Skip to content

JobWrapper: use correct fail method #14210

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
bernt-matthias wants to merge 3 commits into from
Closed

JobWrapper: use correct fail method #14210

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
6803572
JobWrapper: use correct fail method
bernt-matthias Jun 28, 2022
b55b630
add a test
bernt-matthias Jun 28, 2022
66274f0
Revert "JobWrapper: use correct fail method"
bernt-matthias Jun 28, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 3 additions & 1 deletion test/functional/tools/strict_shell.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
<tool id="strict_shell" name="strict_shell" version="1.0.0">
<command strict="true" detect_errors="exit_code"><![CDATA[
echo "Hello" > '$out_file1';
#if $exit_code == "0"
echo "Hello" > '$out_file1';
#end if
sh -c 'exit $exit_code';
sh -c 'exit 0'
]]></command>
Expand Down
8 changes: 5 additions & 3 deletions test/functional/tools/strict_shell_default_off.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
<tool id="strict_shell_default_off" name="strict_shell_default_off" version="1.0.0">
<command detect_errors="exit_code"><![CDATA[
echo 'Hello' > '$out_file1'
; sh -c 'exit $exit_code'
; sh -c 'exit 0'
#if $exit_code == "0"
echo 'Hello' > '$out_file1';
#end if
sh -c 'exit $exit_code';
sh -c 'exit 0'
]]></command>
<inputs>
<param name="exit_code" type="integer" value="0" label="exit code"/>
Expand Down
8 changes: 5 additions & 3 deletions test/functional/tools/strict_shell_profile.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
<tool id="strict_shell_profile" name="strict_shell_profile" version="1.0.0" profile="20.09">
<command detect_errors="exit_code"><![CDATA[
echo 'Hello' > '$out_file1'
; sh -c 'exit $exit_code'
; sh -c 'exit 0'
#if $exit_code == 0
echo 'Hello' > '$out_file1';
#end if
sh -c 'exit $exit_code';
sh -c 'exit 0'
]]></command>
<inputs>
<param name="exit_code" type="integer" value="0" label="exit code"/>
Expand Down
2 changes: 1 addition & 1 deletion test/integration/test_job_outputs_to_working_directory.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,5 +17,5 @@ def handle_galaxy_config_kwds(cls, config):
instance = integration_util.integration_module_instance(JobOutputsToWorkingDirectoryIntegrationInstance)

test_tools = integration_util.integration_tool_runner(
["output_format", "output_empty_work_dir", "collection_creates_pair_from_work_dir"]
["output_format", "output_empty_work_dir", "collection_creates_pair_from_work_dir", "strict_shell_profile"]
)