Include only inputs in staging manifest

galaxyproject · Nov 13, 2024 · 511ee61 · 511ee61
1 parent e827a30
commit 511ee61
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/pulsar/client/client.py b/pulsar/client/client.py
@@ -505,8 +505,7 @@ def launch(
         MANIFEST_SCRIPT = importlib.resources.path(scripts, "collect_output_manifest.py")
 
         with tempfile.NamedTemporaryFile(mode="w") as temp_fh:
-            fixed_manifest = [staging_manifest[0]]
-            temp_fh.write(json_dumps(fixed_manifest))
+            temp_fh.write(json_dumps(staging_manifest))
             temp_fh.flush()
             staging_process = subprocess.run([sys.executable, STAGING_SCRIPT, "--json", temp_fh.name], capture_output=True)
             assert staging_process.returncode == 0, staging_process.stderr.decode()

diff --git a/pulsar/client/staging/up.py b/pulsar/client/staging/up.py
@@ -73,13 +73,14 @@ def submit_job(client, client_job_description, job_config=None):
     launch_kwds["token_endpoint"] = client.token_endpoint
 
     # populate `to_path`
+    staging_manifest = []
     for action in file_stager.action_mapper.actions:
-        name = basename(action.path)
-        input_type = "input"
-        path = file_stager.job_directory.calculate_path(name, input_type)
-        action.write_to_path(path)
+        if action.file_type not in ("output", "output_workdir"):
+            name = basename(action.path)
+            path = file_stager.job_directory.calculate_path(name, action.file_type)
+            action.write_to_path(path)
+            staging_manifest.append(action.finalize())
 
-    staging_manifest = file_stager.action_mapper.finalize()
     if staging_manifest:
         launch_kwds["staging_manifest"] = staging_manifest