import os
import json
import argparse
+import re
from arvados.api import OrderedJsonModel
-from cwltool.process import adjustFiles
+from cwltool.process import adjustFileObjs, adjustDirObjs
from cwltool.load_tool import load_tool
# Print package versions
try:
job_order_object = arvados.current_job()['script_parameters']
+ pdh_path = re.compile(r'^[0-9a-f]{32}\+\d+(/.+)?$')
+
def keeppath(v):
- if arvados.util.keep_locator_pattern.match(v):
- return "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], v)
+ if pdh_path.match(v):
+ return "keep:%s" % v
else:
return v
- job_order_object["cwl:tool"] = keeppath(job_order_object["cwl:tool"])
+ def keeppathObj(v):
+ v["location"] = keeppath(v["location"])
+
+ job_order_object["cwl:tool"] = "file://%s/%s" % (os.environ['TASK_KEEPMOUNT'], job_order_object["cwl:tool"])
for k,v in job_order_object.items():
if isinstance(v, basestring) and arvados.util.keep_locator_pattern.match(v):
job_order_object[k] = {
"class": "File",
- "path": keeppath(v)
+ "location": "keep:%s" % v
}
- adjustFiles(job_order_object, keeppath)
+ adjustFileObjs(job_order_object, keeppathObj)
+ adjustDirObjs(job_order_object, keeppathObj)
- runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()), work_api="jobs")
+ runner = arvados_cwl.ArvCwlRunner(api_client=arvados.api('v1', model=OrderedJsonModel()))
t = load_tool(job_order_object, runner.arvMakeTool)
outputObj = runner.arvExecutor(t, job_order_object, **vars(args))
files = {}
- def capture(path):
+ def capture(fileobj):
+ path = fileobj["location"]
sp = path.split("/")
col = sp[0][5:]
if col not in files:
files[col] = set()
files[col].add("/".join(sp[1:]))
- return path
+ fileobj["location"] = path
- adjustFiles(outputObj, capture)
+ adjustFileObjs(outputObj, capture)
final = arvados.collection.Collection()
for f in c:
final.copy(f, f, c, True)
- def makeRelative(path):
- return "/".join(path.split("/")[1:])
+ def makeRelative(fileobj):
+ fileobj["location"] = "/".join(fileobj["location"].split("/")[1:])
- adjustFiles(outputObj, makeRelative)
+ adjustFileObjs(outputObj, makeRelative)
with final.open("cwl.output.json", "w") as f:
json.dump(outputObj, f, indent=4)