import time
import subprocess
import logging
+import sys
+import errno
import arvados.commands._util as arv_cmd
+import arvados.collection
+
+from arvados._version import __version__
logger = logging.getLogger('arvados.arv-run')
logger.setLevel(logging.INFO)
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, 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.")
-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'")
+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,
+ 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.")
+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'")
+arvrun_parser.add_argument('--version', action='version',
+ version="%s %s" % (sys.argv[0], __version__),
+ help='Print version and exit.')
arvrun_parser.add_argument('args', nargs=argparse.REMAINDER)
class ArvFile(object):
self.prefix = prefix
self.fn = fn
+ def __hash__(self):
+ return (self.prefix+self.fn).__hash__()
+
+ def __eq__(self, other):
+ return (self.prefix == other.prefix) and (self.fn == other.fn)
+
class UploadFile(ArvFile):
pass
else:
sp = os.path.split(root)
return is_in_collection(sp[0], os.path.join(sp[1], branch))
- except IOError, OSError:
+ except (IOError, OSError):
return (None, None)
# Determine the project to place the output of this command by searching upward
else:
sp = os.path.split(root)
return determine_project(sp[0], current_user)
- except IOError, OSError:
+ except (IOError, OSError):
return current_user
# Determine if string corresponds to a file, and if that file is part of a
# 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):
+def statfile(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"):
absfn = os.path.abspath(fn)
- if os.path.exists(absfn):
+ try:
st = os.stat(absfn)
- if stat.S_ISREG(st.st_mode):
- sp = os.path.split(absfn)
- (pdh, branch) = is_in_collection(sp[0], sp[1])
- if pdh:
- return ArvFile(prefix, "$(file %s/%s)" % (pdh, branch))
+ sp = os.path.split(absfn)
+ (pdh, branch) = is_in_collection(sp[0], sp[1])
+ if pdh:
+ if stat.S_ISREG(st.st_mode):
+ return ArvFile(prefix, fnPattern % (pdh, branch))
+ elif stat.S_ISDIR(st.st_mode):
+ return ArvFile(prefix, dirPattern % (pdh, branch))
else:
- # trim leading '/' for path prefix test later
- return UploadFile(prefix, absfn[1:])
- if stat.S_ISDIR(st.st_mode):
- sp = os.path.split(absfn)
- (pdh, branch) = is_in_collection(sp[0], sp[1])
- if pdh:
- return ArvFile(prefix, "$(dir %s/%s/)" % (pdh, branch))
+ raise Exception("%s is not a regular file or directory" % absfn)
+ else:
+ # trim leading '/' for path prefix test later
+ return UploadFile(prefix, absfn[1:])
+ except OSError as e:
+ if e.errno == errno.ENOENT:
+ pass
+ else:
+ raise
return prefix+fn
-def uploadfiles(files, api, dry_run=False, num_retries=0, project=None):
+def write_file(collection, pathprefix, fn):
+ with open(os.path.join(pathprefix, fn)) as src:
+ dst = collection.open(fn, "w")
+ r = src.read(1024*128)
+ while r:
+ dst.write(r)
+ r = src.read(1024*128)
+ dst.close(flush=False)
+
+def uploadfiles(files, api, dry_run=False, num_retries=0,
+ project=None,
+ fnPattern="$(file %s/%s)",
+ name=None):
# Find the smallest path prefix that includes all the files that need to be uploaded.
# This starts at the root and iteratively removes common parent directory prefixes
- # until all file pathes no longer have a common parent.
+ # until all file paths no longer have a common parent.
n = True
pathprefix = "/"
while n:
for c in files:
c.fn = c.fn[len(pathstep):]
- orgdir = os.getcwd()
- os.chdir(pathprefix)
-
logger.info("Upload local files: \"%s\"", '" "'.join([c.fn for c in files]))
if dry_run:
pdh = "$(input)"
else:
files = sorted(files, key=lambda x: x.fn)
- collection = arvados.CollectionWriter(api, num_retries=num_retries)
- stream = None
+ collection = arvados.collection.Collection(api_client=api, num_retries=num_retries)
+ prev = ""
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"])
+ localpath = os.path.join(pathprefix, f.fn)
+ if prev and localpath.startswith(prev+"/"):
+ # If this path is inside an already uploaded subdirectory,
+ # don't redundantly re-upload it.
+ # e.g. we uploaded /tmp/foo and the next file is /tmp/foo/bar
+ # skip it because it starts with "/tmp/foo/"
+ continue
+ prev = localpath
+ if os.path.isfile(localpath):
+ write_file(collection, pathprefix, f.fn)
+ elif os.path.isdir(localpath):
+ for root, dirs, iterfiles in os.walk(localpath):
+ root = root[len(pathprefix):]
+ for src in iterfiles:
+ write_file(collection, pathprefix, os.path.join(root, src))
+
+ filters=[["portable_data_hash", "=", collection.portable_data_hash()],
+ ["name", "like", name+"%"]]
+ if project:
+ filters.append(["owner_uuid", "=", project])
+
+ exists = api.collections().list(filters=filters, limit=1).execute(num_retries=num_retries)
+
+ if exists["items"]:
+ item = exists["items"][0]
+ pdh = item["portable_data_hash"]
+ logger.info("Using collection %s (%s)", pdh, item["uuid"])
+ else:
+ collection.save_new(name=name, owner_uuid=project, ensure_unique_name=True)
+ pdh = collection.portable_data_hash()
+ logger.info("Uploaded to %s (%s)", pdh, collection.manifest_locator())
for c in files:
- c.fn = "$(file %s/%s)" % (pdh, c.fn)
-
- os.chdir(orgdir)
+ c.keepref = "%s/%s" % (pdh, c.fn)
+ c.fn = fnPattern % (pdh, c.fn)
def main(arguments=None):
files = [c for command in slots[1:] for c in command if isinstance(c, UploadFile)]
if files:
- uploadfiles(files, api, dry_run=args.dry_run, num_retries=args.num_retries, project=project)
+ uploadfiles(files, api, dry_run=args.dry_run, num_retries=args.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]]