dockerize app and test dockerized service

.github/workflows/tests.yml

@@ -43,3 +43,61 @@ jobs:
       run: | #jacocoTestReport is for testing code coverage, submits the last report to the link
         ./gradlew jacocoTestReport
         bash <(curl -s https://codecov.io/bash)
+
+  Docker-Test:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Setup Gradle
+      uses: gradle/gradle-build-action@v2
+
+    - name: Setup Docker Buildx
+      id: buildx
+      uses: docker/setup-buildx-action@v1
+
+    - name: Docker Hub Login
+      uses: docker/login-action@v1
+      with: 
+        username: ${{ secrets.DOCKER_HUB_USERNAME }}
+        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+    - name: Set Docker Image Version
+      run: |
+        source ci/set-docker-image-version.sh
+        echo "version=${DOCKER_IMG_VER}" >> $GITHUB_ENV
+
+    - name: Build Docker Image
+      uses: docker/build-push-action@v2
+      with:
+        context: .
+        builder: ${{ steps.buildx.outputs.name }}
+        push: true
+        tags: ga4gh/ga4gh-testbed-api:test
+        build-args: VERSION=${{ env.version }}
+        cache-from: type=gha #GitHub Actions Cache Exporter
+        cache-to: type=gha,mode=max
+
+    - name: Start Services
+      run: docker-compose up -d
+
+    - name: Service Health Check
+      uses: jtalk/url-health-check-action@v2
+      with:
+        url: http://localhost:4500/reports
+        follow-redirect: false
+        max-attempts: 6
+        retry-delay: 10s
+        retry-all: true
+
+    # - name: Setup upterm session # Using Github - SSH for debugging
+    #   uses: lhotari/action-upterm@v1
+    #   with:
+    #     ## limits ssh access and adds the ssh public key for the user which triggered the workflow
+    #     limit-access-to-actor: true
+    #     ## limits ssh access and adds the ssh public keys of the listed GitHub users
+    #     limit-access-to-users: jb-adams
+
+    - name: Docker Test
+      run: ./gradlew test --tests=docker.*

Dockerfile

@@ -0,0 +1,64 @@
+##################################################
+# BUILDER CONTAINER
+##################################################
+
+FROM openjdk:11.0.12 as builder
+
+USER root
+
+WORKDIR /usr/src/dependencies
+
+# INSTALL MAKE
+RUN apt update \
+    && apt install build-essential -y
+
+# INSTALL SQLITE3
+RUN wget https://www.sqlite.org/2021/sqlite-autoconf-3340100.tar.gz \
+    && tar -zxf sqlite-autoconf-3340100.tar.gz \
+    && cd sqlite-autoconf-3340100 \
+    && ./configure \
+    && make \
+    && make install
+
+# USER 'make' and 'sqlite3' to create the dev database
+COPY Makefile Makefile
+COPY database/sqlite database/sqlite
+RUN make sqlite-db-refresh
+
+##################################################
+# GRADLE CONTAINER
+##################################################
+
+FROM gradle:7.3.3-jdk11 as gradleimage
+
+WORKDIR /home/gradle/source
+
+COPY build.gradle build.gradle
+COPY gradlew gradlew
+COPY settings.gradle settings.gradle
+COPY src src
+
+RUN gradle wrapper
+
+RUN ./gradlew bootJar
+
+##################################################
+# FINAL CONTAINER
+##################################################
+
+FROM adoptopenjdk/openjdk12:jre-12.0.2_10-alpine
+
+USER root
+
+ARG VERSION
+
+WORKDIR /usr/src/app
+
+# copy jar, dev db, and dev resource files
+COPY --from=gradleimage /home/gradle/source/build/libs/ga4gh-testbed-api-${VERSION}.jar ga4gh-testbed-api.jar
+COPY --from=builder /usr/src/dependencies/ga4gh-testbed-api.dev.db ga4gh-testbed-api.dev.db
+COPY src/test/resources/ src/test/resources/
+
+RUN chmod 666 ga4gh-testbed-api.dev.db
+
+ENTRYPOINT ["java", "-jar", "ga4gh-testbed-api.jar"]

