Revert "always check output file existence"

This reverts commit 131576f. Reverted because also the user may purge the dataset during the job. Also remove the test tool from the framework tests.
galaxyproject · Aug 5, 2022 · 32207c6 · 32207c6
1 parent 9e46bd3
commit 32207c6
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Showing 3 changed files with 4 additions and 8 deletions.
diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
@@ -1697,12 +1697,6 @@ def fail(message=job.info, exception=None):
                         # Prior to fail we need to set job.state
                         job.set_state(final_job_state)
                         return fail(f"Job {job.id}'s output dataset(s) could not be read")
-        else:
-            # check existence of outputs (tools may delete outputs)
-            for dataset_path in self.get_output_fnames():
-                if not os.path.exists(dataset_path.real_path):
-                    job.set_state(final_job_state)
-                    return fail(f"Job {job.id}'s output dataset(s) could not be read")
 
         job_context = ExpressionContext(dict(stdout=job.stdout, stderr=job.stderr))
         if extended_metadata:

diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
@@ -215,8 +215,6 @@
   <tool file="interactivetool_two_entry_points.xml" />
   <tool file="converter_target_datatype.xml" />
 
-  <tool file="tool_deleting_output.xml" />
-
   <!-- Tools interesting only for building up test workflows. -->
 
   <!-- Next three tools demonstrate concatenating multiple datasets

diff --git a/test/functional/tools/tool_deleting_output.xml b/test/functional/tools/tool_deleting_output.xml
@@ -22,5 +22,9 @@ exit $exit_code
         the job should fail independent of the exit code and the exit code should be correctly checked.
 
         With outputs_to_working_directory this provoked https://github.com/galaxyproject/galaxy/issues/14206
+
+        The tool is currently tested only within  https://github.com/galaxyproject/galaxy/blob/dev/test/integration/test_job_outputs_to_working_directory.python_environment_problem
+        but not in the framework tests since in the framework test setting tool test #1 will
+        not fail (because also the user may purge the output)
     ]]></help>
 </tool>