Merge pull request #291 from uc-cdis/feat/al2-debug

debug: use compose-etl debug branch

.github/workflows/image_build_and_test.yaml

@@ -3,21 +3,23 @@ on: push
 
 jobs:
 
-  # # first, build the image
-  # build:
-  #   name: Build and push image
-  #   uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
-  #   secrets:
-  #     ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
-  #     ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
-  #     QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }}
-  #     QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }}
+  # first, build the image
+  build:
+    name: Build and push image
+    uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master
+    with:
+      BUILD_PLATFORMS: "linux/amd64"
+    secrets:
+      ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
+      ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
+      QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }}
+      QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }}
 
   # then run the tests
   test:
     name: Run tests
     runs-on: ubuntu-20.04
-    # needs: build
+    needs: build
 
     services:
       postgres:

Dockerfile

@@ -44,7 +44,6 @@ FROM base
 COPY --from=builder /venv /venv
 COPY --from=builder /${appname} /${appname}
 
-
 ENV DEBIAN_FRONTEND=noninteractive \
     SQOOP_VERSION="1.4.7" \
     HADOOP_VERSION="3.3.2" \
@@ -67,12 +66,14 @@ ENV ES_HADOOP_HOME_VERSION="${ES_HADOOP_HOME}/elasticsearch-hadoop-${ES_HADOOP_V
 RUN mkdir -p /usr/share/man/man1
 RUN mkdir -p /usr/share/man/man7
 
-
 RUN dnf -y update
 RUN dnf -y install \
-    wget tar unzip vim
-RUN dnf -y install java-11-amazon-corretto
-
+    java-11-amazon-corretto \
+    postgresql15 \
+    tar \
+    unzip \
+    vim \
+    wget
 
 RUN wget ${SQOOP_INSTALLATION_URL} \
     && mkdir -p $SQOOP_HOME \
@@ -117,16 +118,14 @@ ENV HADOOP_CONF_DIR=$HADOOP_HOME/etc/hadoop \
 
 RUN mkdir -p $ACCUMULO_HOME $HIVE_HOME $HBASE_HOME $HCAT_HOME $ZOOKEEPER_HOME
 RUN chown -R gen3:gen3 $HADOOP_HOME
-RUN mkdir -p /result && chown -R gen3:gen3 /result && chmod -R 700 /result
-#RUN hdfs dfs -chown gen3 /result
 
 ENV PATH=${SQOOP_HOME}/bin:${HADOOP_HOME}/sbin:$HADOOP_HOME/bin:${JAVA_HOME}/bin:${PATH}
 
-
 # Switch to non-root user 'gen3' for the serving process
 USER gen3
 
-RUN source /venv/bin/activate
+ENV PATH="/venv/bin:$PATH" \
+    VIRTUAL_ENV="/venv"
 
 ENV PYTHONUNBUFFERED=1 \
     PYTHONIOENCODING=UTF-8