arvrun_parser.add_argument('--git-dir', type=str, default="")
arvrun_parser.add_argument('args', nargs=argparse.REMAINDER)
-class UploadFile(object):
+class ArvFile(object):
def __init__(self, prefix, fn):
self.prefix = prefix
self.fn = fn
+class UploadFile(ArvFile):
+ pass
+
def is_in_collection(root, branch):
if root == "/":
return (None, None)
sp = os.path.split(absfn)
(pdh, branch) = is_in_collection(sp[0], sp[1])
if pdh:
- return "%s$(file %s/%s)" % (prefix, pdh, branch)
+ return ArvFile(prefix, "$(file %s/%s)" % (pdh, branch))
else:
# trim leading '/' for path prefix test later
return UploadFile(prefix, absfn[1:])
else:
pdh = put.main(["--portable-data-hash"]+[c.fn for c in files])
- for i in xrange(1, len(slots)):
- slots[i] = [("%s$(file %s/%s)" % (c.prefix, pdh, c.fn)) if isinstance(c, UploadFile) else c for c in slots[i]]
+ for c in files:
+ c.fn = "$(file %s/%s)" % (pdh, c.fn)
+
+ for i in xrange(1, len(slots)):
+ slots[i] = [("%s%s" % (c.prefix, c.fn)) if isinstance(c, ArvFile) else c for c in slots[i]]
component = {
"script": "run-command",
"script_version": "3609-arv-run",
"repository": "arvados",
"script_parameters": {
- "command": slots[2:]
},
"runtime_constraints": {
"docker_image": args.docker_image
}
task_foreach = []
+ group_parser = argparse.ArgumentParser()
+ group_parser.add_argument('--group', type=str)
+ group_parser.add_argument('args', nargs=argparse.REMAINDER)
+
+ for s in xrange(2, len(slots)):
+ for i in xrange(0, len(slots[s])):
+ if slots[s][i] == '--':
+ inp = "input%i" % s
+ groupargs = group_parser.parse_args(slots[2][i+1:])
+ component["script_parameters"][inp] = groupargs.args
+ if groupargs.group:
+ inpgroups = inp+"_groups"
+ component["script_parameters"][inpgroups] = {"group":inp, "regex":groupargs.group}
+ slots[s] = slots[s][0:i] + [{"foreach": inpgroups, "command": "$(%s)" % inpgroups}]
+ task_foreach.append(inpgroups)
+ else:
+ slots[s] = slots[s][0:i] + ["$(%s)" % inp]
+ task_foreach.append(inp)
+ break
+ if slots[s][i] == '\--':
+ slots[s][i] = '--'
if slots[0]:
component["script_parameters"]["task.stdout"] = slots[0][0]
if task_foreach:
component["script_parameters"]["task.foreach"] = task_foreach
+ component["script_parameters"]["command"] = slots[2:]
+
pipeline = {
"name": "",
"components": {
else:
api = arvados.api('v1')
pi = api.pipeline_instances().create(body=pipeline).execute()
+ print "Running pipeline %s" % pi["uuid"]
#ws.main(["--pipeline", pi["uuid"]])
if __name__ == '__main__':