Makefile

@@ -1,6 +1,6 @@
 DOCKER_ORG := ga4gh
 DOCKER_REPO := ga4gh-testbed-api
-DOCKER_TAG := 0.1.0
+DOCKER_TAG := $(shell cat build.gradle | grep "^version" | cut -f 2 -d ' ' | sed "s/'//g")
 DOCKER_IMG := ${DOCKER_ORG}/${DOCKER_REPO}:${DOCKER_TAG}
 DEVDB := ga4gh-testbed-api.dev.db
 
@@ -47,4 +47,10 @@ sqlite-db-populate-dev-dataset:
 .PHONY: sqlite-db-refresh
 sqlite-db-refresh: clean-sqlite sqlite-db-build sqlite-db-populate-dev-dataset
 
+.PHONY: docker-build
+docker-build:
+	docker build -t ${DOCKER_IMG} --build-arg VERSION=${DOCKER_TAG} .
 
+.PHONY: docker-build-test
+docker-build-test:
+	docker build -t ga4gh/ga4gh-testbed-api:test --build-arg VERSION=${DOCKER_TAG} .

build.gradle

@@ -20,8 +20,8 @@ plugins {
 }
 
 archivesBaseName = 'ga4gh-testbed-api'
-group = 'org.ga4gh'
-version = '0.1.0'
+group 'org.ga4gh'
+version '0.1.0'
 
 repositories {
     // Use jcenter for resolving dependencies.

ci/set-docker-image-version.sh

@@ -0,0 +1 @@
+export DOCKER_IMG_VER=`cat build.gradle | grep "^version" | cut -f 2 -d ' ' | sed "s/'//g"`

database/postgresql/add-dev-dataset.sql

@@ -76,10 +76,14 @@ insert into specification_platform values
 
 insert into report_series values (
     '1edb5213-52a2-434f-a7b8-b101fea8fb30',
+    'k4A2I1FUJrbpN70v4FXrrAqwvcamnZyB',
+    'dcaa1ff102a989efeaebef66e950216d86160303689120e9e76d88d4a70bd003', /* plaintext token is K5pLbwScVu8rEoLLj8pRy5Wv7EXTVahn */
     'refget-compliance',
     'org.ga4gh.refget.starterkit'
 ),(
     '483382e9-f92b-466d-9427-154d56a75fcf',
+    'JQhtM8FvjgaQaNbxTFbawJTWFjbdiiSL',
+    '463bdadca28c206693339fcc5465c9885395a7e03deff93ce1e851c5561bae36', /* plaintext token is l0HiRbbpjVDKc6k3tQ2skzROB1oAP2IV */
     'rnaget-compliance',
     'org.ga4gh.rnaget.starterkit'
 );

database/postgresql/create-tables.sql

@@ -107,6 +107,8 @@ CREATE TABLE IF NOT EXISTS summary
 CREATE TABLE IF NOT EXISTS report_series
 (
     id text PRIMARY KEY,
+    token_salt text NOT NULL,
+    token_hash text NOT NULL,
     fk_testbed_id text NOT NULL,
     fk_platform_id text NOT NULL,
     foreign key (fk_testbed_id) references testbed(id),

database/sqlite/add-dev-dataset.sql

@@ -76,10 +76,14 @@ insert into specification_platform values
 
 insert into report_series values (
     "1edb5213-52a2-434f-a7b8-b101fea8fb30",
+    'k4A2I1FUJrbpN70v4FXrrAqwvcamnZyB',
+    'dcaa1ff102a989efeaebef66e950216d86160303689120e9e76d88d4a70bd003', /* plaintext token is K5pLbwScVu8rEoLLj8pRy5Wv7EXTVahn */
     'refget-compliance',
     'org.ga4gh.refget.starterkit'
 ),(
     "483382e9-f92b-466d-9427-154d56a75fcf",
+    'JQhtM8FvjgaQaNbxTFbawJTWFjbdiiSL',
+    '463bdadca28c206693339fcc5465c9885395a7e03deff93ce1e851c5561bae36', /* plaintext token is l0HiRbbpjVDKc6k3tQ2skzROB1oAP2IV */
     'rnaget-compliance',
     'org.ga4gh.rnaget.starterkit'
 );

