Add Flyway to tefca-viewer container (#2652)

* temp changes * testing * instal plsh * clean up * testing moving flyway to within tefca container * testing continued * most recent attempts * working version of flyway in tefca-viewer * cleanup * remove unrecognized conf * update dockerfile to install flyway at installer * undo changes to migrations * remove unused files * remove flyway parts of workflows * COPY files in Dockerfile; remove volumes * add additional inline comments * have Dockerfile call flyway command * update docker compose commands * add setup step to ensure migrations are fully run before running playwright tests * test change to github url * update url * try with removal of --no-cache * try with other setup func * clean up + increase webServer timeout * add additional wait time after 200 * bump webserver time back down to 5 min * add back --no-cache * add max retries * add logging * increase workflow timeout * add indices for conditions.name and query.query_name * try 60 min while testing other things locally * change timeout back to 15 min * undo testing measures * appease GH timeouts * Allow Flyway to fully manage transactions * Mods for additional workflow testing * [pre-commit.ci] auto fixes from pre-commit hooks * use docker compose not docker-compose * Remove docker compose test * Upgrade Flyway and Java versions to address warnings related to use of Postgres 17 * Introduce test:playwright to start webserver external to Playwright * Use playwright list reporter * Try full command directly in GH workflow * Fix docker compose command * build, up, and test as separate workflow steps * additional logging * state playwright test directory explicitly * Try npm ci and specify config directory * reduce workflow timeout to 10 & clean up * bump min workers to 2 and cleanup playwright config * remove csv-to-fhir work * cleanup * add note about local.env file * note about DATABASE_URL * remove duplicate test * revert workers to max 1 * temporarily remove test for no patients --------- Co-authored-by: DanPaseltiner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
CDCgov · Oct 7, 2024 · d88816d · d88816d
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diff --git a/.github/workflows/buildReleaseContainers.yaml b/.github/workflows/buildReleaseContainers.yaml
@@ -58,22 +58,6 @@ jobs:
           labels: |
             org.opencontainers.image.version=${{ inputs.container-tag }}
 
-      - name: Extract metadata (tags, labels) for Flyway Docker
-        id: flyway-meta
-        uses: docker/metadata-action@v4
-        if: ${{ contains(fromJSON('["tefca-viewer"]'), matrix.container-to-build) }}
-        with:
-          ref: ${{ inputs.container-tag }}
-          images: ghcr.io/${{ github.repository }}/tefca-viewer-flyway
-          # this sets the version for tags and labels for each of the containers to be
-          # be the same as the version/tag where the code was pulled from
-          tags: |
-            type=semver,pattern={{raw}},value=${{ inputs.container-tag }}
-            type=ref,event=branch
-            type=ref,event=tag,pattern={{raw}},value=${{ inputs.container-tag }}
-          labels: |
-            org.opencontainers.image.version=${{ inputs.container-tag }}
-
       - name: Build and push
         uses: docker/build-push-action@v3
         if: ${{ !contains(fromJSON('["ecr-viewer", "tefca-viewer"]'), matrix.container-to-build) }}
@@ -85,18 +69,6 @@ jobs:
           cache-from: type=gha
           cache-to: type=gha,mode=max
 
-      - name: Build Flyway Container
-        uses: docker/build-push-action@v3
-        if: ${{ contains(fromJSON('["tefca-viewer"]'), matrix.container-to-build) }}
-        with:
-          context: .
-          file: ./containers/${{ matrix.container-to-build }}/Dockerfile.flyway
-          push: true
-          tags: ${{ steps.flyway-meta.outputs.tags }}
-          labels: ${{ steps.flyway-meta.outputs.labels }}
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
-
       - name: Build and push with shared-resources
         uses: docker/build-push-action@v3
         if: ${{ contains(fromJSON('["ecr-viewer", "tefca-viewer"]'), matrix.container-to-build) }}

diff --git a/.github/workflows/container-tefca-viewer.yaml b/.github/workflows/container-tefca-viewer.yaml
@@ -75,14 +75,6 @@ jobs:
           push: false
           cache-from: type=gha
           cache-to: type=gha,mode=max
-      - name: Build ${{ env.CONTAINER }} Flyway Container
-        uses: docker/build-push-action@v3
-        with:
-          context: .
-          file: ./containers/${{ env.CONTAINER }}/Dockerfile.flyway
-          push: false
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
 
