#!/usr/bin/env python
import arvados
+import arvados.commands.ws as ws
import argparse
import json
import re
import stat
import put
import time
-#import arvados.command.ws as ws
import subprocess
import logging
+import arvados.commands._util as arv_cmd
logger = logging.getLogger('arvados.arv-run')
-arvrun_parser = argparse.ArgumentParser()
+arvrun_parser = argparse.ArgumentParser(parents=[arv_cmd.retry_opt])
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('--local', action="store_true", help="Run locally using arv-run-pipeline-instance")
arvrun_parser.add_argument('--docker-image', type=str, default="arvados/jobs", help="Docker image to use, default arvados/jobs")
+arvrun_parser.add_argument('--ignore-rcode', action="store_true", help="Commands that return non-zero return codes should not be considered failed.")
+arvrun_parser.add_argument('--no-reuse', action="store_true", help="Do not reuse past jobs.")
+arvrun_parser.add_argument('--no-wait', action="store_true", help="Do not wait and display logs after submitting command, just exit.")
+arvrun_parser.add_argument('--project-uuid', type=str, help="Parent project of the pipeline")
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'")
class UploadFile(ArvFile):
pass
+# Determine if a file is in a collection, and return a tuple consisting of the
+# portable data hash and the path relative to the root of the collection.
+# Return None if the path isn't with an arv-mount collection or there was is error.
def is_in_collection(root, branch):
- if root == "/":
+ try:
+ 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))
+ except IOError, OSError:
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))
+# Determine the project to place the output of this command by searching upward
+# for arv-mount psuedofile indicating the project. If the cwd isn't within
+# an arv-mount project or there is an error, return current_user.
+def determine_project(root, current_user):
+ try:
+ if root == "/":
+ return current_user
+ fn = os.path.join(root, ".arvados#project")
+ if os.path.exists(fn):
+ with file(fn, 'r') as f:
+ c = json.load(f)
+ if 'writable_by' in c and current_user in c['writable_by']:
+ return c["uuid"]
+ else:
+ return current_user
+ else:
+ sp = os.path.split(root)
+ return determine_project(sp[0], current_user)
+ except IOError, OSError:
+ return current_user
+
+# Determine if string corresponds to a file, and if that file is part of a
+# arv-mounted collection or only local to the machine. Returns one of
+# ArvFile() (file already exists in a collection), UploadFile() (file needs to
+# be uploaded to a collection), or simply returns prefix+fn (which yields the
+# original parameter string).
def statfile(prefix, fn):
absfn = os.path.abspath(fn)
if os.path.exists(absfn):
else:
# trim leading '/' for path prefix test later
return UploadFile(prefix, absfn[1:])
+ if stat.S_ISDIR(st.st_mode):
+ sp = os.path.split(absfn)
+ (pdh, branch) = is_in_collection(sp[0], sp[1])
+ if pdh:
+ return ArvFile(prefix, "$(dir %s/%s/)" % (pdh, branch))
+
return prefix+fn
def main(arguments=None):
args = arvrun_parser.parse_args(arguments)
+ if len(args.args) == 0:
+ arvrun_parser.print_help()
+ return
+
+ starting_args = args.args
+
reading_into = 2
+ # Parse the command arguments into 'slots'.
+ # All words following '>' are output arguments and are collected into slots[0].
+ # All words following '<' are input arguments and are collected into slots[1].
+ # slots[2..] store the parameters of each command in the pipeline.
+ #
+ # e.g. arv-run foo arg1 arg2 '|' bar arg3 arg4 '<' input1 input2 input3 '>' output.txt
+ # will be parsed into:
+ # [['output.txt'],
+ # ['input1', 'input2', 'input3'],
+ # ['foo', 'arg1', 'arg2'],
+ # ['bar', 'arg3', 'arg4']]
slots = [[], [], []]
for c in args.args:
if c.startswith('>'):
logger.error("Can only specify a single stdout file (run-command substitutions are permitted)")
return
- patterns = [re.compile("(--[^=]+=)(.*)"),
- re.compile("(-[^=]+=)(.*)"),
- re.compile("(-.)(.+)")]
-
- 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
+ if not args.dry_run:
+ api = arvados.api('v1')
+ if args.project_uuid:
+ project = args.project_uuid
+ else:
+ project = determine_project(os.getcwd(), api.users().current().execute()["uuid"])
+
+ # Identify input files. Look at each parameter and test to see if there is
+ # a file by that name. This uses 'patterns' to look for within
+ # command line arguments, such as --foo=file.txt or -lfile.txt
+ patterns = [re.compile("([^=]+=)(.*)"),
+ re.compile("(-[A-Za-z])(.+)")]
+ for j, command in enumerate(slots[1:]):
+ for i, a in enumerate(command):
+ if j > 0 and i == 0:
+ # j == 0 is stdin, j > 0 is commands
+ # always skip program executable (i == 0) in commands
+ pass
+ elif a.startswith('\\'):
+ # if it starts with a \ then don't do any interpretation
+ command[i] = a[1:]
else:
- # parameter might be a file, so test it
+ # See if it looks like a file
command[i] = statfile('', a)
+ # If a file named command[i] was found, it would now be an
+ # ArvFile or UploadFile. If command[i] is a basestring, that
+ # means it doesn't correspond exactly to a file, so do some
+ # pattern matching.
