issue #3676 - first pass at replacing db2 with postgres in the contai…

…nerized e2e tests

Signed-off-by: Lee Surprenant <lmsurpre@merative.com>

.github/workflows/integration.yml

@@ -8,7 +8,7 @@ on:
       - '.github/workflows/site.yml'
 
 jobs:
-  e2e-db2-with-bulkdata:
+  e2e-postgres:
     runs-on: ubuntu-latest
     if: "!contains(github.event.pull_request.labels.*.name, 'ci-skip')"
     strategy:
@@ -55,7 +55,6 @@ jobs:
         containerId=$(docker ps -a | grep fhir | cut -d ' ' -f 1)
         if [[ -z "${containerId}" ]]; then
             echo "Warning: Could not find fhir container!!!"
-            bash build/docker/docker-cleanup.sh
         else
             echo "fhir container id: $containerId"
 
@@ -66,12 +65,12 @@ jobs:
             docker cp -L $containerId:/logs ${it_results}/server-logs
         fi
         echo "Gathering integration test output"
-        cp -pr ${GITHUB_WORKSPACE}/fhir-server-test/target/surefire-reports/* ${it_results}/fhir-server-test || true
+        cp -r ${GITHUB_WORKSPACE}/fhir-server-test/target/surefire-reports/* ${it_results}/fhir-server-test || true
     - name: Upload logs
       if: always()
       uses: actions/upload-artifact@v2.2.0
       with:
-        name: integration-test-results-db2-${{ matrix.java }}
+        name: integration-test-results-${{ matrix.java }}
         path: integration-test-results
 
 concurrency:

build/.gitignore

@@ -1,5 +1,5 @@
 logs/
-docker/fhir-server/volumes/
+docker/fhir-server/
 deploy.sh
 *.jar
 *.zip

build/docker/bulkdata-setup.sh

@@ -0,0 +1,38 @@
+#!/usr/bin/env sh
+###############################################################################
+# (C) Copyright IBM Corp. 2016, 2022
+#
+# SPDX-License-Identifier: Apache-2.0
+###############################################################################
+set -ex
+
+if [[ -z "${WORKSPACE}" ]]; then
+    echo "ERROR: WORKSPACE environment variable not set!"
+    exit 1
+fi
+
+TEST_RESOURCES="${WORKSPACE}/fhir-server-test/src/test/resources"
+
+BULKDATA="${WORKSPACE}/build/docker/fhir-server/bulkdata/"
+mkdir -p ${BULKDATA}
+cp ${TEST_RESOURCES}/testdata/import-operation/test-import.ndjson ${BULKDATA}
+cp ${TEST_RESOURCES}/testdata/import-operation/test-import-skip.ndjson ${BULKDATA}
+cp ${TEST_RESOURCES}/testdata/import-operation/test-import-neg.ndjson ${BULKDATA}
+cp ${TEST_RESOURCES}/testdata/import-operation/test-import-mismatch.ndjson ${BULKDATA}
+
+S3_BULKDATA="${WORKSPACE}/build/docker/minio/miniodata/fhirbulkdata/"
+mkdir -p ${S3_BULKDATA}
+cp ${TEST_RESOURCES}/testdata/import-operation/test-import.ndjson ${S3_BULKDATA}
+cp ${TEST_RESOURCES}/testdata/import-operation/test-import-skip.ndjson ${S3_BULKDATA}
+cp ${TEST_RESOURCES}/testdata/import-operation/test-import-neg.ndjson ${S3_BULKDATA}
+cp ${TEST_RESOURCES}/testdata/import-operation/test-import-mismatch.ndjson ${S3_BULKDATA}
+
+# Appending the path
+echo "test.bulkdata.path = ${BULKDATA}" >> ${TEST_RESOURCES}/test.properties
+
+# Enable bulkdata export/import tests
+sed -i -e 's/test.bulkdata.export.enabled = false/test.bulkdata.export.enabled = true/g' ${TEST_RESOURCES}/test.properties
+sed -i -e 's/test.bulkdata.import.enabled = false/test.bulkdata.import.enabled = true/g' ${TEST_RESOURCES}/test.properties
+
+#sed -i -e 's/test.bulkdata.useminio = false/test.bulkdata.useminio = true/g' ${WORKSPACE}/fhir-server-test/src/test/resources/test.properties
+#sed -i -e 's/test.bulkdata.useminio.inbuildpipeline = false/test.bulkdata.useminio.inbuildpipeline = true/g' ${WORKSPACE}/fhir-server-test/src/test/resources/test.properties