database/sqlite/create-tables.sql

@@ -107,6 +107,8 @@ CREATE TABLE IF NOT EXISTS summary
 CREATE TABLE IF NOT EXISTS report_series
 (
     id text PRIMARY KEY,
+    token_salt text NOT NULL,
+    token_hash text NOT NULL,
     fk_testbed_id text NOT NULL,
     fk_platform_id text NOT NULL,
     foreign key (fk_testbed_id) references testbed(id),

docker-compose.yml

@@ -0,0 +1,7 @@
+version: "3.9"
+services:
+  testbed-api:
+    image: ga4gh/ga4gh-testbed-api:test
+    hostname: testbed.ga4gh.org
+    ports:
+      - "4500:4500"

src/main/java/org/ga4gh/testbed/api/app/TestbedApiSpringConfig.java

@@ -30,6 +30,7 @@
 import org.ga4gh.testbed.api.utils.hibernate.TestbedApiHibernateUtil;
 import org.ga4gh.testbed.api.utils.logging.TestbedLoggingUtil;
 import org.ga4gh.testbed.api.utils.requesthandler.report.CreateReportHandler;
+import org.ga4gh.testbed.api.utils.requesthandler.report.DeleteReportHandler;
 import org.ga4gh.testbed.api.utils.requesthandler.report.ShowReportHandler;
 import org.ga4gh.testbed.api.utils.secretmanager.AwsSecretManagerUtil;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -230,6 +231,12 @@ public CreateReportHandler createReportHandler() {
         return new CreateReportHandler();
     }
 
+    @Bean
+    @RequestScope
+    public DeleteReportHandler deleteReportHandler() {
+        return new DeleteReportHandler();
+    }
+
     @Bean
     @RequestScope
     public BasicShowRequestHandler<String, ReportSeries> showReportSeriesHandler(

src/main/java/org/ga4gh/testbed/api/controller/Reports.java

@@ -6,8 +6,10 @@
 import org.ga4gh.testbed.api.utils.SerializeView;
 import org.ga4gh.testbed.api.utils.hibernate.TestbedApiHibernateUtil;
 import org.ga4gh.testbed.api.utils.requesthandler.report.CreateReportHandler;
+import org.ga4gh.testbed.api.utils.requesthandler.report.DeleteReportHandler;
 import org.ga4gh.testbed.api.utils.requesthandler.report.ShowReportHandler;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.web.bind.annotation.DeleteMapping;
 import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.PostMapping;
@@ -29,6 +31,9 @@ public class Reports {
     @Autowired
     private CreateReportHandler createReport;
 
+    @Autowired
+    private DeleteReportHandler deleteReport;
+
     @GetMapping
     @JsonView(SerializeView.ReportSimple.class)
     public List<Report> getReports() {
@@ -52,4 +57,14 @@ public Report postReport(
     ) throws Exception {
         return createReport.prepare(reportSeriesId, reportSeriesToken, report).handleRequest();
     }
+
+    @DeleteMapping("/{reportId:.+}")
+    @JsonView(SerializeView.ReportFull.class)
+    public Report deleteReport(
+        @PathVariable String reportId,
+        @RequestHeader("GA4GH-TestbedReportSeriesId") String reportSeriesId,
+        @RequestHeader("GA4GH-TestbedReportSeriesToken") String reportSeriesToken
+    ) throws Exception {
+        return deleteReport.prepare(reportId, reportSeriesId, reportSeriesToken).handleRequest();
+    }
 }

src/main/java/org/ga4gh/testbed/api/model/ReportSeries.java

@@ -35,6 +35,14 @@ public class ReportSeries implements HibernateEntity<String> {
     @JsonView(SerializeView.Always.class)
     private String id;
 
