Unverified Commit 468d5e0c authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #13913 from bgruening/fix_job_stderr 

[22.01] Redirect stderr of trap cleanup
parents e1031759 149af62e

lib/galaxy/jobs/command_factory.py

+2 −2
Original line number Diff line number Diff line
@@ -278,11 +278,11 @@ class CommandsBuilder: 
        self.append_command("; ".join(c for c in commands if c))



    def capture_stdout_stderr(self, stdout_file, stderr_file):

        trap_command = """trap 'rm "$__out" "$__err"' EXIT"""

        trap_command = """trap 'rm -f "$__out" "$__err"' EXIT"""

        if TRAP_KILL_CONTAINER in self.commands:

            # We need to replace the container kill trap with one that removes the named pipes and kills the container

            self.commands = self.commands.replace(TRAP_KILL_CONTAINER, "")

            trap_command = """trap 'rm "$__out" "$__err" 2> /dev/null || true; _on_exit' EXIT"""

            trap_command = """trap 'rm -f "$__out" "$__err"; _on_exit' EXIT"""

        self.prepend_command(

            f"""__out="${{TMPDIR:-.}}/out.$$" __err="${{TMPDIR:-.}}/err.$$"

mkfifo "$__out" "$__err"

lib/galaxy/webapps/galaxy/api/__init__.py

+3 −1
Original line number Diff line number Diff line
@@ -183,7 +183,9 @@ class GalaxyASGIRequest(GalaxyAbstractRequest): 


    @property

    def host(self) -> str:

        return str(self.__request.client.host)

        client = self.__request.client

        assert client is not None

        return str(client.host)





class GalaxyASGIResponse(GalaxyAbstractResponse):

test/unit/app/jobs/test_command_factory.py

+3 −3
Original line number Diff line number Diff line
@@ -22,7 +22,7 @@ CAPTURE_AND_REDIRECT = f"{TEE_REDIRECT}{RETURN_CODE_CAPTURE}" 
CP_WORK_DIR_OUTPUTS = '; \nif [ -f "foo" ] ; then cp "foo" "bar" ; fi'

TEE_LOG = """__out="${TMPDIR:-.}/out.$$" __err="${TMPDIR:-.}/err.$$"

mkfifo "$__out" "$__err"

trap 'rm "$__out" "$__err"' EXIT

trap 'rm -f "$__out" "$__err"' EXIT

tee -a '../outputs/tool_stdout' < "$__out" &

tee -a '../outputs/tool_stderr' < "$__err" >&2 & """
@@ -53,8 +53,8 @@ class TestCommandFactory(TestCase): 
        self.include_work_dir_outputs = False

        self.job_wrapper.command_line = f"{TRAP_KILL_CONTAINER}{MOCK_COMMAND_LINE}"

        expected_command_line = self._surround_command(MOCK_COMMAND_LINE).replace(

            """trap 'rm "$__out" "$__err"' EXIT""",

            """trap 'rm "$__out" "$__err" 2> /dev/null || true; _on_exit' EXIT"""

            """trap 'rm -f "$__out" "$__err"' EXIT""",

            """trap 'rm -f "$__out" "$__err"; _on_exit' EXIT"""

        )

        self.__assert_command_is(expected_command_line)