build/docker/copy-server-config.sh

@@ -12,43 +12,24 @@ if [[ -z "${WORKSPACE}" ]]; then
 fi
 
 echo "Removing the old server config..."
-CONFIG="${WORKSPACE}/build/docker/fhir-server/volumes/config"
-rm -rf $CONFIG/* 2> /dev/null
-mkdir -p $CONFIG
-
-BULKDATA="${WORKSPACE}/build/docker/fhir-server/volumes/bulkdata/"
-mkdir -p ${BULKDATA}
-cp ${WORKSPACE}/fhir-server-test/src/test/resources/testdata/import-operation/test-import.ndjson ${BULKDATA}
-cp ${WORKSPACE}/fhir-server-test/src/test/resources/testdata/import-operation/test-import-skip.ndjson ${BULKDATA}
-cp ${WORKSPACE}/fhir-server-test/src/test/resources/testdata/import-operation/test-import-neg.ndjson ${BULKDATA}
-cp ${WORKSPACE}/fhir-server-test/src/test/resources/testdata/import-operation/test-import-mismatch.ndjson ${BULKDATA}
-
-S3_BULKDATA="${WORKSPACE}/build/docker/minio/miniodata/fhirbulkdata/"
-mkdir -p ${S3_BULKDATA}
-cp ${WORKSPACE}/fhir-server-test/src/test/resources/testdata/import-operation/test-import.ndjson ${S3_BULKDATA}
-cp ${WORKSPACE}/fhir-server-test/src/test/resources/testdata/import-operation/test-import-skip.ndjson ${S3_BULKDATA}
-cp ${WORKSPACE}/fhir-server-test/src/test/resources/testdata/import-operation/test-import-neg.ndjson ${S3_BULKDATA}
-cp ${WORKSPACE}/fhir-server-test/src/test/resources/testdata/import-operation/test-import-mismatch.ndjson ${S3_BULKDATA}
-
-# Appending the path
-echo "test.bulkdata.path = ${BULKDATA}" >> ${WORKSPACE}/fhir-server-test/src/test/resources/test.properties
+CONFIG="${WORKSPACE}/build/docker/fhir-server/config"
+rm -rf ${CONFIG}/* 2> /dev/null
+mkdir -p ${CONFIG}
 
 echo "Copying the server config files..."
 cp -r ${WORKSPACE}/fhir-server-webapp/src/main/liberty/config/config/* ${CONFIG}
 cp -r ${WORKSPACE}/fhir-server-webapp/src/test/liberty/config/config/* ${CONFIG}
-bash ${WORKSPACE}/build/update-server-registry-resource.sh ${WORKSPACE}/fhir-server-webapp/src/main/liberty/config/config/default/fhir-server-config-db2.json
-cp -r ${WORKSPACE}/fhir-server-webapp/src/main/liberty/config/config/default/fhir-server-config-db2.json ${CONFIG}/default/fhir-server-config.json
+bash ${WORKSPACE}/build/update-server-registry-resource.sh ${WORKSPACE}/fhir-server-webapp/src/main/liberty/config/config/default/fhir-server-config-postgresql.json
+cp -r ${WORKSPACE}/fhir-server-webapp/src/main/liberty/config/config/default/fhir-server-config-postgresql.json ${CONFIG}/default/fhir-server-config.json
 
 echo "Replacing datasource content in server configDropins..."
-OVERRIDES="${WORKSPACE}/build/docker/fhir-server/volumes/overrides"
+OVERRIDES="${WORKSPACE}/build/docker/fhir-server/configDropins/overrides"
+rm -rf ${OVERRIDES}/* 2> /dev/null
 mkdir -p ${OVERRIDES}
 
-# Just in case it already exists, let's wipe the datsource*.xml files
-rm -f ${OVERRIDES}/datasource*.xml
-
-# Copy over both the db2 (default_default) and derby (tenant1_*) datasource definitions
-cp ${WORKSPACE}/fhir-server-webapp/src/main/liberty/config/configDropins/disabled/datasource-db2.xml ${OVERRIDES}/
-cp ${WORKSPACE}/fhir-server-webapp/src/main/liberty/config/configDropins/disabled/db2/bulkdata.xml ${OVERRIDES}/
+# Copy over both the postgres (default_default) and derby (tenant1_*) datasource definitions
+cp ${WORKSPACE}/fhir-server-webapp/src/main/liberty/config/configDropins/disabled/datasource-postgresql.xml ${OVERRIDES}/
+cp ${WORKSPACE}/fhir-server-webapp/src/main/liberty/config/configDropins/disabled/postgres/bulkdata.xml ${OVERRIDES}/
 cp ${WORKSPACE}/fhir-server-webapp/src/test/liberty/config/configDropins/overrides/datasource-derby.xml ${OVERRIDES}/
 
 echo "Finished copying the server config."

build/docker/copy-test-operations.sh

@@ -1,18 +1,18 @@
 #!/usr/bin/env bash
 ###############################################################################
-# (C) Copyright IBM Corp. 2016, 2020
+# (C) Copyright IBM Corp. 2016, 2022
 #
 # SPDX-License-Identifier: Apache-2.0
 ###############################################################################
-set -e
+set -ex
 
 if [[ -z "${WORKSPACE}" ]]; then
     echo "ERROR: WORKSPACE environment variable not set!"
     exit 1
 fi
 
 echo "Removing old test operations..."
-USERLIB="${WORKSPACE}/build/docker/fhir-server/volumes/userlib"
+USERLIB="${WORKSPACE}/build/docker/fhir-server/userlib"
 rm -rf $USERLIB/* 2> /dev/null
 mkdir -p $USERLIB