   playwright-tests:
     timeout-minutes: 10
@@ -96,10 +88,16 @@ jobs:
           node-version: ${{env.NODE_VERSION}}
       - name: Install dependencies
         working-directory: ./containers/${{env.CONTAINER}}
-        run: npm install
+        run: npm ci
       - name: Install Playwright Browsers
         working-directory: ./containers/${{env.CONTAINER}}
         run: npx playwright install --with-deps
-      - name: Run Playwright tests
+      - name: Build Query Connector
+        working-directory: ./containers/${{env.CONTAINER}}
+        run: docker compose build --no-cache
+      - name: Run Query Connector
+        working-directory: ./containers/${{env.CONTAINER}}
+        run: docker compose up -d
+      - name: Playwright Tests
         working-directory: ./containers/${{env.CONTAINER}}
-        run: npx playwright test
+        run: npx playwright test e2e --reporter=list --config playwright.config.ts
diff --git a/containers/tefca-viewer/Dockerfile b/containers/tefca-viewer/Dockerfile
@@ -1,11 +1,11 @@
 FROM node:18-alpine AS base
 
 FROM base AS builder
-# Check https://github.com/nodejs/docker-node/tree/b4117f9333da4138b03a546ec926ef50a31506c3#nodealpine to understand why libc6-compat might be needed.
+# Install necessary packages for building
 RUN apk update
 RUN apk add --no-cache libc6-compat
 
-# Set working directory 
+# Set working directory
 WORKDIR /app
 RUN npm i -g turbo
 COPY . .
@@ -18,6 +18,20 @@ 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
+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 \
+    && ln -s /flyway/flyway /usr/local/bin/flyway \
+    && rm flyway.tar.gz \
+    && rm -rf /flyway/jre \
+    && chmod +x /flyway/flyway
+
 # First install the dependencies
 COPY .gitignore .gitignore
 COPY --from=builder /app/out/json/ .
@@ -32,9 +46,18 @@ ENV TURBO_TELEMETRY_DISABLED=1
 
 RUN npx turbo build --filter=tefca-viewer...
 
+# Final stage for running the app
 FROM base AS runner
 WORKDIR /app
 
+RUN apk add --no-cache bash openjdk17-jre
+
+# Copy Flyway from the installer stage
+COPY --from=installer /flyway /flyway
+RUN chmod +x /flyway/flyway
+# Create symlink to run Flyway from anywhere in the container
+RUN ln -s /flyway/flyway /usr/local/bin/flyway
+
 # Don't run production as root
 RUN addgroup --system --gid 1001 nodejs
 RUN adduser --system --uid 1001 nextjs
@@ -43,17 +66,24 @@ USER nextjs
 # Set hostname to localhost
 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
 
 # Automatically leverage output traces to reduce image size
-# https://nextjs.org/docs/advanced-features/output-file-tracing
 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
 
+# 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 ["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 containers/tefca-viewer/server.js"]
diff --git a/containers/tefca-viewer/Dockerfile.flyway b/containers/tefca-viewer/Dockerfile.flyway
diff --git a/containers/tefca-viewer/docker-compose-dev.yaml b/containers/tefca-viewer/docker-compose-dev.yaml
@@ -8,6 +8,8 @@ services:
       - POSTGRES_USER=postgres
       - POSTGRES_PASSWORD=pw
       - POSTGRES_DB=tefca_db
+      # Note: you must have a local .env file with the DATABASE_URL set to the following:
+      # DATABASE_URL=postgresql://postgres:pw@localhost:5432/tefca_db
     healthcheck:
       test: ["CMD-SHELL", "pg_isready -U postgres"]
       interval: 2s

diff --git a/containers/tefca-viewer/docker-compose.yaml b/containers/tefca-viewer/docker-compose.yaml
@@ -14,23 +14,13 @@ services:
       timeout: 5s
       retries: 20
 
-  # Flyway migrations and DB version control
-  flyway:
-    image: flyway/flyway:10.16-alpine
-    command: -configFiles=/flyway/conf/flyway.conf -schemas=public -connectRetries=60 migrate
-    volumes:
-      - ./flyway/sql:/flyway/sql
-      - ./flyway/conf/flyway.conf:/flyway/conf/flyway.conf
-    depends_on:
-      db:
-        condition: service_started
-
-  # Next.js app
+  # Next.js app with Flyway
   tefca-viewer:
     platform: linux/amd64
     build:
       context: ../../
       dockerfile: ./containers/tefca-viewer/Dockerfile
+    tty: true
     ports:
       - "3000:3000"
     environment:
@@ -39,5 +29,3 @@ services:
     depends_on:
       db:
         condition: service_healthy
-      flyway:
-        condition: service_completed_successfully
diff --git a/containers/tefca-viewer/e2e/query_workflow.spec.ts b/containers/tefca-viewer/e2e/query_workflow.spec.ts
@@ -1,6 +1,5 @@
 // @ts-check
 
