Make blj_go and similar functions into stand-alone scripts; not funct…

…ions. This is for compatibility with non-bash shells.
mjzapata · Mar 9, 2020 · 3b18467 · 3b18467
1 parent a182da2
commit 3b18467
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Showing 19 changed files with 82 additions and 90 deletions.
diff --git a/resources/aws/ec2_head_node_profile b/resources/aws/ec2_head_node_profile
@@ -35,7 +35,7 @@ set_ec2_owner() {
 }
 
 # Initialize bash environment
-source "${BLJ_SCRIPT}/blj_config"
+source "${BLJ}/script/blj_config"
 [ "$(get_blj_prop docker.user)" != "" ] && export DOCKER_ID="$(get_blj_prop docker.user)"
 ######=========================================######
 ######   BioLockJ AWS ~/.bash_profile LOADED   ###### 

diff --git a/script/aws_config_lib b/script/aws_config_lib
@@ -2,7 +2,7 @@
 ##############################################################
 ##  This script contains functions to work with AWS Config  ##
 ##############################################################
-. ${BLJ_SCRIPT}/docker_functions
+. ${BLJ}/script/docker_functions
 
 AWS_CONF=~/.aws/aws_config
 STANDARD_CONFIG="${BLJ}/resources/config/default/standard.properties"

diff --git a/script/aws_functions b/script/aws_functions
@@ -3,11 +3,11 @@
 ##  This script is used for AWS core functions + logic      ##
 ##############################################################
 
-. ${BLJ_SCRIPT}/aws_config_lib
-. ${BLJ_SCRIPT}/aws_head_node_lib
-. ${BLJ_SCRIPT}/aws_upload_lib
-. ${BLJ_SCRIPT}/aws_clean_lib
-. ${BLJ_SCRIPT}/blj_functions
+. ${BLJ}/script/aws_config_lib
+. ${BLJ}/script/aws_head_node_lib
+. ${BLJ}/script/aws_upload_lib
+. ${BLJ}/script/aws_clean_lib
+. ${BLJ}/script/blj_functions
 
 alias clearPipes="sudo rm -rf ${EFS}/pipelines/*; echo AWS pipelines removed"
 alias tailnf="tail -1000f /.nextflow.log"

diff --git a/script/aws_upload_lib b/script/aws_upload_lib
@@ -101,7 +101,7 @@ stage_blj_config() {
 	console_log "Starting --> [ stage_blj_config  ]: Upload Pipeline Config --> EFS: $(basename $(get_config ec2))"
 	upload_to_efs "$(local_nf_conf)" "${EC2_HOME}/.nextflow/config"
 	upload_to_efs "${BLJ}/resources/aws/ec2_head_node_profile"
-	upload_to_efs "${BLJ_SCRIPT}" "${EFS}"
+	upload_to_efs "${BLJ}/script" "${EFS}"
 	upload_to_efs "$(get_config local)" "${BLJ_CONFIG}"
 	exe_remote_cmd 'mv ~/.bash_profile ~/.bash_profile~; mv ~/ec2_head_node_profile ~/.bash_profile'
 	localS3=$(get_property $(get_config local) aws.s3)

diff --git a/script/biolockj-api b/script/biolockj-api
@@ -25,8 +25,8 @@ main(){
     fi
 }
 
-. ${BLJ_SCRIPT}/blj_functions
-. ${BLJ_SCRIPT}/blj_user_arg_lib # note that several functions are over-written
+. ${BLJ}/script/blj_functions
+. ${BLJ}/script/blj_user_arg_lib # note that several functions are over-written
 
 # Optionally print a message, then show help, then exit with status 1
 # over-witten from blj_functions

diff --git a/script/blj_complete b/script/blj_complete
@@ -3,7 +3,7 @@
 ##  This script manually completes current module and pipeline status.       ##
 ##  All modules numbered below than the current module will also be reset.   ##
 ###############################################################################
-. ${BLJ_SCRIPT}/blj_functions
+. ${BLJ}/script/blj_functions
 
 if [ ${#1} -gt 0 ]; then myDir="${1}"; else myDir="$PWD"; fi
 echo "Starting [ blj_complete ] to reset status of modules before/including $myDir to --> \"biolockjComplete\""

diff --git a/script/blj_download b/script/blj_download
@@ -8,7 +8,7 @@
 ##  Users can copy the command and execute it from a local workstation.   ##
 ##                                                                        ##
 ############################################################################
-. ${BLJ_SCRIPT}/blj_functions
+. ${BLJ}/script/blj_functions
 
