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Merge branch '10186-crunch2-slurm-partition' closes #10186
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
runner.py
diff --git
a/sdk/cwl/arvados_cwl/runner.py
b/sdk/cwl/arvados_cwl/runner.py
index 07f85bbc479d7104cb9308f3013eea75c829b758..e5b4e006e8cce7cac780436fc06c6dcd79882730 100644
(file)
--- a/
sdk/cwl/arvados_cwl/runner.py
+++ b/
sdk/cwl/arvados_cwl/runner.py
@@
-21,7
+21,7
@@
from .pathmapper import ArvPathMapper
logger = logging.getLogger('arvados.cwl-runner')
logger = logging.getLogger('arvados.cwl-runner')
-cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"
^[a-zA-Z0-9._+-]+$
")
+cwltool.draft2tool.ACCEPTLIST_RE = re.compile(r"
.*
")
def trim_listing(obj):
"""Remove 'listing' field from Directory objects that are keep references.
def trim_listing(obj):
"""Remove 'listing' field from Directory objects that are keep references.
@@
-114,13
+114,15
@@
def upload_docker(arvrunner, tool):
class Runner(object):
class Runner(object):
- def __init__(self, runner, tool, job_order, enable_reuse):
+ def __init__(self, runner, tool, job_order, enable_reuse
, output_name
):
self.arvrunner = runner
self.tool = tool
self.job_order = job_order
self.running = False
self.enable_reuse = enable_reuse
self.uuid = None
self.arvrunner = runner
self.tool = tool
self.job_order = job_order
self.running = False
self.enable_reuse = enable_reuse
self.uuid = None
+ self.final_output = None
+ self.output_name = output_name
def update_pipeline_component(self, record):
pass
def update_pipeline_component(self, record):
pass
@@
-169,7
+171,11
@@
class Runner(object):
outputs = None
try:
try:
outputs = None
try:
try:
- outc = arvados.collection.Collection(record["output"])
+ self.final_output = record["output"]
+ outc = arvados.collection.CollectionReader(self.final_output,
+ api_client=self.arvrunner.api,
+ keep_client=self.arvrunner.keep_client,
+ num_retries=self.arvrunner.num_retries)
with outc.open("cwl.output.json") as f:
outputs = json.load(f)
def keepify(fileobj):
with outc.open("cwl.output.json") as f:
outputs = json.load(f)
def keepify(fileobj):