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Merge branch 'release_21.05' into dev

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Nicola Soranzo
2021-09-06 17:09:58 +01:00
parent 508bbc60b4 4629832187
commit 20dd06b54e
4 changed files with 12 additions and 5 deletions
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lib/galaxy/dependencies/dev-requirements.txt
+1 -1
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@@ -32,7 +32,7 @@ celery==5.0.5; python_version >= "3.6"
certifi==2020.12.5; python_version >= "3.6" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4" and python_version >= "3.6"
cffi==1.14.5; implementation_name == "pypy" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")
chardet==4.0.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
cheetah3==3.2.6.post2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
cheetah3==3.2.6.post1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
circus==0.17.1
click-didyoumean==0.0.3; python_version >= "3.6"
click-plugins==1.1.1; python_version >= "3.6"
lib/galaxy/dependencies/pinned-requirements.txt
+1 -1
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@@ -30,7 +30,7 @@ celery==5.0.5; python_version >= "3.6"
certifi==2020.12.5; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
cffi==1.14.5; implementation_name == "pypy" and python_version >= "3.6" and (python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.4.0")
chardet==4.0.0; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
cheetah3==3.2.6.post2; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
cheetah3==3.2.6.post1; (python_version >= "2.7" and python_full_version < "3.0.0") or (python_full_version >= "3.4.0")
circus==0.17.1
click-didyoumean==0.0.3; python_version >= "3.6"
click-plugins==1.1.1; python_version >= "3.6"
lib/galaxy/jobs/runners/pulsar.py
+8 -3
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@@ -6,6 +6,7 @@ More information on Pulsar can be found at https://pulsar.readthedocs.io/ .
import errno
import logging
import os
import re
import subprocess
from time import sleep
@@ -759,6 +760,10 @@ class PulsarJobRunner(AsynchronousJobRunner):
output_files = self.get_output_files(job_wrapper)
metadata_directory = os.path.join(job_wrapper.working_directory, "metadata")
metadata_strategy = job_wrapper.get_destination_configuration('metadata_strategy', None)
tool = job_wrapper.tool
tool_provided_metadata_file_path = tool.provided_metadata_file
tool_provided_metadata_style = tool.provided_metadata_style
dynamic_outputs = None # use default
if metadata_strategy == "extended" and PulsarJobRunner.__remote_metadata(client):
# if Pulsar is doing remote metadata and the remote metadata is extended,
@@ -767,10 +772,10 @@ class PulsarJobRunner(AsynchronousJobRunner):
else:
# otherwise collect everything we might need
dynamic_outputs = DEFAULT_DYNAMIC_COLLECTION_PATTERN[:]
# grab discovered outputs...
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
# grab tool provided metadata (galaxy.json) also...
dynamic_outputs.append(re.escape(tool_provided_metadata_file_path))
dynamic_file_sources = [
{"path": tool_provided_metadata_file_path, "type": "galaxy" if tool_provided_metadata_style == "default" else "legacy_galaxy"}
]
test/integration/test_pulsar_embedded.py
+2
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@@ -29,4 +29,6 @@ test_tools = integration_util.integration_tool_runner([
"vcf_bgzip_test",
"environment_variables",
"multi_output_assign_primary_ext_dbkey",
"strict_shell",
"tool_provided_metadata_9",
])