirect/smart/oauth_callback`
+   - `https://jhe.example.org/auth/callback`
 
    c. Client type: Public
 
