Fix issues reported by ShellCheck

arash77 · Jun 13, 2019 · 90a6c6d · 90a6c6d
1 parent 421eca8
commit 90a6c6d
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Showing 25 changed files with 55 additions and 58 deletions.
diff --git a/create_db.sh b/create_db.sh
@@ -1,9 +1,9 @@
 #!/bin/sh
 
-cd `dirname $0`
+cd "$(dirname "$0")"
 
 . ./scripts/common_startup_functions.sh
 
 setup_python
 
-python ./scripts/create_db.py $@
+python ./scripts/create_db.py "$@"
diff --git a/extract_dataset_parts.sh b/extract_dataset_parts.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 
-cd `dirname $0`
+cd "$(dirname "$0")"
 
 . ./scripts/common_startup_functions.sh
 
@@ -9,5 +9,5 @@ setup_python
 for file in $1/split_info*.json
 do
     # echo processing $file
-    python ./scripts/extract_dataset_part.py $file
+    python ./scripts/extract_dataset_part.py "$file"
 done
diff --git a/run_tests.sh b/run_tests.sh
@@ -1,7 +1,6 @@
 #!/bin/sh
 
-pwd_dir=$(pwd)
-cd `dirname $0`
+cd "$(dirname "$0")"
 
 rm -f run_functional_tests.log
 
@@ -318,8 +317,8 @@ then
         -e "GALAXY_TEST_DATABASE_TYPE=$db_type" \
         -e "LC_ALL=C" \
         --rm \
-        -v `pwd`:/galaxy \
-        -v `pwd`/test/docker/base/run_test_wrapper.sh:/usr/local/bin/run_test_wrapper.sh $DOCKER_IMAGE "$@"
+        -v "$(pwd)":/galaxy \
+        -v "$(pwd)"/test/docker/base/run_test_wrapper.sh:/usr/local/bin/run_test_wrapper.sh "$DOCKER_IMAGE" "$@"
     exit $?
 fi
 
@@ -607,7 +606,7 @@ elif [ -n "$toolshed_script" ]; then
 elif [ -n "$api_script" ]; then
     extra_args="$api_script"
 elif [ -n "$section_id" ]; then
-    extra_args=`python tool_list.py $section_id`
+    extra_args=$(python tool_list.py "$section_id")
 elif [ -n "$unit_extra" ]; then
     extra_args="$unit_extra"
 elif [ -n "$integration_extra" ]; then

diff --git a/scripts/cleanup_datasets/delete_datasets.sh b/scripts/cleanup_datasets/delete_datasets.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -6 -r $@ >> ./scripts/cleanup_datasets/delete_datasets.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -6 -r "$@" >> ./scripts/cleanup_datasets/delete_datasets.log
diff --git a/scripts/cleanup_datasets/delete_userless_histories.sh b/scripts/cleanup_datasets/delete_userless_histories.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -1 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -1 "$@" >> ./scripts/cleanup_datasets/delete_userless_histories.log
diff --git a/scripts/cleanup_datasets/populate_uuid.sh b/scripts/cleanup_datasets/populate_uuid.sh
@@ -1,5 +1,5 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
+cd "$(dirname "$0")"/../..
 export PYTHONPATH=./lib/
-python ./scripts/cleanup_datasets/populate_uuid.py ./config/galaxy.ini $@
+python ./scripts/cleanup_datasets/populate_uuid.py ./config/galaxy.ini "$@"
diff --git a/scripts/cleanup_datasets/purge_datasets.sh b/scripts/cleanup_datasets/purge_datasets.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -3 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -3 -r "$@" >> ./scripts/cleanup_datasets/purge_datasets.log
diff --git a/scripts/cleanup_datasets/purge_folders.sh b/scripts/cleanup_datasets/purge_folders.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -5 -r $@ >> ./scripts/cleanup_datasets/purge_folders.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -5 -r "$@" >> ./scripts/cleanup_datasets/purge_folders.log
diff --git a/scripts/cleanup_datasets/purge_histories.sh b/scripts/cleanup_datasets/purge_histories.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -2 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -2 -r "$@" >> ./scripts/cleanup_datasets/purge_histories.log
diff --git a/scripts/cleanup_datasets/purge_libraries.sh b/scripts/cleanup_datasets/purge_libraries.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log
+cd "$(dirname "$0")"/../..
+python ./scripts/cleanup_datasets/cleanup_datasets.py -d 10 -4 -r "$@" >> ./scripts/cleanup_datasets/purge_libraries.log
diff --git a/scripts/cleanup_datasets/update_metadata.sh b/scripts/cleanup_datasets/update_metadata.sh
@@ -6,4 +6,4 @@
 . ./scripts/get_python.sh
 . ./setup_paths.sh
 
-$GALAXY_PYTHON ./scripts/cleanup_datasets/update_metadata.py ./config/galaxy.ini $@
+"$GALAXY_PYTHON" ./scripts/cleanup_datasets/update_metadata.py ./config/galaxy.ini "$@"
diff --git a/scripts/maintenance.sh b/scripts/maintenance.sh
@@ -6,7 +6,7 @@
 set -e
 
 display_help(){
-  scriptname=`basename $0`
+  scriptname=$(basename "$0")
   printf "./$scriptname [--help] [--no-dry-run] [--days 10] 
 Will run the galaxy cleanup scripts in the recommend order. By default a 'dry-run' is started. Specify --no-dry-run to do the actual cleanup.
 
