#!/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.commands.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-run-pipeline-instance")
arvrun_parser.add_argument('--docker-image', type=str, default="arvados/jobs", help="Docker image to use, default arvados/jobs")
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):
try:
if root == "/":
else:
sp = os.path.split(root)
return is_in_collection(sp[0], os.path.join(sp[1], branch))
- except:
+ except IOError, OSError:
return (None, None)
+# 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 == "/":
else:
sp = os.path.split(root)
return determine_project(sp[0], current_user)
- except:
+ 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):
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('>'):
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:
# if it starts with a \ then don't do any interpretation
command[i] = a[1:]
else:
- # 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))
- matched = True
- break
- if not matched:
- # parameter might be a file, so test it
- command[i] = statfile('', a)
+ # 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 = "/"
print("Upload local files: \"%s\"" % '" "'.join([c.fn for c in files]))
if args.dry_run:
- print("cd %s" % pathprefix)
+ print("$(input) is %s" % pathprefix.rstrip('/'))
pdh = "$(input)"
else:
files = sorted(files, key=lambda x: x.fn)
- collection = arvados.CollectionWriter(api, num_retries=3)
+ collection = arvados.CollectionWriter(api, num_retries=args.retries)
stream = None
for f in files:
sp = os.path.split(f.fn)
if slots[1]:
task_foreach.append("stdin")
component["script_parameters"]["stdin"] = slots[1]
- component["script_parameters"]["task.stdin"] = "$(stdin)"\
+ component["script_parameters"]["task.stdin"] = "$(stdin)"
if task_foreach:
component["script_parameters"]["task.foreach"] = task_foreach
print(json.dumps(pipeline, indent=4))
else:
pipeline["owner_uuid"] = project
- pi = api.pipeline_instances().create(body=pipeline).execute()
+ pi = api.pipeline_instances().create(body=pipeline, ensure_unique_name=True).execute()
print "Running pipeline %s" % pi["uuid"]
if args.local:
projects / arvados.git / blobdiff