#!/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')
+logger.setLevel(logging.INFO)
-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")
+arvrun_parser.add_argument('--docker-image', type=str, help="Docker image to use, otherwise use instance default.")
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.")
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, "$(dir %s/%s/)" % (pdh, branch))
+
return prefix+fn
+def uploadfiles(files, api, dry_run=False, num_retries=0, project=None):
+ # Find the smallest path prefix that includes all the files that need to be uploaded.
+ # This starts at the root and iteratively removes common parent directory prefixes
+ # until all file pathes no longer have a common parent.
+ n = True
+ pathprefix = "/"
+ while n:
+ pathstep = None
+ for c in files:
+ if pathstep is None:
+ sp = c.fn.split('/')
+ if len(sp) < 2:
+ # no parent directories left
+ n = False
+ break
+ # path step takes next directory
+ pathstep = sp[0] + "/"
+ else:
+ # check if pathstep is common prefix for all files
+ if not c.fn.startswith(pathstep):
+ n = False
+ break
+ if n:
+ # pathstep is common parent directory for all files, so remove the prefix
+ # from each path
+ pathprefix += pathstep
+ for c in files:
+ c.fn = c.fn[len(pathstep):]
+
+ orgdir = os.getcwd()
+ os.chdir(pathprefix)
+
+ logger.info("Upload local files: \"%s\"", '" "'.join([c.fn for c in files]))
+
+ if dry_run:
+ logger.info("$(input) is %s", pathprefix.rstrip('/'))
+ pdh = "$(input)"
+ else:
+ files = sorted(files, key=lambda x: x.fn)
+ collection = arvados.CollectionWriter(api, num_retries=num_retries)
+ stream = None
+ for f in files:
+ sp = os.path.split(f.fn)
+ if sp[0] != stream:
+ stream = sp[0]
+ collection.start_new_stream(stream)
+ collection.write_file(f.fn, sp[1])
+ item = api.collections().create(body={"owner_uuid": project, "manifest_text": collection.manifest_text()}).execute()
+ pdh = item["portable_data_hash"]
+ logger.info("Uploaded to %s", item["uuid"])
+
+ for c in files:
+ c.fn = "$(file %s/%s)" % (pdh, c.fn)
+
+ os.chdir(orgdir)
+
+
def main(arguments=None):
args = arvrun_parser.parse_args(arguments)
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("(-.)(.+)")]
-
+ 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 = "/"
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):]
-
- 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)
- pdh = "$(input)"
- else:
- files = sorted(files, key=lambda x: x.fn)
- collection = arvados.CollectionWriter(api, num_retries=3)
- stream = None
- for f in files:
- sp = os.path.split(f.fn)
- if sp[0] != stream:
- stream = sp[0]
- collection.start_new_stream(stream)
- collection.write_file(f.fn, sp[1])
- item = api.collections().create(body={"owner_uuid": project, "manifest_text": collection.manifest_text()}).execute()
- pdh = item["portable_data_hash"]
- print "Uploaded to %s" % item["uuid"]
-
- for c in files:
- c.fn = "$(file %s/%s)" % (pdh, c.fn)
-
- os.chdir(orgdir)
+ if files:
+ uploadfiles(files, api, dry_run=args.dry_run, num_retries=args.num_retries, project=project)
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]]
"repository": args.repository,
"script_parameters": {
},
- "runtime_constraints": {
- "docker_image": args.docker_image
- }
+ "runtime_constraints": {}
}
+ if args.docker_image:
+ component["runtime_constraints"]["docker_image"] = args.docker_image
+
task_foreach = []
group_parser = argparse.ArgumentParser()
group_parser.add_argument('-b', '--batch-size', type=int)
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()
- print "Running pipeline %s" % pi["uuid"]
+ pi = api.pipeline_instances().create(body=pipeline, ensure_unique_name=True).execute()
+ logger.info("Running pipeline %s", pi["uuid"])
if args.local:
subprocess.call(["arv-run-pipeline-instance", "--instance", pi["uuid"], "--run-jobs-here"] + (["--no-reuse"] if args.no_reuse else []))
ws.main(["--pipeline", pi["uuid"]])
pi = api.pipeline_instances().get(uuid=pi["uuid"]).execute()
- print "Pipeline is %s" % pi["state"]
+ logger.info("Pipeline is %s", pi["state"])
if "output_uuid" in pi["components"]["command"]:
- print "Output is %s" % pi["components"]["command"]["output_uuid"]
+ logger.info("Output is %s", pi["components"]["command"]["output_uuid"])
else:
- print "No output"
+ logger.info("No output")
if __name__ == '__main__':
main()
projects / arvados.git / blobdiff