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Update LWR client to pass along tool id and version, required if LWR server is configured to point to a toolbox. The LWR server uses this information to match the job up with a tool and uses the tool to validate inputs.

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For more information see:
https://lwr.readthedocs.org/en/latest/#setting-up-a-public-lwr-server
https://bitbucket.org/jmchilton/lwr/src/tip/test/validator_test.py

Updates the LWR client to revision 8a249f4254eb6aa1eed8669f738c5a9764caccdb of the LWR.
https://bitbucket.org/jmchilton/lwr/commits/8a249f4254eb6aa1eed8669f738c5a9764caccdb
This commit is contained in:
John Chilton
2013-02-28 23:56:56 -06:00
parent 15ca057151
commit 9d31f3499d
2 changed files with 15 additions and 7 deletions
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lib/galaxy/jobs/runners/lwr.py
+3 -2
View File
@@ -69,7 +69,8 @@ class LwrJobRunner( AsynchronousJobRunner ):
output_files = self.get_output_files(job_wrapper)
input_files = job_wrapper.get_input_fnames()
working_directory = job_wrapper.working_directory
file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir, working_directory)
tool = job_wrapper.tool
file_stager = FileStager(client, tool, command_line, job_wrapper.extra_filenames, input_files, output_files, working_directory)
rebuilt_command_line = file_stager.get_rewritten_command_line()
job_id = file_stager.job_id
client.launch( rebuilt_command_line )
@@ -228,4 +229,4 @@ class LwrJobRunner( AsynchronousJobRunner ):
elif job.get_state() == model.Job.states.QUEUED:
# LWR doesn't queue currently, so this indicates galaxy was shutoff while
# job was being staged. Not sure how to recover from that.
job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." )
job_state.job_wrapper.fail( "This job was killed when Galaxy was restarted. Please retry the job." )
lib/galaxy/jobs/runners/lwr_client/__init__.py
+12 -5
View File
@@ -132,7 +132,7 @@ class FileStager(object):
"""
def __init__(self, client, command_line, config_files, input_files, output_files, tool_dir, working_directory):
def __init__(self, client, tool, command_line, config_files, input_files, output_files, working_directory):
"""
"""
self.client = client
@@ -140,7 +140,9 @@ class FileStager(object):
self.config_files = config_files
self.input_files = input_files
self.output_files = output_files
self.tool_dir = os.path.abspath(tool_dir)
self.tool_id = tool.id
self.tool_version = tool.version
self.tool_dir = os.path.abspath(tool.tool_dir)
self.working_directory = working_directory
# Setup job inputs, these will need to be rewritten before
@@ -161,7 +163,7 @@ class FileStager(object):
self.__upload_rewritten_config_files()
def __handle_setup(self):
job_config = self.client.setup()
job_config = self.client.setup(self.tool_id, self.tool_version)
self.new_working_directory = job_config['working_directory']
self.new_outputs_directory = job_config['outputs_directory']
@@ -480,11 +482,16 @@ class Client(object):
self.__raw_execute("clean", {"job_id": self.job_id})
@parseJson()
def setup(self):
def setup(self, tool_id=None, tool_version=None):
"""
Setup remote LWR server to run this job.
"""
return self.__raw_execute("setup", {"job_id": self.job_id})
setup_args = {"job_id": self.job_id}
if tool_id:
setup_args["tool_id"] = tool_id
if tool_version:
setup_args["tool_version"] = tool_version
return self.__raw_execute("setup", setup_args)
def _read(path):