From ea960be59b8a4e4ae1c82b68f6d24324dd63374e Mon Sep 17 00:00:00 2001
From: oboulle <olivier.boulle@inria.fr>
Date: Thu, 14 Apr 2022 16:38:21 +0200
Subject: [PATCH] updated parsing
---
dna_add.sh | 30 +++++++++++++++---------------
dna_create.sh | 24 ++++++++++++------------
dna_del.sh | 32 +++++++++++++++++++++++++-------
dna_list.sh | 7 ++++---
dna_quick_complete_test.sh | 2 +-
dna_workflow.sh | 2 +-
6 files changed, 58 insertions(+), 39 deletions(-)
diff --git a/dna_add.sh b/dna_add.sh
index beadae6..04d4df8 100755
--- a/dna_add.sh
+++ b/dna_add.sh
@@ -9,9 +9,9 @@ source "$project_dir"/workflow_commands/log_manager.sh #load the log manager scr
help_function() {
echo ""
- echo "Usage: dna_add Cname Dname [-nocd]"
- echo -e "\tCname : path to the container"
- echo -e "\tDname : path to the document"
+ echo "Usage: dna_add container document [-nocd]"
+ echo -e "\tcontainer : path to the container"
+ echo -e "\tdocument : path to the document"
echo -e "\t-nocd : turn off channel encoding"
echo ""
exit 1 # Exit script after printing help
@@ -42,18 +42,18 @@ channel_coding=true
#-----------------------------------------------#
while [[ "$#" -gt 0 ]]; do
- case "$1" in
- -nocd ) channel_coding=false ; shift ;;
- -h | --help ) help_function ; exit 1 ;;
- -* ) echo "unknown parameter $1" ; exit 1 ;;
- * ) if test -z "${container_path:-}" ; then
- container_path="${1}" ; shift ;
- elif test -z "${document_path:-}" ; then
- document_path="${1}" ; shift ;
- else
- echo "unknown parameter $1" ; exit 1 ;
- fi ;;
- esac
+ case "$1" in
+ -nocd ) channel_coding=false ; shift ;;
+ -h | --help ) help_function ; exit 1 ;;
+ -* ) echo "unknown parameter $1" ; exit 1 ;;
+ * ) if test -z "${container_path:-}" ; then
+ container_path="${1}" ; shift ;
+ elif test -z "${document_path:-}" ; then
+ document_path="${1}" ; shift ;
+ else
+ echo "unknown parameter $1" ; exit 1 ;
+ fi ;;
+ esac
done
if test -z "${container_path:-}"
diff --git a/dna_create.sh b/dna_create.sh
index ce384b6..b1d5c05 100755
--- a/dna_create.sh
+++ b/dna_create.sh
@@ -8,11 +8,11 @@ source "$project_dir"/workflow_commands/metadata_manager.sh #load the xml manage
help_function() {
echo ""
- echo "Usage: dna_create [-sim] [-fl int] [-sp string] Cname"
+ echo "Usage: dna_create [-sim] [-fl int] [-sp string] container"
echo -e "\t-sim : turn on simulator mode"
echo -e "\t-fl : specify fragment length [default = 100]"
echo -e "\t-sp : specify spacer [default = AAAAAAAACCCCCCCC]"
- echo -e "\tCname : name of the container"
+ echo -e "\tcontainer : name of the container"
echo ""
exit 1 # Exit script after printing help
}
@@ -26,15 +26,15 @@ spacer="AAAAAAAACCCCCCCC"
######### ====== read parameters ====== #########
#-----------------------------------------------#
-while true; do
- case "$1" in
- -sim ) simulation=true ; shift ;;
- -fl ) frag_length=$2 ; shift 2 ;;
- -sp ) spacer=$2 ; shift 2 ;;
- -h | --help ) help_function ; exit 1;;
- -* ) echo "unknown parameter $1" ; exit 1;;
- * ) container_name="${1}" ; break ;;
- esac
+while [[ "$#" -gt 0 ]]; do
+ case "$1" in
+ -sim ) simulation=true ; shift ;;
+ -fl ) frag_length=$2 ; shift 2 ;;
+ -sp ) spacer=$2 ; shift 2 ;;
+ -h | --help ) help_function ; exit 1;;
+ -* ) echo "unknown parameter $1" ; exit 1;;
+ * ) container_name="${1}" ; break ;;
+ esac
done
int_regex='^[0-9]+$'
@@ -49,7 +49,7 @@ then
