Update Dockerfile with starting scripts

packaging/docker_compose/local_executor/cwl_airflow/Dockerfile

@@ -20,6 +20,9 @@ WORKDIR /tmp
 
 ENV CWL_AIRFLOW_VERSION "master"
 ENV CWL_AIRFLOW_URL "https://github.com/Barski-lab/cwl-airflow"
+COPY ./scripts/start_webserver.sh /usr/local/bin/start_webserver.sh
+COPY ./scripts/start_scheduler.sh /usr/local/bin/start_scheduler.sh
+COPY ./scripts/start_apiserver.sh /usr/local/bin/start_apiserver.sh
 
 RUN apt-get update && \
     # installing dependencies (including docker dependencies)

packaging/docker_compose/local_executor/cwl_airflow/scripts/start_apiserver.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+echo "Set parameters from the environment variables or apply defaults"
+: "${MYSQL_USER:=airflow}"
+: "${MYSQL_PASSWORD:=airflow}"
+: "${MYSQL_DATABASE:=airflow}"
+
+echo "Wait until required database and tables are ready"
+until mysql -h mysql -u ${MYSQL_USER} -p${MYSQL_PASSWORD} -e "select * from ${MYSQL_DATABASE}.dag_run"
+do
+    echo "Sleep 1 sec"
+    sleep 1;
+done
+
+echo "Start cwl-airflow api"
+cwl-airflow api "$@"

packaging/docker_compose/local_executor/cwl_airflow/scripts/start_scheduler.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+echo "Set parameters from the environment variables or apply defaults"
+: "${MYSQL_USER:=airflow}"
+: "${MYSQL_PASSWORD:=airflow}"
+: "${MYSQL_DATABASE:=airflow}"
+
+echo "Wait until required database is ready"
+until mysql -h mysql -u ${MYSQL_USER} -p${MYSQL_PASSWORD} -e "USE ${MYSQL_DATABASE}"
+do
+    echo "Sleep 1 sec"
+    sleep 1;
+done
+
+echo "Run initial configuration for CWL-Airflow"
+cwl-airflow init --upgrade
+
+echo "Start airflow scheduler"
+airflow scheduler "$@"

packaging/docker_compose/local_executor/cwl_airflow/scripts/start_webserver.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+
+echo "Set parameters from the environment variables or apply defaults"
+: "${AIRFLOW_HOME:=airflow}"
+: "${MYSQL_USER:=airflow}"
+: "${MYSQL_PASSWORD:=airflow}"
+: "${MYSQL_DATABASE:=airflow}"
+
+echo "Wait until required database and tables are ready"
+until mysql -h mysql -u ${MYSQL_USER} -p${MYSQL_PASSWORD} -e "select * from ${MYSQL_DATABASE}.dag_run"
+do
+    echo "Sleep 1 sec"
+    sleep 1;
+done
+
+echo "Wait until required files are ready"
+until [ -e ${AIRFLOW_HOME}/webserver_config.py ]
+do
+    echo "Sleep 1 sec"
+    sleep 1;
+done
+
+echo "Disable authentication in Airflow UI"
+sed -i'.backup' -e 's/^# AUTH_ROLE_PUBLIC.*/AUTH_ROLE_PUBLIC = "Admin"/g' ${AIRFLOW_HOME}/webserver_config.py
+
+echo "Start airflow webserver"
+airflow webserver "$@"

packaging/docker_compose/local_executor/docker-compose.yml

@@ -38,7 +38,7 @@ services:
         privileged: true                                               # maybe I don't actully need it here
         restart: always
         <<: *airflow_env_var
-        command: bash -c "EXIT_CODE=1 && while [ $$EXIT_CODE -ne 0 ]; do (airflow db check); EXIT_CODE=$$?; sleep 5; done && cwl-airflow init --upgrade && airflow scheduler"
+        command: start_scheduler.sh
         depends_on:
             - mysql
 
@@ -52,7 +52,7 @@ services:
         <<: *airflow_volumes
         <<: *airflow_env_var
         restart: always
-        command: bash -c "EXIT_CODE=1 && while [ $$EXIT_CODE -ne 0 ]; do (mysql -h mysql -u ${MYSQL_USER} -p${MYSQL_PASSWORD} -e 'select * from ${MYSQL_DATABASE}.dag_run'); EXIT_CODE=$$?; sleep 5; done && airflow webserver"
+        command: start_webserver.sh
         depends_on:
             - scheduler  # need to start only after cwl-airflow init was run
 
@@ -67,7 +67,7 @@ services:
         <<: *airflow_volumes        
         <<: *airflow_env_var
         restart: always
-        command: bash -c "EXIT_CODE=1 && while [ $$EXIT_CODE -ne 0 ]; do (mysql -h mysql -u ${MYSQL_USER} -p${MYSQL_PASSWORD} -e 'select * from ${MYSQL_DATABASE}.dag_run'); EXIT_CODE=$$?; sleep 5; done && cwl-airflow api --replay 60 --host 0.0.0.0"
+        command: start_apiserver.sh --replay 60 --host 0.0.0.0
         depends_on:
             - scheduler  # need to start only after cwl-airflow init was run