moved pipeline_wrapper_sh to new function; new flags --deployment and --analysis

scripts/deploy_all_pipelines.sh

@@ -18,8 +18,10 @@ ${bold}Description:${normal}
 Deploy all pipelines in the scope of the BfR-ABC-Harmonization repository
 
 ${bold}Optional Named Arguments:${normal}
--d, --deploy_paths              Override deploy base path (default: <git_parent_dir> from paths.cfg)
--a, --auto                      Do not ask for interactive confirmation, e.g. for automated deployments
+-d, --deployment                Deploy BfR-ABC pipelines to <deploy_path>
+-a, --analysis                  Analyse BfR-ABC pipelines test datasets
+-p, --deploy_path               Override deploy base path (default: <git_parent_dir> from paths.cfg)
+--auto                          Do not ask for interactive confirmation, e.g. for automated deployments
 --imeanit                       Do not perform a dryrun
 
 ${bold}Example:${normal}
@@ -35,10 +37,12 @@ parse_args() {
   ## default values of variables
   repo_path=$(dirname "$script_path")
   args_git_parent_dir=""
-
-  ## default values of switches
   args_dryrun="--dryrun"
   args_interactive=""
+
+  ## default values of switches
+  args_deployment=false
+  args_analysis=false
   dryrun=true
   interactive=true
 
@@ -50,7 +54,15 @@ parse_args() {
       set -x
       shift
       ;;
-    -d | --deploy_paths)
+    -d | --deployment)
+      args_deployment=true
+      shift
+      ;;
+    -a | --analysis)
+      args_analysis=true
+      shift
+      ;;
+    -p | --deploy_paths)
       args_git_parent_dir=${2:-}
       shift 2
       ;;
@@ -59,7 +71,7 @@ parse_args() {
       dryrun=false
       shift
       ;;
-    -a | --auto)
+    --auto) # -a is already taken
       args_interactive="--auto"
       interactive=false
       shift
@@ -154,7 +166,6 @@ deploy_single_pipeline() {
   skip_git_pull=true
   skip_setup_env=true
   skip_setup_data=true
-  skip_test_analysis=false # TODO: change to true
 
   pipeline=$1
   branch=${2:-main}
@@ -178,22 +189,17 @@ branch:|$branch
 
   ## setup mamba environment
   [[ ! "${conda_envs[*]}" =~ ${pipeline,,} && -f "$pipeline_dir/${pipeline_setup_sh[$pipeline]}" ]] && skip_setup_env=false || logwarn "Conda environment already exists or setup script not found"
-  [[ $skip_setup_env == false ]] && logexec bash "$pipeline_dir"/"${pipeline_setup_sh[$pipeline]}" $args_interactive ${setup_args_env[$pipeline]}
+  [[ $skip_setup_env == false ]] && logexec bash "$pipeline_dir"/"${pipeline_setup_sh[$pipeline]}" $args_interactive "${setup_args_env[$pipeline]}"
 
   ## setup data dependencies
   [[ -f "$pipeline_dir/${pipeline_setup_sh[$pipeline]}" && $(find $pipeline_dir/test_data -type f \( -name "*.sha256" -o -name "*.md5" \) | wc -l) -lt 1 ]] && skip_setup_data=false || logwarn "Data already retrieved or setup script not found"
-  [[ $skip_setup_data == false ]] && logexec bash "$pipeline_dir"/"${pipeline_setup_sh[$pipeline]}" $args_interactive ${setup_args_data[$pipeline]}
-
-  ## analyze test data
-  # TODO: create a test for successful data analysis, maybe pipeline status
-  [[ $skip_test_analysis == false ]] && logexec bash "$pipeline_dir"/"${pipeline_wrapper_sh[$pipeline]}" $args_interactive --norun
+  [[ $skip_setup_data == false ]] && logexec bash "$pipeline_dir"/"${pipeline_setup_sh[$pipeline]}" $args_interactive "${setup_args_data[$pipeline]}"
 
   logsuccess "Pipeline $pipeline deployed successfully"
-  return 0
 }
 
 deploy_bfr_abc() {
-  ## [Rationale] create_symlinks() This is the Rationale for create_symlinks() and mode "create"
+  ## [Rationale] deploy_bfr_abc() This is the Rationale for deploy_bfr_abc() and mode "--deployment"
 
   local pipeline branch="feature/harmonization"
 
@@ -226,14 +232,60 @@ deploy_bfr_abc() {
 
   # deploy pipelines from branch
   for pipeline in "${!repository_origin_urls[@]}"; do
-    echo
-    interactive_query "Deploy pipeline $pipeline?" || continue
+    [[ $interactive == true ]] && (
+      echo
+      interactive_query "Analyse pipeline ${magenta}$pipeline${normal}?" || continue # TODO: interactive_query exits upon "no"; This only exits the subshell caused by the (..) group.
+    )
     deploy_single_pipeline "$pipeline" "$branch"
   done
 
   echo
 }
 
+analyse_single_pipeline() {
+  ## [Rationale] analyse_single_pipeline() This is the Rationale for analyse_single_pipeline() which is looped in analyse_bfr_abc()
+
+  local pipeline pipeline_dir skip_test_analysis
+  skip_test_analysis=true
+
+  pipeline=$1
+  logheader "Test data analysis of pipeline $pipeline:"
+
+  ## check if directory exists
+  pipeline_dir="$git_parent_dir/$pipeline"
+
+  echo "
+pipeline_dir:|$pipeline_dir
+" | column -t -s "|" | logpipe
+
+  ## analyse test data
+  [[ $(find "$pipeline_dir/test_data" -type f -name "pipeline_status*" | wc -l) -lt 1 ]] && skip_test_analysis=false || logwarn "No test data found"
+  [[ $skip_test_analysis == false ]] && logexec bash "$pipeline_dir"/"${pipeline_wrapper_sh[$pipeline]}" $args_interactive --norun
+
+  logsuccess "Pipeline $pipeline test data analysed successfully"
+}
+
+analyse_bfr_abc() {
+  ## [Rationale] analyse_bfr_abc() This is the Rationale for deploy_bfr_abc() and mode "--analysis"
+
+  local pipeline
+
+  pipeline_table_column2array "pipeline_wrapper_sh"
+  declare -g -A pipeline_wrapper_sh
+  for key in "${!column_array[@]}"; do pipeline_wrapper_sh["$key"]="${column_array[$key]}"; done
+
+  # deploy pipelines from branch
+  for pipeline in "${!pipeline_wrapper_sh[@]}"; do
+    [[ $interactive == true ]] && (
+      echo
+      interactive_query "Analyse pipeline ${magenta}$pipeline${normal}?" || continue # TODO: interactive_query exits upon "no"; This only exits the subshell caused by the (..) group.
+    )
+    analyse_single_pipeline "$pipeline"
+  done
+
+  echo
+}
+
 ## (3) Main
 
 define_paths
@@ -242,8 +294,9 @@ logglobal "Arguments: ${*:-"No arguments provided"}"
 show_info
 
 ## Workflow
-deploy_bfr_abc
+[[ $args_deployment == true ]] && deploy_bfr_abc
+[[ $args_analysis == true ]] && analyse_bfr_abc
 
 logglobal "All steps were logged to: $logfile"
 logglobal "[STOP] $script_real"
-echo "Thank you for deploying the BfR-ABC"
+echo "Thank you for using the BfR-ABC"