Unverified Commit 7c68c878 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #14105 from mvdbeek/more_robust_test_exit_code_127_k8s_test 

Improve robustness of test_exit_code_127 k8s test
parents 24690547 13c34e97

lib/galaxy/datatypes/text.py

+2 −2
Original line number Diff line number Diff line
@@ -6,7 +6,6 @@ import json 
import logging

import os

import re

import shlex

import subprocess

import tempfile
@@ -28,6 +27,7 @@ from galaxy.datatypes.sniff import ( 
)

from galaxy.util import (

    nice_size,

    shlex_join,

    string_as_bool,

    unicodify,

)
@@ -219,7 +219,7 @@ class Ipynb(Json): 
                ofilename = dataset.file_name

                log.exception(

                    'Command "%s" failed. Could not convert the Jupyter Notebook to HTML, defaulting to plain text.',

                    " ".join(map(shlex.quote, cmd)),

                    shlex_join(cmd),

                )

            return open(ofilename, mode="rb"), headers

lib/galaxy/tool_util/deps/conda_util.py

+2 −2
Original line number Diff line number Diff line
@@ -4,7 +4,6 @@ import json 
import logging

import os

import re

import shlex

import shutil

import sys

import tempfile
@@ -18,6 +17,7 @@ import packaging.version 
from galaxy.util import (

    commands,

    listify,

    shlex_join,

    smart_str,

    which,

)
@@ -237,7 +237,7 @@ class CondaContext(installable.InstallableContext): 
        env = {}

        if self.condarc_override:

            env["CONDARC"] = self.condarc_override

        cmd_string = " ".join(map(shlex.quote, cmd))

        cmd_string = shlex_join(cmd)

        kwds = dict()

        try:

            if stdout_path:

lib/galaxy/tool_util/deps/mulled/mulled_build.py

+2 −2
Original line number Diff line number Diff line
@@ -12,7 +12,6 @@ Build a mulled image with: 
import json

import logging

import os

import shlex

import shutil

import stat

import string
@@ -31,6 +30,7 @@ from galaxy.tool_util.deps.docker_util import command_list as docker_command_lis 
from galaxy.util import (

    commands,

    safe_makedirs,

    shlex_join,

    unicodify,

)

from ._cli import arg_parser
@@ -301,7 +301,7 @@ def mull_targets( 
            involucro_args.insert(6, "-set")

            involucro_args.insert(7, f"TEST_BINDS={','.join(test_bind)}")

    cmd = involucro_context.build_command(involucro_args)

    print(f"Executing: {' '.join(shlex.quote(_) for _ in cmd)}")

    print(f"Executing: {shlex_join(cmd)}")

    if dry_run:

        return 0

    ensure_installed(involucro_context, True)

lib/galaxy/util/__init__.py

+9 −0
Original line number Diff line number Diff line
@@ -13,6 +13,7 @@ import json 
import os

import random

import re

import shlex

import shutil

import smtplib

import stat
@@ -77,6 +78,14 @@ from .path import ( # noqa: F401 
    safe_relpath,

)



try:

    shlex_join = shlex.join  # type: ignore[attr-defined]

except AttributeError:

    # Python < 3.8

    def shlex_join(split_command):

        return " ".join(map(shlex.quote, split_command))





inflector = Inflector()



log = get_logger(__name__)

lib/galaxy/util/path/__init__.py

+1 −1
Original line number Diff line number Diff line
@@ -365,7 +365,7 @@ def external_chown(path, pwent, external_chown_script, description="file"): 


        cmd = shlex.split(external_chown_script)

        cmd.extend([path, pwent[0], str(pwent[3])])

        log.debug(f"Changing ownership of {path} with: {' '.join(map(shlex.quote, cmd))}")

        log.debug(f"Changing ownership of {path} with: '{galaxy.util.shlex_join(cmd)}'")

        galaxy.util.commands.execute(cmd)

        return True

    except galaxy.util.commands.CommandLineException as e: