import time
#import arvados.command.ws as ws
import subprocess
+import logging
+
+logger = logging.getLogger('arvados.arv-run')
arvrun_parser = argparse.ArgumentParser()
-arvrun_parser.add_argument('--dry-run', action="store_true")
-arvrun_parser.add_argument('--local', action="store_true")
-arvrun_parser.add_argument('--docker-image', type=str, default="arvados/jobs")
-arvrun_parser.add_argument('--git-dir', type=str, default="")
-arvrun_parser.add_argument('command')
+arvrun_parser.add_argument('--dry-run', action="store_true", help="Print out the pipeline that would be submitted and exit")
+arvrun_parser.add_argument('--local', action="store_true", help="Run locally using arv-crunch-job")
+arvrun_parser.add_argument('--docker-image', type=str, default="arvados/jobs", help="Docker image to use, default arvados/jobs")
+arvrun_parser.add_argument('--git-dir', type=str, default="", help="Git repository passed to arv-crunch-job when using --local")
+arvrun_parser.add_argument('--repository', type=str, default="arvados", help="repository field of component, default 'arvados'")
+arvrun_parser.add_argument('--script-version', type=str, default="master", help="script_version field of component, default 'master'")
arvrun_parser.add_argument('args', nargs=argparse.REMAINDER)
-needupload_files = []
-
class ArvFile(object):
def __init__(self, prefix, fn):
self.prefix = prefix
self.fn = fn
-def statfile(prefix, fn, pattern):
+class UploadFile(ArvFile):
+ pass
+
+def is_in_collection(root, branch):
+ if root == "/":
+ return (None, None)
+ fn = os.path.join(root, ".arvados#collection")
+ if os.path.exists(fn):
+ with file(fn, 'r') as f:
+ c = json.load(f)
+ return (c["portable_data_hash"], branch)
+ else:
+ sp = os.path.split(root)
+ return is_in_collection(sp[0], os.path.join(sp[1], branch))
+
+def statfile(prefix, fn):
absfn = os.path.abspath(fn)
if os.path.exists(absfn):
- fn = os.path.abspath(fn)
- st = os.stat(fn)
+ st = os.stat(absfn)
if stat.S_ISREG(st.st_mode):
- mount = os.path.dirname(fn)+"/.arvados#collection"
- if os.path.exists(mount):
- with file(mount, 'r') as f:
- c = json.load(f)
- return prefix+"$(file "+c["portable_data_hash"]+"/" + os.path.basename(fn) + ")"
+ sp = os.path.split(absfn)
+ (pdh, branch) = is_in_collection(sp[0], sp[1])
+ if pdh:
+ return ArvFile(prefix, "$(file %s/%s)" % (pdh, branch))
else:
- needupload_files.append(fn)
- return ArvFile(prefix, fn[1:])
+ # trim leading '/' for path prefix test later
+ return UploadFile(prefix, absfn[1:])
return prefix+fn
def main(arguments=None):
args = arvrun_parser.parse_args(arguments)
+ if len(args.args) == 0:
+ arvrun_parser.print_help()
+ return
+
+ reading_into = 2
+
+ slots = [[], [], []]
+ for c in args.args:
+ if c.startswith('>'):
+ reading_into = 0
+ if len(c) > 1:
+ slots[reading_into].append(c[1:])
+ elif c.startswith('<'):
+ reading_into = 1
+ if len(c) > 1:
+ slots[reading_into].append(c[1:])
+ elif c == '|':
+ reading_into = len(slots)
+ slots.append([])
+ else:
+ slots[reading_into].append(c)
+
+ if slots[0] and len(slots[0]) > 1:
+ logger.error("Can only specify a single stdout file (run-command substitutions are permitted)")
+ return
+
patterns = [re.compile("(--[^=]+=)(.*)"),
re.compile("(-[^=]+=)(.*)"),
re.compile("(-.)(.+)")]
- commandargs = []
-
- for a in args.args:
- if a[0] == '-':
- matched = False
- for p in patterns:
- m = p.match(a)
- if m:
- commandargs.append(statfile(m.group(1), m.group(2), p))
- matched = True
- break
- if not matched:
- commandargs.append(a)
- else:
- commandargs.append(statfile('', a, None))
+ for command in slots[1:]:
+ for i in xrange(0, len(command)):
+ a = command[i]
+ if a[0] == '-':
+ # parameter starts with '-' so it might be a command line
+ # parameter with a file name, do some pattern matching
+ matched = False
+ for p in patterns:
+ m = p.match(a)
+ if m:
+ command[i] = statfile(m.group(1), m.group(2))
+ break
+ else:
+ # parameter might be a file, so test it
+ command[i] = statfile('', a)
n = True
pathprefix = "/"
- files = [c for c in commandargs if isinstance(c, ArvFile)]
+ files = [c for command in slots[1:] for c in command if isinstance(c, UploadFile)]
if len(files) > 0:
+ # Find the smallest path prefix that includes all the files that need to be uploaded.