-import { RETURN_TO_STEP_ONE_LABEL } from "@/app/query/components/PatientSearchResults";
 import { test, expect } from "@playwright/test";
 
 test.describe("querying with the TryTEFCA viewer", () => {
@@ -30,6 +29,31 @@ test.describe("querying with the TryTEFCA viewer", () => {
     ).toBeVisible();
   });
 
+  //TODO: Add this test back in once you no longer have to click to select the query from the dropdown
+  // test("unsuccessful user query: no patients", async ({ page }) => {
+  //   await page.getByRole("button", { name: "Go to the demo" }).click();
+  //   await page
+  //     .getByLabel("Query", { exact: true })
+  //     .selectOption("social-determinants");
+  //   await page.getByRole("button", { name: "Fill fields" }).click();
+
+  //   await page.getByLabel("First Name").fill("Ellie");
+  //   await page.getByLabel("Last Name").fill("Williams");
+  //   await page.getByLabel("Phone Number").fill("5555555555");
+  //   await page.getByLabel("Medical Record Number").fill("TLOU1TLOU2");
+  //   await page.getByRole("button", { name: "Search for patient" }).click();
+
+  //   // Better luck next time, user!
+  //   await expect(
+  //     page.getByRole("heading", { name: "No Patients Found" })
+  //   ).toBeVisible();
+  //   await expect(page.getByText("There are no patient records")).toBeVisible();
+  //   await page.getByRole("link", { name: "Search for a new patient" }).click();
+  //   await expect(
+  //     page.getByRole("heading", { name: "Search for a Patient", exact: true })
+  //   ).toBeVisible();
+  // });
+
   test("successful demo user query: the quest for watermelon mcgee", async ({
     page,
   }) => {
@@ -92,35 +116,6 @@ test.describe("querying with the TryTEFCA viewer", () => {
     ).toBeVisible();
   });
 
-  test("unsuccessful user query: no patients", async ({ page }) => {
-    await page.getByRole("button", { name: "Go to the demo" }).click();
-    await page
-      .getByLabel("Query", { exact: true })
-      .selectOption("social-determinants");
-    await page.getByRole("button", { name: "Advanced" }).click();
-    await page
-      .getByLabel("FHIR Server (QHIN)", { exact: true })
-      .selectOption("HELIOS Meld: Direct");
-
-    await page.getByLabel("First Name").fill("Ellie");
-    await page.getByLabel("Last Name").fill("Williams");
-    await page.getByLabel("Date of Birth").fill("2019-07-07");
-    await page.getByLabel("Medical Record Number").fill("TLOU1TLOU2");
-    await page.getByRole("button", { name: "Search for patient" }).click();
-
-    // Better luck next time, user!
-    await expect(
-      page.getByRole("heading", { name: "No Records Found" }),
-    ).toBeVisible();
-    await expect(
-      page.getByText("No records were found for your search"),
-    ).toBeVisible();
-    await page.getByText(RETURN_TO_STEP_ONE_LABEL).click();
-    await expect(
-      page.getByRole("heading", { name: "Search for a Patient", exact: true }),
-    ).toBeVisible();
-  });
-
   test("query using form-fillable demo patient by phone number", async ({
     page,
   }) => {

diff --git a/containers/tefca-viewer/flyway/sql/V01_01__tcr_custom_query_schema.sql b/containers/tefca-viewer/flyway/sql/V01_01__tcr_custom_query_schema.sql
@@ -1,4 +1,3 @@
-BEGIN;
 CREATE EXTENSION IF NOT EXISTS "uuid-ossp";
 
 CREATE TABLE IF NOT EXISTS conditions (
@@ -81,6 +80,7 @@ CREATE TABLE IF NOT EXISTS query_included_concepts (
 -- Create indexes for all primary and foreign keys
 
 CREATE INDEX IF NOT EXISTS conditions_id_index ON conditions (id);
+CREATE INDEX IF NOT EXISTS conditions_name_index ON conditions (name);
 
 CREATE INDEX IF NOT EXISTS valuesets_id_index ON valuesets (id);
 
@@ -97,6 +97,7 @@ CREATE INDEX IF NOT EXISTS valueset_to_concept_concept_id_index ON valueset_to_c
 CREATE INDEX IF NOT EXISTS icd_crosswalk_id_index ON icd_crosswalk (id);
 
 CREATE INDEX IF NOT EXISTS query_id_index ON query (id);
+CREATE INDEX IF NOT EXISTS query_name_index ON query (query_name);
 
