Merge branch 'main' into bob/2663-query-flow-redirect

.github/pull_request_template.md

@@ -1,19 +1,27 @@
 # PULL REQUEST
 
 ## Summary
+
 What changes are being proposed?
 
 ## Related Issue
+
 Fixes #
 
 ## Acceptance Criteria
+
 Please copy the acceptance criteria from your ticket and paste it here for your reviewer(s)
 
+For frontend PR’s - include a description (including anything that’s out of scope) for what you want the designers to review
+
+- ex: _“Check out the whitespace on the page, as well as the dropdowns in the form. Here is the corresponding Figma link. You can ignore everything else. Also, the button at the bottom doesn’t work now”_
+
 ## Additional Information
+
 Anything else the review team should know?
 
 ## Checklist
 
 - [ ] If this code affects the other scrum team, have they been notified? (In Slack, as reviewers, etc.)
 
-[//]: # (PR title: Remember to name your PR descriptively!)
+[//]: # "PR title: Remember to name your PR descriptively!"

.github/workflows/container-tefca-viewer.yaml

@@ -50,30 +50,6 @@ jobs:
         working-directory: ./containers/${{env.CONTAINER}} # Navigate to your Node.js app directory
         run: npm test
 
-  build-container:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-
-      - name: Check Out Changes
-        uses: actions/checkout@v4
-
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-
-      - name: Build ${{ env.CONTAINER }} Container
-        uses: docker/build-push-action@v3
-        with:
-          context: .
-          file: ./containers/${{ env.CONTAINER }}/Dockerfile
-          push: false
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
-
   playwright-tests:
     timeout-minutes: 10
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -1,19 +1,19 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.7
+    rev: v0.6.9
     hooks:
       # Run the linter.
       - id: ruff
         args: [--fix]
       # Run the formatter.
       - id: ruff-format
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: pretty-format-json
         args: [--autofix, --no-sort-keys]
   - repo: https://github.com/pre-commit/mirrors-eslint
-    rev: "v9.9.0"
+    rev: "v9.12.0"
     hooks:
       - id: eslint
         name: ESLint for ECR Viewer

containers/tefca-viewer/Dockerfile

@@ -1,29 +1,16 @@
 FROM node:18-alpine AS base
 
-FROM base AS builder
-# Install necessary packages for building
+FROM base AS installer
+
 RUN apk update
 RUN apk add --no-cache libc6-compat
+RUN apk add --no-cache bash curl
 
-# Set working directory
 WORKDIR /app
-RUN npm i -g turbo
 COPY . .
-ENV TURBO_TELEMETRY_DISABLED=1
-RUN turbo prune tefca-viewer --docker
-
-# Add lockfile and package.json's of isolated subworkspace
-FROM base AS installer
-RUN apk update
-RUN apk add --no-cache libc6-compat
-WORKDIR /app
-
-ENV FLYWAY_VERSION=10.19.0
-
-# Add bash to enable running Flyway
-RUN apk add --no-cache bash curl
 
 # Install Flyway and remove JRE directory to force flyway to use the openjdk11 version in the runner
+ENV FLYWAY_VERSION=10.19.0
 RUN curl -L https://repo1.maven.org/maven2/org/flywaydb/flyway-commandline/${FLYWAY_VERSION}/flyway-commandline-${FLYWAY_VERSION}-linux-x64.tar.gz -o flyway.tar.gz \
     && tar -zxvf flyway.tar.gz \
     && mv flyway-${FLYWAY_VERSION} /flyway \
@@ -32,19 +19,10 @@ RUN curl -L https://repo1.maven.org/maven2/org/flywaydb/flyway-commandline/${FLY
     && rm -rf /flyway/jre \
     && chmod +x /flyway/flyway
 
-# First install the dependencies
-COPY .gitignore .gitignore
-COPY --from=builder /app/out/json/ .
-COPY --from=builder /app/out/package-lock.json ./package-lock.json
-RUN npm i
-
 # Build the project
-COPY --from=builder /app/out/full/ .
-COPY turbo.json turbo.json
 ENV NEXT_TELEMETRY_DISABLED=1
-ENV TURBO_TELEMETRY_DISABLED=1
-
-RUN npx turbo build --filter=tefca-viewer...
+RUN npm ci
+RUN npm run build
 
 # Final stage for running the app
 FROM base AS runner
@@ -64,26 +42,25 @@ RUN adduser --system --uid 1001 nextjs
 USER nextjs
 
