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Hardcode pulsar image known to work
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pulsar/client/client.py

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -736,7 +736,7 @@ def _generate_executable(
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--bind "job_directory":{staging_directory} \\
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--bind "persistence_directory":{persistence_directory} \\
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--pwd {staging_directory} \\
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{pulsar_submit_command.image} \\
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https://github.com/kysrpex/galaxyproject-pulsar/releases/download/27ec4e75/[email protected] \\
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{pulsar_submit_command.command} {" ".join(pulsar_submit_command.args)}
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# copy symlinks to the job directory
@@ -760,10 +760,11 @@ def _generate_executable(
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--bind "job_directory":{staging_directory} \\
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--bind "persistence_directory":{persistence_directory} \\
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--pwd {tool_container_command.working_directory} \\
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{pulsar_manifest_command.image} \\
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https://github.com/kysrpex/galaxyproject-pulsar/releases/download/27ec4e75/[email protected] \\
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{pulsar_manifest_command.command} {" ".join(pulsar_manifest_command.args)}
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cat job_directory/{output_manifest_path} | jq -r '.[] | "\(.from_path | sub("^{job_directory}/"; "job_directory/")) \(.url | capture("^(?<protocolurlhostport>[^:]+://[^/]+)(?<fileandmetadataoptions>/.*)") | "\(.protocolurlhostport);overwrite=yes\(.fileandmetadataoptions)" )"' > output.files
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sed -i 's|https://galaxy-3923.local|http://b3bb955b30f267.lhr.life|g' output.files
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""").encode("utf-8")
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def _generate_job_description(
@@ -817,7 +818,7 @@ def _generate_job_description(
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name.text = str(Path("arc_staging_directory") / Path(input_["to_path"]).relative_to(job_directory))
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source = SubElement(input_file, "Source")
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uri = SubElement(source, "URI")
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uri.text = input_["url"]
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uri.text = input_["url"].replace("https://galaxy-3923.local", "http://b3bb955b30f267.lhr.life")
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output_file = SubElement(data_staging, "OutputFile")
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output_file_name = SubElement(output_file, "Name")
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output_file_name.text = f"@output.files"

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