[WIP] mongo7 upgrade

.github/workflows/test.yml

@@ -21,15 +21,15 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - python-version: '3.7'
+          - python-version: '3.9.19'
             mongo-version: '3.6'
-          # - python-version: '3.7'
-          #   mongo-version: '7.0.4'
+          - python-version: '3.9.19'
+            mongo-version: '7.0.4'
     services:
       mongo:
         image: mongo:${{matrix.mongo-version}}
         ports:
-            - 27017:27017
+            - 27018:27017
         options: --name mongo${{matrix.mongo-version}}
 
     steps:
@@ -43,6 +43,12 @@ jobs:
         with:
           python-version: ${{matrix.python-version}}
 
+      - name: Install Docker Compose
+        run: |
+          sudo curl -L "https://github.com/docker/compose/releases/download/v2.32.1/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
+          sudo chmod +x /usr/local/bin/docker-compose
+          docker-compose --version
+
       - name: Install dependencies and set up test config
         shell: bash
         env:
@@ -52,7 +58,7 @@ jobs:
         run: |
 
           # test mongo connection
-          curl http://localhost:27017
+          curl http://localhost:27018
           returncode=$?
           if [ $returncode != 0 ]; then exit $returncode; fi
 
@@ -77,6 +83,9 @@ jobs:
           sed -i "s#^nms-admin-token.*#nms-admin-token=$KBASE_CI_TOKEN#" test/test.cfg
           sed -i "s#^method-spec-admin-users.*#method-spec-admin-users=$ADMIN_USER#" test/test.cfg
 
+          # setup env variables in docker-compose_nms.yml file
+          echo "ADMIN_USER=$ADMIN_USER" >> $GITHUB_ENV
+
       - name: Run tests
         shell: bash
         run: make test

Makefile

@@ -103,7 +103,7 @@ setup-tests:
 	mkdir -p $(TESTDIR)/nms
 	rsync -av lib/biokbase/* $(TESTLIB)/biokbase/. --exclude *.bak-*
 	rsync -av kbapi_common/lib/biokbase/* $(TESTLIB)/biokbase/.
-	cd narrative_method_store; make; make build-classpath-list;
+#	cd narrative_method_store; make; make build-classpath-list;
 #	rsync -av narrative_method_store/lib/biokbase/* $(TESTLIB)/biokbase/.
 
 

requirements.txt

@@ -1,4 +1,4 @@
-pymongo==3.10
+pymongo==4.7.2
 docker>=3.5
 gitpython
 pyyaml

test/docker-compose_nms.yml

@@ -0,0 +1,47 @@
+version: '3.4'
+
+services:
+  nms:
+    image: ghcr.io/kbase/narrative_method_store:v0.3.12
+    platform: linux/amd64
+    ports:
+      - "7125:7125"
+    depends_on: ["mongo"]
+    environment:
+      # see deployment/conf/.templates for more environment variables
+      - method_spec_git_repo=https://github.com/kbase/narrative_method_specs_ci
+      - method_spec_git_repo_branch=master
+      - method_spec_git_repo_local_dir=narrative_method_specs_recreated_at_startup
+      - method_spec_git_repo_refresh_rate=2
+      - method_spec_cache_size=5000
+      - method_spec_temp_dir=narrative_method_store_temp
+      - method_spec_mongo_host=mongo:27017
+      - method_spec_mongo_dbname=method_store_repo_db
+      - method_spec_admin_users=${ADMIN_USER}
+      - endpoint_host=https://ci.kbase.us
+      - endpoint_base=/services
+      - method_spec_default_tag=dev
+      - auth_service_url=https://ci.kbase.us/services/auth/api/legacy/KBase/Sessions/Login
+      - auth_service_url_allow_insecure=false
+      - service_port=7125
+    command:
+      - "-wait"
+      - "tcp://mongo:27017"
+      - "-timeout"
+      - "120s"
+      - "-template"
+      - "/kb/deployment/conf/.templates/deployment.cfg.templ:/kb/deployment/conf/deployment.cfg"
+      - "-template"
+      - "/kb/deployment/conf/.templates/http.ini.templ:/kb/deployment/services/narrative_method_store/start.d/http.ini"
+      - "-template"
+      - "/kb/deployment/conf/.templates/server.ini.templ:/kb/deployment/services/narrative_method_store/start.d/server.ini"
+      - "-template"
+      - "/kb/deployment/conf/.templates/start_server.sh.templ:/kb/deployment/bin/start_server.sh"
+      - "-stdout"
+      - "/kb/deployment/services/narrative_method_store/logs/request.log"
+      - "/kb/deployment/bin/start_server.sh"
+
+  mongo:
+    image: "mongo:7.0.4"
+    ports:
+      - "27017:27017"

test/run_tests.sh

@@ -11,8 +11,7 @@
 # start the test NMS endpoint
 echo 'Starting NMS...'
 export KB_DEPLOYMENT_CONFIG=test.cfg
-classpath=`cat ../narrative_method_store/dist/jar.classpath.txt`
-java -cp $classpath us.kbase.narrativemethodstore.NarrativeMethodStoreServer 7125 > nms/error.log 2>&1 &
+docker-compose -f docker-compose_nms.yml up -d
 NMS_PID=$!
 
 echo 'Starting Mock Auth API...'
@@ -62,5 +61,6 @@ kill -9 $NMS_PID
 #stop Docker containers
 docker stop mock-auth
 docker stop registry
+docker-compose -f docker-compose_nms.yml down
 
 exit ${TEST_RETURN_CODE}

test/test.cfg.example

@@ -24,8 +24,8 @@ test-user-2 = wstester2
 test-module-repo-1 = https://github.com/kbaseIncubator/catalog_test_module
 test-module-repo-2 = https://github.com/kbaseIncubator/catalog_test_module.git
 
-# host where mongo lives, e.g. localhost:27017, for tests there should be not authentication required
-mongodb-host = localhost:27017
+# host where mongo lives, e.g. localhost:27018, for tests there should be not authentication required
+mongodb-host = localhost:27018
 
 # docker registry host endpoint
 docker-registry-host = localhost:5000