Merge branch 'refs/heads/devel'

src/ingest-pipeline/misc/tools/auto_deploy.sh

@@ -2,15 +2,31 @@
 
 # What variables do we need?
 # Define HIVE machines
-#hive_machines=("l001.hive.psc.edu" "gpu002.pvt.hive.psc.edu")
+# hive_machines=("l001.hive.psc.edu" "gpu002.pvt.hive.psc.edu")
 hive_machines=()
-#b2_machines=("v004.pvt.bridges2.psc.edu")
+# b2_machines=("v004.pvt.bridges2.psc.edu")
 b2_machines=()
-repo_env="dev"
-repo_dir="/opt/repositories/$(hostname -s)-$repo_env/ingest-pipeline"
+
+priority_list=("-prod" "-test" "-dev")
+base_name="airflow"
+file_dir="/etc/sysconfig"
 
 regenerate_env=false
 
+function set_main_environment(){
+  for ending in "${priority_list[@]}"; do
+    file="$file_dir/$base_name$ending"
+    if [ -f "$file" ]; then
+        echo "Selected file: $file"
+        source $file
+        repo_env="$HUBMAP_INSTANCE"
+        python_version="$HUBMAP_PYTHON_VERSION"
+        repo_dir="/opt/repositories/$(hostname -s)-$repo_env/ingest-pipeline"
+        break
+    fi
+done
+}
+
 while getopts ":g" opt; do
   case $opt in
     g)
@@ -23,23 +39,30 @@ while getopts ":g" opt; do
 done
 
 set -x
-for machine in ${hive_machines[@]}; do
+
+set_main_environment
+
+if [ -z "$repo_env" ]; then
+    exit "The environment variable HUBMAP_INSTANCE is not set."
+fi
+
+for machine in "${codcc_machines[@]}"; do
        	# Rsync repo to machine
         rsync -a --exclude "src/ingest-pipeline/airflow/logs" $repo_dir/ $machine:$repo_dir
 
        	# If flag set, run the conda environment regenerations
         if $regenerate_env ; then
-                ssh $machine "/usr/local/bin/update_hubmap.sh $repo_dir $repo_env"
+                ssh $machine "/usr/local/bin/update_hubmap.sh $repo_dir $repo_env $python_version"
         fi
 done
 
 # Separate because its easier to loop twice over a small list than insert string checking and manipulation
-for machine in ${b2_machines[@]}; do
+for machine in "${b2_machines[@]}"; do
         # Rsync repo to machine
         rsync -a --exclude "src/ingest-pipeline/airflow/logs" 'ssh -J bridges2.psc.edu' $repo_dir/ $machine:$repo_dir
 
         # If flag set, run the conda environment regenerations
         if $regenerate_env ; then
-                ssh -J "bridges2.psc.edu" $machine "/usr/local/bin/update_hubmap.sh $repo_dir $repo_env"
+                ssh -J "bridges2.psc.edu" $machine "/usr/local/bin/update_hubmap.sh $repo_dir $repo_env $python_version"
         fi
 done