diff --git a/lib/galaxy/dependencies/dev-requirements.txt b/lib/galaxy/dependencies/dev-requirements.txt index 5290b553919..d1346637796 100644 --- a/lib/galaxy/dependencies/dev-requirements.txt +++ b/lib/galaxy/dependencies/dev-requirements.txt @@ -143,7 +143,7 @@ prompt-toolkit==3.0.3; python_version >= "3.6" protobuf==3.15.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" prov==1.5.1; python_version >= "3.6" and python_version < "4" psutil==5.8.0; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0") -pulsar-galaxy-lib==0.14.8 +pulsar-galaxy-lib==0.14.10 py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or python_full_version >= "3.4.0" and python_version >= "3.6" and implementation_name == "pypy" pyasn1-modules==0.2.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" pyasn1==0.4.8; python_version >= "3.5" and python_version < "4" diff --git a/lib/galaxy/dependencies/pinned-requirements.txt b/lib/galaxy/dependencies/pinned-requirements.txt index 87a30062242..b3db1a5e313 100644 --- a/lib/galaxy/dependencies/pinned-requirements.txt +++ b/lib/galaxy/dependencies/pinned-requirements.txt @@ -126,7 +126,7 @@ prompt-toolkit==3.0.3; python_version >= "3.6" protobuf==3.15.8; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" and python_version >= "3.6" prov==1.5.1; python_version >= "3.6" and python_version < "4" psutil==5.8.0; (python_version >= "2.6" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0") -pulsar-galaxy-lib==0.14.8 +pulsar-galaxy-lib==0.14.10 py==1.10.0; python_version >= "3.6" and python_full_version < "3.0.0" and implementation_name == "pypy" or implementation_name == "pypy" and python_version >= "3.6" and python_full_version >= "3.4.0" pyasn1-modules==0.2.8; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.6.0" pyasn1==0.4.8; python_version >= "3.5" and python_version < "4" diff --git a/lib/galaxy/jobs/runners/pulsar.py b/lib/galaxy/jobs/runners/pulsar.py index fbbf2148a0f..bf7c9d9a2a3 100644 --- a/lib/galaxy/jobs/runners/pulsar.py +++ b/lib/galaxy/jobs/runners/pulsar.py @@ -767,6 +767,12 @@ class PulsarJobRunner(AsynchronousJobRunner): # otherwise collect everything we might need dynamic_outputs = DEFAULT_DYNAMIC_COLLECTION_PATTERN[:] dynamic_outputs.extend(job_wrapper.tool.output_discover_patterns) + tool = job_wrapper.tool + tool_provided_metadata_file_path = tool.provided_metadata_file + tool_provided_metadata_style = tool.provided_metadata_style + dynamic_file_sources = [ + {"path": tool_provided_metadata_file_path, "type": "galaxy" if tool_provided_metadata_style == "default" else "legacy_galaxy"} + ] client_outputs = ClientOutputs( working_directory=job_wrapper.tool_working_directory, metadata_directory=metadata_directory, @@ -774,6 +780,7 @@ class PulsarJobRunner(AsynchronousJobRunner): output_files=output_files, version_file=job_wrapper.get_version_string_path(), dynamic_outputs=dynamic_outputs, + dynamic_file_sources=dynamic_file_sources, ) return client_outputs diff --git a/pyproject.toml b/pyproject.toml index 70b0bf64603..1019ed57a0e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -56,7 +56,7 @@ paramiko = "*" Parsley = "*" Paste = "*" psutil = "*" -pulsar-galaxy-lib = ">=0.14.5" +pulsar-galaxy-lib = ">=0.14.9" pycryptodome = "*" pykwalify = "*" pyparsing = "*" diff --git a/test/integration/test_pulsar_embedded.py b/test/integration/test_pulsar_embedded.py index 282b5fa64e1..db9bd8baedf 100644 --- a/test/integration/test_pulsar_embedded.py +++ b/test/integration/test_pulsar_embedded.py @@ -21,6 +21,7 @@ class EmbeddedPulsarIntegrationInstance(integration_util.IntegrationInstance): instance = integration_util.integration_module_instance(EmbeddedPulsarIntegrationInstance) test_tools = integration_util.integration_tool_runner([ + "collection_creates_dynamic_nested_from_json", "composite", "simple_constructs", "multi_data_param",