 pipeline=$(most_recent_pipeline)
 SUM=summary.txt

diff --git a/script/blj_go b/script/blj_go
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+## This script navigates the $USER to their most recent pipeline and lists the current directory
+
+. $BLJ/script/blj_functions 
+
+[ ! -d "${BLJ_PROJ}" ] && exit_script "Exit program - BLJ_PROJ: directory not found: ${BLJ_PROJ}" && return
+pipeline=$(most_recent_pipeline)
+if [ ${#pipeline} -gt 0 ]; then
+	echo "Goto latest BioLockJ pipeline: ${pipeline}"
+	cd "${pipeline}" && ls "${pipeline}"
+else
+	echo "No pipelines found in BLJ_PROJ: ${BLJ_PROJ}"
+fi
diff --git a/script/blj_log b/script/blj_log
@@ -0,0 +1,26 @@
+#!/bin/bash
+
+# This script tails 1K lines from the current pipelines Java log file.
+# If the current directory is not a BioLockJ pipeline, print last 1K lines from the most recent pipeline executed.  
+# If param is passed, pass it to tail command in place of -1000 parameter.
+
+. $BLJ/script/blj_functions 
+
+
+pipeline=$(current_pipeline)
+if [ ${#pipeline} -gt 0 ]; then
+echo "Tail current BioLockJ pipeline log: $pipeline"
+else
+	pipeline=$(most_recent_pipeline)
+	[ ${#pipeline} -gt 0 ] && echo "Tail most recent BioLockJ pipeline log: $pipeline"
+fi
+
+if [ ${#pipeline} -gt 0 ]; then
+	if [ ${#1} -gt 0 ]; then
+		\tail $1 $pipeline/*.log 
+	else
+		\tail -1000 $pipeline/*.log 
+	fi
+else
+	echo "No pipelines found in BLJ_PROJ: ${BLJ_PROJ}"
+fi
diff --git a/script/blj_reset b/script/blj_reset
@@ -18,7 +18,7 @@ main(){
 	echo "Reset complete."
 }
 
-. ${BLJ_SCRIPT}/blj_functions
+. ${BLJ}/script/blj_functions
 
 set_pipeline_dir(){
 	if $(is_pipeline_dir "$myDir"); then

diff --git a/script/blj_summary b/script/blj_summary
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+# This script prints the Summary BioModule output of current pipeline.
+# If the current directory is not a BioLockJ pipeline, print the summary of the most recent pipeline executed.
+
+. $BLJ/script/blj_functions 
+
+pipeline=$(most_recent_pipeline)
+SUM=summary.txt
+if [ -f $SUM ]; then
+	echo "Print summary file: $SUM"
+	cat $SUM
+elif [ ${#pipeline} -gt 0 ]; then
+	echo "Print summary file: $pipeline/$SUM"
+	cat "$pipeline/$SUM"
+else
+	echo "No pipeline summary found in BLJ_PROJ: ${BLJ_PROJ}"
+fi
diff --git a/script/blj_test b/script/blj_test
@@ -9,7 +9,7 @@
 ##  Otherwise exit script if any pipeline fails.                         ##
 ##                                                                       ##
 ###########################################################################
-. ${BLJ_SCRIPT}/blj_functions
+. ${BLJ}/script/blj_functions
 
 
 # Get pipeline status

diff --git a/script/blj_user_arg_lib b/script/blj_user_arg_lib
@@ -9,7 +9,7 @@
 ##                                                               ##
 ###################################################################
 
-. ${BLJ_SCRIPT}/blj_functions
+. ${BLJ}/script/blj_functions
 
 # example: take_standard_biolockj_args "$@"
 take_standard_biolockj_args(){

diff --git a/script/blj_user_lib b/script/blj_user_lib
diff --git a/script/docker_functions b/script/docker_functions
@@ -4,8 +4,8 @@
 ##  This script contains common functions used in BioLockJ.      ##
 ##                                                               ##
 ###################################################################
-. "${BLJ_SCRIPT}/docker_config"
-. ${BLJ_SCRIPT}/blj_functions
+. "${BLJ}/script/docker_config"
+. ${BLJ}/script/blj_functions
 
 alias bljb="build_blj_only"
 alias bljd="build_blj_only; clearDock; push_blj_only"

diff --git a/script/launch_aws b/script/launch_aws
@@ -25,7 +25,7 @@ main(){
 	fi
 }
 
-. ${BLJ_SCRIPT}/blj_user_arg_lib
-. ${BLJ_SCRIPT}/aws_functions
+. ${BLJ}/script/blj_user_arg_lib
+. ${BLJ}/script/aws_functions
 
 main $@
diff --git a/script/launch_docker b/script/launch_docker
@@ -52,8 +52,8 @@ main(){
 	ifArgUsed $GUI_ARG && startBrowser # if the gui has its own docker container, this CMD would be defined there
 }
 
-. ${BLJ_SCRIPT}/blj_user_arg_lib
-. ${BLJ_SCRIPT}/docker_config
+. ${BLJ}/script/blj_user_arg_lib
+. ${BLJ}/script/docker_config
 
 # Read script args and bash env vars
 # Param 1 - Array of launch_docker script args

diff --git a/script/launch_java b/script/launch_java
@@ -25,8 +25,8 @@ main(){
 	after_java_start
 }
 
-. ${BLJ_SCRIPT}/blj_functions
-. ${BLJ_SCRIPT}/blj_user_arg_lib
+. ${BLJ}/script/blj_functions
+. ${BLJ}/script/blj_user_arg_lib
 
 # Make sure required variables exist and are valid
 check_env_vars(){

diff --git a/script/make_nextflow b/script/make_nextflow
@@ -7,7 +7,7 @@
 ##  substituting "_" for each "." characters in the Java class name           ##
 ################################################################################
 . /app/biolockj/script/blj_config
-. ${BLJ_SCRIPT}/aws_functions
+. ${BLJ}/script/aws_functions
 
 # Build the template file that NextflowUtil.java will use to create the pipeline main.nf
 # Param 1 - All make_nextflow script args