 CREATE INDEX IF NOT EXISTS query_to_valueset_id_index ON query_to_valueset (id);
 CREATE INDEX IF NOT EXISTS query_to_valueset_query_id_index ON query_to_valueset (query_id);
@@ -105,5 +106,3 @@ CREATE INDEX IF NOT EXISTS query_to_valueset_valueset_id_index ON query_to_value
 CREATE INDEX IF NOT EXISTS query_included_concepts_id_index ON query_included_concepts (id);
 CREATE INDEX IF NOT EXISTS query_included_concepts_query_by_valueset_id_index ON query_included_concepts (query_by_valueset_id);
 CREATE INDEX IF NOT EXISTS query_included_concepts_concept_id_index ON query_included_concepts (concept_id);
-
-COMMIT;
diff --git a/containers/tefca-viewer/flyway/sql/V01_02__load_tcr_data.sql b/containers/tefca-viewer/flyway/sql/V01_02__load_tcr_data.sql
@@ -1,4 +1,3 @@
-BEGIN;
 
 INSERT INTO valuesets VALUES('2.16.840.1.113762.1.4.1146.6_20230602','2.16.840.1.113762.1.4.1146.6','20230602','Diphtheria (Disorders) (SNOMED)','CSTE Steward','dxtc');
 INSERT INTO valuesets VALUES('2.16.840.1.113762.1.4.1146.2030_20230125','2.16.840.1.113762.1.4.1146.2030','20230125','Bartonella henselae infection (Disorders) (SNOMED)','CSTE Steward','dxtc');
@@ -175313,8 +175312,3 @@ INSERT INTO icd_crosswalk VALUES('81590','Z993','V463','00000');
 INSERT INTO icd_crosswalk VALUES('81591','Z9981','V462','00000');
 INSERT INTO icd_crosswalk VALUES('81592','Z9989','V468','10000');
 INSERT INTO icd_crosswalk VALUES('81593','Z9989','V469','10000');
-COMMIT;
-
-
-
-
diff --git a/containers/tefca-viewer/flyway/sql/V01_03__insert_hardcoded_values.sql b/containers/tefca-viewer/flyway/sql/V01_03__insert_hardcoded_values.sql
@@ -1,5 +1,3 @@
-BEGIN;
-
 INSERT INTO conditions VALUES('1','DIBBs Local Code System','Newborn Screening','20240909');
 INSERT INTO conditions VALUES('2','DIBBs Local Code System','Cancer (Leukemia)','20240909');
 INSERT INTO conditions VALUES('3','DIBBs Local Code System','Social Determinants of Health','20240909'); -- has no valuesets
@@ -157,7 +155,3 @@ INSERT INTO valueset_to_concept VALUES('45314','14_20240923','1_1255068005');
 INSERT INTO valueset_to_concept VALUES('45315','14_20240923','1_9484.100004300');
 INSERT INTO valueset_to_concept VALUES('45316','15_20240923','1_363346000');
 INSERT INTO valueset_to_concept VALUES('45317','2_20240909','1_418689008');
-
-
-
-COMMIT;
diff --git a/containers/tefca-viewer/flyway/sql/V01_04__insert_tcr_default_queries.sql b/containers/tefca-viewer/flyway/sql/V01_04__insert_tcr_default_queries.sql
@@ -1,4 +1,3 @@
-BEGIN;
 -- Select data from the TCR that will be used to create default queries
 WITH tcr_data AS (
     SELECT
@@ -57,6 +56,3 @@ select
 from qic_data
 join valueset_to_concept vtc 
 on qic_data.valueset_id = vtc.valueset_id;
-
-COMMIT;
-
diff --git a/containers/tefca-viewer/package.json b/containers/tefca-viewer/package.json
@@ -4,9 +4,9 @@
   "version": "1.0.1",
   "private": true,
   "scripts": {
-    "dev": "docker-compose -f docker-compose-dev.yaml up -d && next dev",
-    "dev-win": "start docker-compose -f docker-compose-dev.yaml up && next dev",
-    "dev:db": "docker-compose -f docker-compose-dev.yaml up",
+    "dev": "docker compose -f docker-compose-dev.yaml up -d && next dev",
+    "dev-win": "start docker compose -f docker-compose-dev.yaml up && next dev",
+    "dev:db": "docker compose -f docker-compose-dev.yaml up",
     "dev:next": "dotenv -e ./tefca.env.local -e ./tefca.env -- next dev",
     "setup-local-env": "./setup-env.sh",
     "build": "next build && cp -r .next/static .next/standalone/.next && cp -r public .next/standalone/",
@@ -16,6 +16,7 @@
     "test:unit": "jest --testPathPattern=tests/unit",
     "test:unit:watch": "jest --watch",
     "test:integration": "jest --testPathPattern=tests/integration",
+    "test:playwright": "docker compose build --no-cache && docker compose up -d && npx playwright test --reporter=list",
     "cypress:open": "cypress open",
     "cypress:run": "cypress run"
   },