1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/dc67550cf28a/ Changeset: dc67550cf28a User: jmchilton Date: 2014-03-26 16:00:22 Summary: Update LWR client through LWR commit 2fec198. Makes parsing LWR host more robust - auto-adding http to beginning and trailing / if needed. Also makes LWR runn compatible with forthcoming job metrics pull request and pulls in Python 3 fix for job_script module. Affected #: 3 files
diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/lwr_client/interface.py --- a/lib/galaxy/jobs/runners/lwr_client/interface.py +++ b/lib/galaxy/jobs/runners/lwr_client/interface.py @@ -36,8 +36,13 @@
def __init__(self, destination_params, transport): self.transport = transport - self.remote_host = destination_params.get("url") - assert self.remote_host is not None, "Failed to determine url for LWR client." + remote_host = destination_params.get("url") + assert remote_host is not None, "Failed to determine url for LWR client." + if not remote_host.endswith("/"): + remote_host = "%s/" % remote_host + if not remote_host.startswith("http"): + remote_host = "http://%s" % remote_host + self.remote_host = remote_host self.private_key = destination_params.get("private_token", None)
def execute(self, command, args={}, data=None, input_path=None, output_path=None):
diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/lwr_client/staging/down.py --- a/lib/galaxy/jobs/runners/lwr_client/staging/down.py +++ b/lib/galaxy/jobs/runners/lwr_client/staging/down.py @@ -14,7 +14,7 @@ # this pattern picks up attiditional files to copy back - such as those # associated with multiple outputs and metadata configuration. Set to .* to just # copy everything -COPY_FROM_WORKING_DIRECTORY_PATTERN = compile(r"primary_.*|galaxy.json|metadata_.*|dataset_\d+.dat|dataset_\d+_files.+") +COPY_FROM_WORKING_DIRECTORY_PATTERN = compile(r"primary_.*|galaxy.json|metadata_.*|dataset_\d+.dat|__instrument_.*|dataset_\d+_files.+")
def finish_job(client, cleanup_job, job_completed_normally, client_outputs, lwr_outputs):
diff -r 62146f92190c00c621a3ce2ed7860f3f0c2c7ec4 -r dc67550cf28a3e32f8cc867ce82cb8a7b1495335 lib/galaxy/jobs/runners/util/job_script/__init__.py --- a/lib/galaxy/jobs/runners/util/job_script/__init__.py +++ b/lib/galaxy/jobs/runners/util/job_script/__init__.py @@ -2,11 +2,11 @@ from pkg_resources import resource_string
DEFAULT_JOB_FILE_TEMPLATE = Template( - resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh') + resource_string(__name__, 'DEFAULT_JOB_FILE_TEMPLATE.sh').decode('UTF-8') )
SLOTS_STATEMENT_CLUSTER_DEFAULT = \ - resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh') + resource_string(__name__, 'CLUSTER_SLOTS_STATEMENT.sh').decode('UTF-8')
SLOTS_STATEMENT_SINGLE = """ GALAXY_SLOTS="1"
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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