Wait for wait

lib/galaxy/datatypes/text.py

@@ -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

@@ -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

@@ -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

@@ -13,6 +13,7 @@ import json
 import os
 import random
 import re
+import shlex
 import shutil
 import smtplib
 import stat
@@ -77,6 +78,12 @@ from .path import (  # noqa: F401
     safe_relpath,
 )
 
+try:
+    shlex_join = shlex.join  # type: ignore[attr-defined]
+except AttributeError:
+    # Python < 3.8
+    shlex_join = lambda split_command: " ".join(map(shlex.quote, split_command))  # noqa: E731
+
 inflector = Inflector()
 
 log = get_logger(__name__)

lib/galaxy/util/path/__init__.py

@@ -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:

test/integration/test_kubernetes_runner.py

@@ -11,10 +11,14 @@ import time
 
 import pytest
 
-from galaxy.util import unicodify
+from galaxy.util import (
+    shlex_join,
+    unicodify,
+)
 from galaxy_test.base.populators import (
     DatasetPopulator,
     skip_without_tool,
+    wait_on,
 )
 from galaxy_test.driver import integration_util
 from .test_containerized_jobs import MulledJobTestCases
@@ -323,13 +327,21 @@ class BaseKubernetesIntegrationTestCase(BaseJobEnvironmentIntegrationTestCase, M
         self._wait_for_external_state(sa_session=sa_session, job=job, expected=app.model.Job.states.RUNNING)
 
         external_id = job.job_runner_external_id
-        log_cmd = ["kubectl", "logs", "-l", f"job-name={external_id}"]
-        p = subprocess.run(log_cmd, capture_output=True, text=True)
-        if p.returncode:
-            raise Exception(
-                f"Command '{' '.join(log_cmd)}' failed with exit code: {p.returncode}.\nstdout: {p.stdout}\nstderr: {p.stderr}"
-            )
-        output = p.stdout
+
+        def get_kubectl_logs(allow_wait=True):
+            log_cmd = ["kubectl", "logs", "-l", f"job-name={external_id}"]
+            p = subprocess.run(log_cmd, capture_output=True, text=True)
+            if p.returncode:
+                if allow_wait and "is waiting to start" in p.stderr:
+                    return None
+                raise Exception(
+                    f"Command '{shlex_join}' failed with exit code: {p.returncode}.\nstdout: {p.stdout}\nstderr: {p.stderr}"
+                )
+            return p.stdout
+
+        wait_on(get_kubectl_logs, "k8s logs")
+        output = get_kubectl_logs(allow_wait=False)
+
         EXPECTED_STDOUT = "The bool is not true"
         EXPECTED_STDERR = "The bool is very not true"
         assert EXPECTED_STDOUT in output