Merge remote-tracking branch 'upstream/release_23.0' into dev

galaxyproject · Apr 10, 2023 · 3774cc3 · 3774cc3
2 parents d84f0dc + 629655d
commit 3774cc3
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Showing 3 changed files with 8 additions and 7 deletions.
diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt
@@ -121,7 +121,7 @@ pkgutil-resolve-name==1.3.10 ; python_version >= "3.7" and python_version < "3.9
 prompt-toolkit==3.0.38 ; python_version >= "3.7" and python_version < "3.12"
 prov==1.5.1 ; python_version >= "3.7" and python_version < "3.12"
 psutil==5.9.4 ; python_version >= "3.7" and python_version < "3.12"
-pulsar-galaxy-lib==0.15.0.dev1 ; python_version >= "3.7" and python_version < "3.12"
+pulsar-galaxy-lib==0.15.0.dev2 ; python_version >= "3.7" and python_version < "3.12"
 pyasn1==0.4.8 ; python_version >= "3.7" and python_version < "3.12"
 pycparser==2.21 ; python_version >= "3.7" and python_version < "3.12"
 pycryptodome==3.17 ; python_version >= "3.7" and python_version < "3.12"

diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
@@ -104,12 +104,12 @@ def build_command(
         else:
             commands_builder = CommandsBuilder(externalized_commands)
 
-    if not for_pulsar:
-        # Galaxy writes I/O files to outputs, Pulsar instruments own I/O redirection
-        io_directory = "../outputs"
-        commands_builder.capture_stdout_stderr(
-            f"{io_directory}/tool_stdout", f"{io_directory}/tool_stderr", stream_stdout_stderr=stream_stdout_stderr
-        )
+    # Galaxy writes I/O files to outputs, Pulsar uses metadata. metadata seems like
+    # it should be preferred - at least if the directory exists.
+    io_directory = "../metadata" if for_pulsar else "../outputs"
+    commands_builder.capture_stdout_stderr(
+        f"{io_directory}/tool_stdout", f"{io_directory}/tool_stderr", stream_stdout_stderr=stream_stdout_stderr
+    )
 
     # Don't need to create a separate tool working directory for Pulsar
     # jobs - that is handled by Pulsar.

diff --git a/test/integration/test_pulsar_embedded.py b/test/integration/test_pulsar_embedded.py
@@ -36,5 +36,6 @@ def handle_galaxy_config_kwds(cls, config):
         "tool_provided_metadata_9",
         "simple_constructs_y",
         "composite_output",
+        "detect_errors",
     ]
 )