+ # This starts at the root and iteratively removes common parent directory prefixes
+ # until all file pathes no longer have a common parent.
while n:
pathstep = None
for c in files:
if pathstep is None:
sp = c.fn.split('/')
if len(sp) < 2:
+ # no parent directories left
n = False
break
+ # path step takes next directory
pathstep = sp[0] + "/"
else:
+ # check if pathstep is common prefix for all files
if not c.fn.startswith(pathstep):
n = False
break
if n:
+ # pathstep is common parent directory for all files, so remove the prefix
+ # from each path
pathprefix += pathstep
for c in files:
c.fn = c.fn[len(pathstep):]
else:
pdh = put.main(["--portable-data-hash"]+[c.fn for c in files])
- commandargs = [("%s$(file %s/%s)" % (c.prefix, pdh, c.fn)) if isinstance(c, ArvFile) else c for c in commandargs]
-
- cut = None
- i = -1
- stdio = [None, None]
- for j in xrange(0, len(commandargs)):
- c = commandargs[j]
- if c == '<':
- stdio[0] = []
- i = 0
- cut = j if cut is None else cut
- elif c == '>':
- stdio[1] = []
- i = 1
- cut = j if cut is None else cut
- elif i > -1:
- stdio[i].append(c)
-
- if cut is not None:
- commandargs = commandargs[:cut]
+ for c in files:
+ c.fn = "$(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": "0fdfa049801418ecd1faf33ec1415f3b689ea761",
- "repository": "arvados",
+ "script_version": args.script_version,
+ "repository": args.repository,
"script_parameters": {
- "command": [args.command]+commandargs
},
"runtime_constraints": {
"docker_image": args.docker_image
}
}
- if stdio[0]:
- component["script_parameters"]["task.stdin"] = stdio[0][0]
- if stdio[1]:
- component["script_parameters"]["task.stdout"] = stdio[1][0]
+ task_foreach = []
+ group_parser = argparse.ArgumentParser()
+ group_parser.add_argument('--batch-size', type=int)
+ 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-2)
+ groupargs = group_parser.parse_args(slots[2][i+1:])
+ if groupargs.batch_size:
+ component["script_parameters"][inp] = {"batch":groupargs.args, "size":groupargs.batch_size}
+ slots[s] = slots[s][0:i] + [{"foreach": inp, "command": "$(%s)" % inp}]
+ else:
+ component["script_parameters"][inp] = groupargs.args
+ slots[s] = slots[s][0:i] + ["$(%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 slots[1]:
+ task_foreach.append("stdin")
+ component["script_parameters"]["stdin"] = slots[1]
+ component["script_parameters"]["task.stdin"] = "$(stdin)"\
+
+ if task_foreach:
+ component["script_parameters"]["task.foreach"] = task_foreach
+
+ component["script_parameters"]["command"] = slots[2:]
pipeline = {
"name": "",
"components": {
- args.command: component
+ "command": component
},
"state":"RunningOnServer"
}
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__':
projects / arvados.git / blobdiff