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14198: Bringing unit tests up to date WIP
[arvados.git]
/
sdk
/
cwl
/
arvados_cwl
/
crunch_script.py
diff --git
a/sdk/cwl/arvados_cwl/crunch_script.py
b/sdk/cwl/arvados_cwl/crunch_script.py
index 5024e95f77df785abf668c68364dadc4d49fb2a4..7512d5bef27f28014f650d897d24e3d59cb7b3c4 100644
(file)
--- a/
sdk/cwl/arvados_cwl/crunch_script.py
+++ b/
sdk/cwl/arvados_cwl/crunch_script.py
@@
-27,6
+27,7
@@
from cwltool.process import shortname
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, normalizeFilesDirs
from cwltool.load_tool import load_tool
from cwltool.errors import WorkflowException
from cwltool.pathmapper import adjustFileObjs, adjustDirObjs, normalizeFilesDirs
from cwltool.load_tool import load_tool
from cwltool.errors import WorkflowException
+from arvados_cwl.context import ArvRuntimeContext
from .fsaccess import CollectionFetcher, CollectionFsAccess
from .fsaccess import CollectionFetcher, CollectionFsAccess
@@
-97,25
+98,27
@@
def run():
debug = job_order_object["arv:debug"]
del job_order_object["arv:debug"]
debug = job_order_object["arv:debug"]
del job_order_object["arv:debug"]
- runner = arvados_cwl.ArvCwlRunner(api_client=arvados.safeapi.ThreadSafeApiCache(
+ arvargs = argparse.Namespace()
+ arvargs.work_api = "jobs"
+ arvargs.output_name = output_name
+ arvargs.output_tags = output_tags
+ arvargs.thread_count = 1
+
+ runner = arvados_cwl.ArvCwlExecutor(api_client=arvados.safeapi.ThreadSafeApiCache(
api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),
api_params={"model": OrderedJsonModel()}, keep_params={"num_retries": 4}),
-
output_name=output_name, output_tags=output_ta
gs)
+
arvargs=arvar
gs)
make_fs_access = functools.partial(CollectionFsAccess,
collection_cache=runner.collection_cache)
make_fs_access = functools.partial(CollectionFsAccess,
collection_cache=runner.collection_cache)
- t = load_tool(toolpath, runner.arv_make_tool,
- fetcher_constructor=functools.partial(CollectionFetcher,
- api_client=runner.api,
- fs_access=make_fs_access(""),
- num_retries=runner.num_retries))
+ t = load_tool(toolpath, runner.loadingContext)
if debug:
logger.setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
logging.getLogger("cwltool").setLevel(logging.DEBUG)
if debug:
logger.setLevel(logging.DEBUG)
logging.getLogger('arvados').setLevel(logging.DEBUG)
logging.getLogger("cwltool").setLevel(logging.DEBUG)
- args =
argparse.Namespace(
)
+ args =
ArvRuntimeContext(vars(arvargs)
)
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
args.on_error = on_error
args.project_uuid = arvados.current_job()["owner_uuid"]
args.enable_reuse = enable_reuse
args.on_error = on_error
@@
-134,7
+137,7
@@
def run():
args.disable_js_validation = False
args.tmp_outdir_prefix = "tmp"
args.disable_js_validation = False
args.tmp_outdir_prefix = "tmp"
- runner.arv_executor(t, job_order_object,
**vars(args)
)
+ runner.arv_executor(t, job_order_object,
args, logger=logger
)
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)
except Exception as e:
if isinstance(e, WorkflowException):
logging.info("Workflow error %s", e)