echo "error: spacer ($spacer) is not a dna sequence" ; exit 1
fi
-if test -z "$container_name"
+if test -z "${container_name:-}"
then
echo "container name missing"
help_function
diff --git a/dna_del.sh b/dna_del.sh
index 67dcd58..3ae9568 100755
--- a/dna_del.sh
+++ b/dna_del.sh
@@ -8,8 +8,8 @@ source "$project_dir"/workflow_commands/metadata_manager.sh #load the xml manage
help_function() {
echo ""
- echo "Usage: dna_del Cname DI"
- echo -e "\tCname : path to the container"
+ echo "Usage: dna_del container DI"
+ echo -e "\tcontainer : path to the container"
echo -e "\tDI : index of the document to delete"
echo ""
exit 1 # Exit script after printing help
@@ -19,12 +19,30 @@ help_function() {
######### ====== read parameters ====== #########
#-----------------------------------------------#
-container_path="${1}"
-doc_index="${2}"
+while [[ "$#" -gt 0 ]]; do
+ case "$1" in
+ -h | --help ) help_function ; exit 1 ;;
+ -* ) echo "unknown parameter $1" ; exit 1 ;;
+ * ) if test -z "${container_path:-}" ; then
+ container_path="${1}" ; shift ;
+ elif test -z "${doc_index:-}" ; then
+ doc_index="${1}" ; shift ;
+ else
+ echo "unknown parameter $1" ; exit 1 ;
+ fi ;;
+ esac
+done
-if [ "$#" != 2 ]
+if test -z "${container_path:-}"
then
- echo "error invalid number of arguments"
+ echo "container path missing"
+ help_function
+ exit 1
+fi
+
+if test -z "${doc_index:-}"
+then
+ echo "document index missing"
help_function
exit 1
fi
@@ -37,7 +55,7 @@ fi
if [ ! -d "$container_path"/$doc_index ]
then
- echo "error : $container_path does not contain a document of index $doc_index"
+ echo "error : container $container_path does not contain a document of index $doc_index"
exit 1
fi
diff --git a/dna_list.sh b/dna_list.sh
index a032fa5..6dbaba0 100755
--- a/dna_list.sh
+++ b/dna_list.sh
@@ -12,19 +12,20 @@ source "$project_dir"/workflow_commands/metadata_manager.sh #load the xml manage
help_function() {
echo ""
- echo "Usage: dna_list Cname"
- echo -e "\tCname : path to the container"
+ echo "Usage: dna_list container"
+ echo -e "\tcontainer : path to the container"
echo ""
exit 1 # Exit script after printing help
}
-container_path="${1}"
if [ "$#" != 1 ]
then
echo "error invalid number of arguments"
help_function
exit 1
+else
+ container_path="${1}"
fi
if [ ! -d "$container_path" ]
diff --git a/dna_quick_complete_test.sh b/dna_quick_complete_test.sh
index 809c9b9..604591d 100755
--- a/dna_quick_complete_test.sh
+++ b/dna_quick_complete_test.sh
@@ -27,7 +27,7 @@ rm -rf "$container_path"
"$commands_dir"/dna_create.sh -sim -fl 100 "$container_path"
-call_function "$commands_dir"/dna_add.sh -nocd "$commands_dir"/documents_test/doc.txt "$container_path"
+call_function "$commands_dir"/dna_add.sh -nocd "$container_path" "$commands_dir"/documents_test/doc.txt
#call_function "$commands_dir"/dna_add.sh -nocd "$commands_dir"/documents_test/img_50.png "$container_path"
diff --git a/dna_workflow.sh b/dna_workflow.sh
index daafe13..ef06ffb 100755
--- a/dna_workflow.sh
+++ b/dna_workflow.sh
@@ -60,7 +60,7 @@ fi
call_function "$commands_dir"/dna_create.sh -sim -fl 100 "$container_path" #TODO fl
-call_function "$commands_dir"/dna_add.sh "$document_path" "$container_path"
+call_function "$commands_dir"/dna_add.sh "$container_path" "$document_path"
call_function "$commands_dir"/dna_store.sh "$container_path"
--
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