+ if isinstance(command[i], basestring):
+ for p in patterns:
+ m = p.match(a)
+ if m:
+ command[i] = statfile(m.group(1), m.group(2))
+ break
+
n = True
pathprefix = "/"
files = [c for command in slots[1:] for c in command if isinstance(c, UploadFile)]
for c in files:
c.fn = c.fn[len(pathstep):]
+ orgdir = os.getcwd()
os.chdir(pathprefix)
+ print("Upload local files: \"%s\"" % '" "'.join([c.fn for c in files]))
+
if args.dry_run:
- print("cd %s" % pathprefix)
- print("arv-put \"%s\"" % '" "'.join([c.fn for c in files]))
+ print("$(input) is %s" % pathprefix.rstrip('/'))
pdh = "$(input)"
else:
- pdh = put.main(["--portable-data-hash"]+[c.fn for c in files])
+ files = sorted(files, key=lambda x: x.fn)
+ collection = arvados.CollectionWriter(api, num_retries=args.retries)
+ stream = None
+ for f in files:
+ sp = os.path.split(f.fn)
+ if sp[0] != stream:
+ stream = sp[0]
+ collection.start_new_stream(stream)
+ collection.write_file(f.fn, sp[1])
+ item = api.collections().create(body={"owner_uuid": project, "manifest_text": collection.manifest_text()}).execute()
+ pdh = item["portable_data_hash"]
+ print "Uploaded to %s" % item["uuid"]
for c in files:
c.fn = "$(file %s/%s)" % (pdh, c.fn)
+ os.chdir(orgdir)
+
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]]
task_foreach = []
group_parser = argparse.ArgumentParser()
- group_parser.add_argument('--batch-size', type=int)
+ group_parser.add_argument('-b', '--batch-size', type=int)
group_parser.add_argument('args', nargs=argparse.REMAINDER)
for s in xrange(2, len(slots)):
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}
+ component["script_parameters"][inp] = {"value": {"batch":groupargs.args, "size":groupargs.batch_size}}
slots[s] = slots[s][0:i] + [{"foreach": inp, "command": "$(%s)" % inp}]
else:
component["script_parameters"][inp] = groupargs.args
if slots[1]:
task_foreach.append("stdin")
component["script_parameters"]["stdin"] = slots[1]
- component["script_parameters"]["task.stdin"] = "$(stdin)"\
+ component["script_parameters"]["task.stdin"] = "$(stdin)"
if task_foreach:
component["script_parameters"]["task.foreach"] = task_foreach
component["script_parameters"]["command"] = slots[2:]
+ if args.ignore_rcode:
+ component["script_parameters"]["task.ignore_rcode"] = args.ignore_rcode
pipeline = {
- "name": "",
+ "name": "arv-run " + " | ".join([s[0] for s in slots[2:]]),
+ "description": "@" + " ".join(starting_args) + "@",
"components": {
"command": component
},
- "state":"RunningOnServer"
+ "state": "RunningOnClient" if args.local else "RunningOnServer"
}
if args.dry_run:
print(json.dumps(pipeline, indent=4))
- elif args.local:
- subprocess.call(["arv-crunch-job", "--job", json.dumps(component), "--git-dir", args.git_dir])
else:
- api = arvados.api('v1')
- pi = api.pipeline_instances().create(body=pipeline).execute()
+ pipeline["owner_uuid"] = project
+ pi = api.pipeline_instances().create(body=pipeline, ensure_unique_name=True).execute()
print "Running pipeline %s" % pi["uuid"]
- #ws.main(["--pipeline", pi["uuid"]])
+
+ if args.local:
+ subprocess.call(["arv-run-pipeline-instance", "--instance", pi["uuid"], "--run-jobs-here"] + (["--no-reuse"] if args.no_reuse else []))
+ elif not args.no_wait:
+ ws.main(["--pipeline", pi["uuid"]])
+
+ pi = api.pipeline_instances().get(uuid=pi["uuid"]).execute()
+ print "Pipeline is %s" % pi["state"]
+ if "output_uuid" in pi["components"]["command"]:
+ print "Output is %s" % pi["components"]["command"]["output_uuid"]
+ else:
+ print "No output"
if __name__ == '__main__':
main()