@@ -52,7 +52,7 @@ do
   esac
 done
 
-cd "$(cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd)"/../
+cd "$(dirname "$0")"/..
 
 . scripts/common_startup_functions.sh
 

diff --git a/scripts/migrate_tools/0002_tools.sh b/scripts/migrate_tools/0002_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0002_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0002_tools.xml "$@"
diff --git a/scripts/migrate_tools/0003_tools.sh b/scripts/migrate_tools/0003_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0003_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0003_tools.xml "$@"
diff --git a/scripts/migrate_tools/0004_tools.sh b/scripts/migrate_tools/0004_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0004_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0004_tools.xml "$@"
diff --git a/scripts/migrate_tools/0005_tools.sh b/scripts/migrate_tools/0005_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0005_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0005_tools.xml "$@"
diff --git a/scripts/migrate_tools/0006_tools.sh b/scripts/migrate_tools/0006_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0006_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0006_tools.xml "$@"
diff --git a/scripts/migrate_tools/0007_tools.sh b/scripts/migrate_tools/0007_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0007_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0007_tools.xml "$@"
diff --git a/scripts/migrate_tools/0008_tools.sh b/scripts/migrate_tools/0008_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml "$@"
diff --git a/scripts/migrate_tools/0009_tools.sh b/scripts/migrate_tools/0009_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0009_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0009_tools.xml "$@"
diff --git a/scripts/migrate_tools/0010_tools.sh b/scripts/migrate_tools/0010_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0010_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0010_tools.xml "$@"
diff --git a/scripts/migrate_tools/0011_tools.sh b/scripts/migrate_tools/0011_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0011_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0011_tools.xml "$@"
diff --git a/scripts/migrate_tools/0012_tools.sh b/scripts/migrate_tools/0012_tools.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
-python ./scripts/migrate_tools/migrate_tools.py 0012_tools.xml $@
+cd "$(dirname "$0")"/../..
+python ./scripts/migrate_tools/migrate_tools.py 0012_tools.xml "$@"
diff --git a/scripts/tool_shed/migrate_tools_to_repositories.sh b/scripts/tool_shed/migrate_tools_to_repositories.sh
@@ -1,4 +1,4 @@
 #!/bin/sh
 
-cd `dirname $0`/../..
+cd "$(dirname "$0")"/../..
 python ./scripts/tool_shed/migrate_tools_to_repositories.py ./community_wsgi.ini >> ./scripts/tool_shed/migrate_tools_to_repositories.log
diff --git a/scripts/validate_tools.sh b/scripts/validate_tools.sh
@@ -1,33 +1,31 @@
 #!/bin/sh
 
-cd `dirname $0`/..
+cd "$(dirname "$0")"/..
 
 GALAXY_SKIP_CLIENT_BUILD=1 ./scripts/common_startup.sh
 GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-.venv}"
-if [ -d "$GALAXY_VIRTUAL_ENV" ];
-then
+if [ -d "$GALAXY_VIRTUAL_ENV" ]; then
     printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
     . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
 xsd_path="lib/galaxy/tool_util/xsd/galaxy.xsd"
 
-err_tmp=`mktemp`
+err_tmp=$(mktemp)
 count=0
 exit=0
 for p in "$@"; do
     count=$((count+1))
     path="$p"
-    echo $path
+    echo "$path"
     PYTHONPATH=lib:$PYTHONPATH
     export PYTHONPATH
-    result=`python -c "import galaxy.tool_util.loader; import xml.etree; xml.etree.ElementTree.dump(galaxy.tool_util.loader.load_tool('$path').getroot())" | xmllint --nowarning --noout --schema "$xsd_path" - 2> "$err_tmp"`
-    if [ $? -eq 0 ]
-    then
+    python -c "import galaxy.tool_util.loader; import xml.etree; xml.etree.ElementTree.dump(galaxy.tool_util.loader.load_tool('$path').getroot())" | xmllint --nowarning --noout --schema "$xsd_path" - 2> "$err_tmp"
+    if [ $? -eq 0 ]; then
         echo "ok $count";
     else
         echo "not ok $count $path";
-        cat "$err_tmp" | sed 's/^/    /'
+        sed 's/^/    /' "$err_tmp"
         exit=1
     fi
 done