 # Set hostname to localhost
-ENV HOSTNAME "0.0.0.0"
+ENV HOSTNAME="0.0.0.0"
 
 # Copy necessary app files
-COPY --from=installer /app/containers/tefca-viewer/next.config.js .
-COPY --from=installer /app/containers/tefca-viewer/package.json .
-COPY --from=installer /app/containers/tefca-viewer/flyway/conf/flyway.conf /flyway/conf/flyway.conf
-COPY --from=installer /app/containers/tefca-viewer/flyway/sql /flyway/sql
+COPY --from=installer /app/next.config.js .
+COPY --from=installer /app/package.json .
+COPY --from=installer /app/flyway/conf/flyway.conf ../flyway/conf/flyway.conf
+COPY --from=installer /app/flyway/sql ../flyway/sql
 
 # Automatically leverage output traces to reduce image size
-COPY --from=installer --chown=nextjs:nodejs /app/containers/tefca-viewer/.next/standalone ./
-COPY --from=installer --chown=nextjs:nodejs /app/containers/tefca-viewer/.next/static ./containers/tefca-viewer/.next/static
-COPY --from=installer --chown=nextjs:nodejs /app/containers/tefca-viewer/public ./containers/tefca-viewer/public
-
+COPY --from=installer --chown=nextjs:nodejs /app/.next/standalone ./
+COPY --from=installer --chown=nextjs:nodejs /app/.next/static ./.next/static
+COPY --from=installer --chown=nextjs:nodejs /app/public ./public
+RUN ls -R
 # Set environment variables for Flyway and Node.js telemetry
-ENV TURBO_TELEMETRY_DISABLED=1
 ENV NEXT_TELEMETRY_DISABLED=1
 
 # Set JAVA_HOME to the OpenJDK version installed by apk for Flyway
 ENV JAVA_HOME=/usr/lib/jvm/default-jvm
 # Add the OpenJDK to the PATH so the java command is available for Flways
 ENV PATH=$JAVA_HOME/bin:$PATH
 
-CMD ["sh", "-c","flyway -configFiles=/flyway/conf/flyway.conf -schemas=public -connectRetries=60 migrate && echo done with flyway && node containers/tefca-viewer/server.js"]
+CMD ["sh", "-c","flyway -configFiles=../flyway/conf/flyway.conf -schemas=public -connectRetries=60 migrate && echo done with flyway && node server.js"]

containers/tefca-viewer/docker-compose-dev.yaml

@@ -22,6 +22,7 @@ services:
   flyway:
     image: flyway/flyway:10.16-alpine
     command: -configFiles=/flyway/conf/flyway.conf -schemas=public -connectRetries=60 migrate
+    platform: linux/amd64
     volumes:
       - ./flyway/sql:/flyway/sql
       - ./flyway/conf/flyway.conf:/flyway/conf/flyway.conf

containers/tefca-viewer/docker-compose.yaml

@@ -18,8 +18,8 @@ services:
   tefca-viewer:
     platform: linux/amd64
     build:
-      context: ../../
-      dockerfile: ./containers/tefca-viewer/Dockerfile
+      context: .
+      dockerfile: Dockerfile
     tty: true
     ports:
       - "3000:3000"

containers/tefca-viewer/e2e/query_workflow.spec.ts

@@ -87,6 +87,7 @@ test.describe("querying with the TryTEFCA viewer", () => {
     await page.getByLabel("Medical Record Number").fill("18091");
     await page.getByLabel("Phone Number").fill("5555555555");
     await page.getByRole("button", { name: "Search for patient" }).click();
+    await expect(page.getByText("Loading")).toHaveCount(0, { timeout: 10000 });
 
     await page.getByRole("link", { name: "Select patient" }).click();
     await expect(
@@ -143,6 +144,7 @@ test.describe("querying with the TryTEFCA viewer", () => {
 
     // Among verification, make sure phone number is right
     await page.getByRole("button", { name: "Search for patient" }).click();
+    await expect(page.getByText("Loading")).toHaveCount(0, { timeout: 10000 });
     await expect(
       page.getByRole("heading", { name: "Patient Record" }),
     ).toBeVisible();
@@ -174,8 +176,9 @@ test.describe("querying with the TryTEFCA viewer", () => {
     await page.getByRole("button", { name: "Go to the demo" }).click();
     await page.getByLabel("Query", { exact: true }).selectOption("chlamydia");
     await page.getByRole("button", { name: "Fill fields" }).click();
-    // await page.getByLabel("Phone Number").fill("");
     await page.getByRole("button", { name: "Search for patient" }).click();
+    await expect(page.getByText("Loading")).toHaveCount(0, { timeout: 10000 });
+
     await expect(
       page.getByRole("heading", { name: "Patient Record" }),
     ).toBeVisible();