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Implement galaxy.json dynamic file collection in Pulsar.

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This commit is contained in:
John Chilton
2021-07-17 15:52:48 -04:00
parent a0b10d7968
commit d7cf4acd7c
5 changed files with 11 additions and 3 deletions
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lib/galaxy/dependencies/dev-requirements.txt
+1 -1
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@@ -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"
lib/galaxy/dependencies/pinned-requirements.txt
+1 -1
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@@ -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"
lib/galaxy/jobs/runners/pulsar.py
+7
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@@ -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
pyproject.toml
+1 -1
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@@ -56,7 +56,7 @@ paramiko = "*"
Parsley = "*"
Paste = "*"
psutil = "*"
pulsar-galaxy-lib = ">=0.14.5"
pulsar-galaxy-lib = ">=0.14.9"
pycryptodome = "*"
pykwalify = "*"
pyparsing = "*"
test/integration/test_pulsar_embedded.py
+1
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@@ -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",