job_directory -> jobs_directory

#360 Merged at a146d10
Repository
galaxy-central
Branch
default
Author
  1. Trevor Wennblom
Reviewers
Description

job_directory -> jobs_directory

Comments (3)

  1. Trevor Wennblom author

    Keeping job vs jobs clear seems tricky, maybe something more obvious like multiple_jobs_directory if a distinction is needed?

    % ack "jobs_directory"
    job_conf.xml.sample_advanced
    27:               queue, ensure jobs_directory is specified on destinations and all
    118:            <!-- <param id="jobs_directory">/path/to/remote/lwr/lwr_staging/</param> -->
    
    lib/galaxy/jobs/runners/lwr_client/client.py
    32:        if "jobs_directory" in (destination_params or {}):
    33:            staging_directory = destination_params["jobs_directory"]
    
    lib/galaxy/jobs/runners/lwr_client/setup_handler.py
    37:        self.jobs_directory = destination_args["jobs_directory"]
    
    % ack "job_directory"
    job_conf.xml.sample_advanced
    113:                 on client by uncommenting job_directory and
    
    lib/galaxy/jobs/runners/lwr_client/client.py
    6:from .job_directory import RemoteJobDirectory
    35:            job_directory = RemoteJobDirectory(
    41:            job_directory = None
    43:        self.job_directory = job_directory
    65:        return self.job_directory is None
    289:        if not self.job_directory:
    290:            error_message = "Message-queue based LWR client requires destination define a remote job_directory to stage files into."
    
    lib/galaxy/jobs/runners/lwr_client/job_directory.py
    33:        self.job_directory = self.path_helper.remote_join(
    58:        return self.job_directory
    84:        return self.path_helper.remote_join(self.job_directory, name)
    
    lib/galaxy/jobs/runners/lwr_client/setup_handler.py
    11:    if client.job_directory:
    35:        system_properties["sep"] = client.job_directory.separator
    42:            job_directory=self.client.job_directory,
    74:def build_job_config(job_id, job_directory, system_properties={}, tool_id=None, tool_version=None):
    77:    inputs_directory = job_directory.inputs_directory()
    78:    working_directory = job_directory.working_directory()
    79:    outputs_directory = job_directory.outputs_directory()
    80:    configs_directory = job_directory.configs_directory()
    81:    tools_directory = job_directory.tool_files_directory()
    82:    unstructured_files_directory = job_directory.unstructured_files_directory()
    
    lib/galaxy/jobs/runners/lwr_client/staging/up.py
    350:                job_directory = self.client.job_directory
    351:                assert job_directory, "job directory required for action %s" % action
    355:                get_path = lambda: job_directory.calculate_path(name, type)
    
    1. John Chilton

      Fair point - I think jobs_directory is more of a deployer facing configuration file not really used in the code and I will try to avoid its usage - the concept it maps to is generally called staging_directory in the code - I will stick with that.