+    @Column(name = "token_salt", nullable = false)
+    @JsonView(SerializeView.Never.class)
+    private String tokenSalt;
+
+    @Column(name = "token_hash", nullable = false)
+    @JsonView(SerializeView.Never.class)
+    private String tokenHash;
+
     @ManyToOne(fetch = FetchType.EAGER,
                cascade = {CascadeType.PERSIST, CascadeType.MERGE,
                           CascadeType.DETACH, CascadeType.REFRESH})

src/main/java/org/ga4gh/testbed/api/utils/requesthandler/report/CreateReportHandler.java

@@ -1,8 +1,6 @@
 package org.ga4gh.testbed.api.utils.requesthandler.report;
 
-import java.util.HashMap;
 import java.util.UUID;
-
 import org.apache.commons.codec.digest.DigestUtils;
 import org.ga4gh.starterkit.common.exception.ConflictException;
 import org.ga4gh.starterkit.common.exception.ResourceNotFoundException;
@@ -25,7 +23,7 @@ public class CreateReportHandler extends BasicCreateRequestHandler<String, Repor
     private String reportSeriesId;
     private String reportSeriesToken;
     private Report report;
-    private static final String TESTBED_TOKENS_SECRET_NAME = "ga4gh-testbed-reportseries-tokens";
+    // private static final String TESTBED_TOKENS_SECRET_NAME = "ga4gh-testbed-reportseries-tokens";
 
     @Autowired
     TestbedApiHibernateUtil hibernateUtil;
@@ -53,20 +51,29 @@ public Report handleRequest() {
         }
         report.setReportSeries(reportSeries);
 
-        // get the token salt and token hash from AWS SM
-        HashMap<String, String> tokenMap;
-        try  {
-            tokenMap = awsSecretManagerUtil.retrieveSecret(TESTBED_TOKENS_SECRET_NAME);
-        } catch(Exception ex){
-            // TODO: log the original exception message
-            throw new ResourceNotFoundException(String.format("Retrieval of token salt and hash failed for report series id: %s",reportSeriesId));
-        }
-        String tokenSalt = tokenMap.get("token-salt-"+reportSeriesId);
-        String tokenHash = tokenMap.get("token-hash-"+reportSeriesId);
-        if (tokenSalt == null || tokenHash == null){
-            // TODO: log this
-            System.err.println(String.format("token salt or token hash is not available in the secret manager for report series id: %s",reportSeriesId) );
+        // first, look up the db for token salt and hash
+        String tokenSalt = reportSeries.getTokenSalt();
+        String tokenHash = reportSeries.getTokenHash();
+
+        /*
+        if (tokenSalt == null || tokenHash == null) {
+            // AWS SECRET MANAGER
+            // get the token salt and token hash from AWS SM
+            HashMap<String, String> tokenMap;
+            try  {
+                tokenMap = awsSecretManagerUtil.retrieveSecret(TESTBED_TOKENS_SECRET_NAME);
+            } catch(Exception ex){
+                // TODO: log the original exception message
+                throw new ResourceNotFoundException(String.format("Retrieval of token salt and hash failed for report series id: %s",reportSeriesId));
+            }
+            tokenSalt = tokenMap.get("token-salt-"+reportSeriesId);
+            tokenHash = tokenMap.get("token-hash-"+reportSeriesId);
+            if (tokenSalt == null || tokenHash == null){
+                // TODO: log this
+                System.err.println(String.format("token salt or token hash is not available in the secret manager for report series id: %s",reportSeriesId) );
+            }
         }
+        */
 
         // calculate the input token hash based on input token and salt
         // compare the input token hash to the report series's token hash in the AWS SM