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Fix issues reported by ShellCheck

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This commit is contained in:
Nicola Soranzo
2019-06-13 12:53:26 +01:00
parent 421eca8eb7
commit 90a6c6d46b
25 changed files with 55 additions and 58 deletions
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scripts/cleanup_datasets/delete_datasets.sh
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@@ -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
scripts/cleanup_datasets/delete_userless_histories.sh
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@@ -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
scripts/cleanup_datasets/populate_uuid.sh
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@@ -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 $@
python ./scripts/cleanup_datasets/populate_uuid.py ./config/galaxy.ini "$@"
scripts/cleanup_datasets/purge_datasets.sh
+2 -2
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@@ -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
scripts/cleanup_datasets/purge_folders.sh
+2 -2
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@@ -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
scripts/cleanup_datasets/purge_histories.sh
+2 -2
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@@ -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
scripts/cleanup_datasets/purge_libraries.sh
+2 -2
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@@ -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
scripts/cleanup_datasets/update_metadata.sh
+1 -1
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@@ -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 "$@"
scripts/maintenance.sh
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@@ -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
scripts/migrate_tools/0002_tools.sh
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@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`/../..
python ./scripts/migrate_tools/migrate_tools.py 0002_tools.xml $@
cd "$(dirname "$0")"/../..
python ./scripts/migrate_tools/migrate_tools.py 0002_tools.xml "$@"
scripts/migrate_tools/0003_tools.sh
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@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`/../..
python ./scripts/migrate_tools/migrate_tools.py 0003_tools.xml $@
cd "$(dirname "$0")"/../..
python ./scripts/migrate_tools/migrate_tools.py 0003_tools.xml "$@"
scripts/migrate_tools/0004_tools.sh
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@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`/../..
python ./scripts/migrate_tools/migrate_tools.py 0004_tools.xml $@
cd "$(dirname "$0")"/../..
python ./scripts/migrate_tools/migrate_tools.py 0004_tools.xml "$@"
scripts/migrate_tools/0005_tools.sh
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@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`/../..
python ./scripts/migrate_tools/migrate_tools.py 0005_tools.xml $@
cd "$(dirname "$0")"/../..
python ./scripts/migrate_tools/migrate_tools.py 0005_tools.xml "$@"
scripts/migrate_tools/0006_tools.sh
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@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`/../..
python ./scripts/migrate_tools/migrate_tools.py 0006_tools.xml $@
cd "$(dirname "$0")"/../..
python ./scripts/migrate_tools/migrate_tools.py 0006_tools.xml "$@"
scripts/migrate_tools/0007_tools.sh
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@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`/../..
python ./scripts/migrate_tools/migrate_tools.py 0007_tools.xml $@
cd "$(dirname "$0")"/../..
python ./scripts/migrate_tools/migrate_tools.py 0007_tools.xml "$@"
scripts/migrate_tools/0008_tools.sh
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@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`/../..
python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml $@
cd "$(dirname "$0")"/../..
python ./scripts/migrate_tools/migrate_tools.py 0008_tools.xml "$@"
scripts/migrate_tools/0009_tools.sh
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@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`/../..
python ./scripts/migrate_tools/migrate_tools.py 0009_tools.xml $@
cd "$(dirname "$0")"/../..
python ./scripts/migrate_tools/migrate_tools.py 0009_tools.xml "$@"
scripts/migrate_tools/0010_tools.sh
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@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`/../..
python ./scripts/migrate_tools/migrate_tools.py 0010_tools.xml $@
cd "$(dirname "$0")"/../..
python ./scripts/migrate_tools/migrate_tools.py 0010_tools.xml "$@"
scripts/migrate_tools/0011_tools.sh
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@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`/../..
python ./scripts/migrate_tools/migrate_tools.py 0011_tools.xml $@
cd "$(dirname "$0")"/../..
python ./scripts/migrate_tools/migrate_tools.py 0011_tools.xml "$@"
scripts/migrate_tools/0012_tools.sh
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@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`/../..
python ./scripts/migrate_tools/migrate_tools.py 0012_tools.xml $@
cd "$(dirname "$0")"/../..
python ./scripts/migrate_tools/migrate_tools.py 0012_tools.xml "$@"
scripts/tool_shed/migrate_tools_to_repositories.sh
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@@ -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
scripts/validate_tools.sh
+7 -9
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@@ -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