Mongo7 upgrade

.github/workflows/test.yml

@@ -21,22 +21,25 @@ 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:${{matrix.mongo-version}}
         ports:
             - 27017:27017
         options: --name mongo${{matrix.mongo-version}}
 
+    env:
+      KBASE_CI_TOKEN: ${{ secrets.KBASE_CI_TOKEN }}
+      # This env var is also used in the catalog test docker compose file for starting NMS
+      ADMIN_USER: ${{ secrets.KBASE_BOT_USER_CI }}
+
     steps:
       - name: Repo checkout
         uses: actions/checkout@v4
-        with:
-          submodules: recursive
 
       - name: Setup Python
         uses: actions/setup-python@v5
@@ -45,9 +48,6 @@ jobs:
 
       - name: Install dependencies and set up test config
         shell: bash
-        env:
-          KBASE_CI_TOKEN: ${{ secrets.KBASE_CI_TOKEN }}
-          ADMIN_USER: ${{ secrets.KBASE_BOT_USER_CI }}
 
         run: |
 

Dockerfile

@@ -1,25 +1,38 @@
-FROM kbase/sdkbase2:python AS build
+FROM python:3.9.19 AS build
 
+# The rsync installation is required for the Makefile
+RUN apt-get update && apt-get install -y rsync
+RUN mkdir -p /kb/deployment/lib/biokbase
 
 COPY . /tmp/catalog
 RUN cd /tmp/catalog && make deploy-service deploy-server-control-scripts
 
-FROM kbase/sdkbase2:python
+FROM python:3.9.19
 # These ARGs values are passed in via the docker build command
 ARG BUILD_DATE
 ARG VCS_REF
 ARG BRANCH
 
+RUN apt-get update && apt-get install -y wget uwsgi
+
+# install dockerize
+WORKDIR /opt
+RUN wget -q https://github.com/kbase/dockerize/raw/master/dockerize-linux-amd64-v0.6.1.tar.gz \
+    && tar xvzf dockerize-linux-amd64-v0.6.1.tar.gz \
+    && rm dockerize-linux-amd64-v0.6.1.tar.gz
+RUN mkdir -p /kb/deployment/bin/
+RUN ln -s /opt/dockerize /kb/deployment/bin/dockerize
+
 ENV KB_DEPLOYMENT_CONFIG "/kb/deployment/conf/deploy.cfg"
 
 COPY --from=build /kb/deployment/lib/biokbase /kb/deployment/lib/biokbase
 COPY --from=build /kb/deployment/services /kb/deployment/services
 COPY --from=build /tmp/catalog/deployment/conf /kb/deployment/conf
 
-SHELL ["/bin/bash", "-c"]
+WORKDIR /tmp/catalog
+RUN pip install --upgrade pip
 COPY requirements.txt requirements.txt
-RUN source activate root && \
-    pip install -r requirements.txt
+RUN pip install -r requirements.txt
 
 LABEL org.label-schema.build-date=$BUILD_DATE \
       org.label-schema.vcs-url="https://github.com/kbase/catalog.git" \

Makefile

@@ -27,11 +27,6 @@ LIB_DIR = lib
 
 PATH := kb_sdk/bin:$(PATH)
 
-default: init
-
-init:
-	git submodule init
-	git submodule update
 
 compile-kb-module:
 	kb-sdk compile $(SPEC_FILE) \
@@ -102,10 +97,6 @@ setup-tests:
 	mkdir -p $(TESTLIB)/biokbase
 	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;
-#	rsync -av narrative_method_store/lib/biokbase/* $(TESTLIB)/biokbase/.
-
 
 
 test: setup-tests