X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/2375573bd5a7f909433435c607803df8d2b7bb38..fcf3ca5baf89bdd944e3a7dcdc1b65f8ff4945ca:/sdk/python/arvados/commands/arv_copy.py diff --git a/sdk/python/arvados/commands/arv_copy.py b/sdk/python/arvados/commands/arv_copy.py index 71820b3d2e..8850d0bfd5 100755 --- a/sdk/python/arvados/commands/arv_copy.py +++ b/sdk/python/arvados/commands/arv_copy.py @@ -1,4 +1,6 @@ -#! /usr/bin/env python +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 # arv-copy [--recursive] [--no-recursive] object-uuid src dst # @@ -16,6 +18,12 @@ # instances src and dst. If either of these files is not found, # arv-copy will issue an error. +from __future__ import division +from future import standard_library +from future.utils import listvalues +standard_library.install_aliases() +from past.builtins import basestring +from builtins import object import argparse import contextlib import getpass @@ -25,7 +33,7 @@ import shutil import sys import logging import tempfile -import urlparse +import urllib.parse import arvados import arvados.config @@ -113,7 +121,7 @@ def main(): copy_opts.set_defaults(recursive=True) parser = argparse.ArgumentParser( - description='Copy a pipeline instance, template or collection from one Arvados instance to another.', + description='Copy a pipeline instance, template, workflow, or collection from one Arvados instance to another.', parents=[copy_opts, arv_cmd.retry_opt]) args = parser.parse_args() @@ -152,7 +160,7 @@ def main(): abort("cannot copy object {} of type {}".format(args.object_uuid, t)) # Clean up any outstanding temp git repositories. - for d in local_repo_dir.values(): + for d in listvalues(local_repo_dir): shutil.rmtree(d, ignore_errors=True) # If no exception was thrown and the response does not have an @@ -344,7 +352,7 @@ def migrate_components_filters(template_components, dst_git_repo): be None if that is not known. """ errors = [] - for cname, cspec in template_components.iteritems(): + for cname, cspec in template_components.items(): def add_error(errmsg): errors.append("{}: {}".format(cname, errmsg)) if not isinstance(cspec, dict): @@ -425,33 +433,47 @@ def copy_workflow(wf_uuid, src, dst, args): # fetch the workflow from the source instance wf = src.workflows().get(uuid=wf_uuid).execute(num_retries=args.retries) + # copy collections and docker images if args.recursive: wf_def = yaml.safe_load(wf["definition"]) if wf_def is not None: - colls = [] + locations = [] + docker_images = {} graph = wf_def.get('$graph', None) if graph is not None: - workflow_collections(graph, colls) + workflow_collections(graph, locations, docker_images) else: - workflow_collections(wf_def, colls) - copy_collections(colls, src, dst, args) + workflow_collections(wf_def, locations, docker_images) + + if locations: + copy_collections(locations, src, dst, args) + for image in docker_images: + copy_docker_image(image, docker_images[image], src, dst, args) + + # copy the workflow itself del wf['uuid'] wf['owner_uuid'] = args.project_uuid - return dst.workflows().create(body=wf).execute(num_retries=args.retries) -def workflow_collections(obj, colls): +def workflow_collections(obj, locations, docker_images): if isinstance(obj, dict): loc = obj.get('location', None) if loc is not None: if loc.startswith("keep:"): - colls.append(loc[5:]) + locations.append(loc[5:]) + + docker_image = obj.get('dockerImageId', None) or obj.get('dockerPull', None) + if docker_image is not None: + ds = docker_image.split(":", 1) + tag = ds[1] if len(ds)==2 else 'latest' + docker_images[ds[0]] = tag + for x in obj: - workflow_collections(obj[x], colls) - if isinstance(obj, list): + workflow_collections(obj[x], locations, docker_images) + elif isinstance(obj, list): for x in obj: - workflow_collections(x, colls) + workflow_collections(x, locations, docker_images) # copy_collections(obj, src, dst, args) # @@ -539,7 +561,7 @@ def migrate_jobspec(jobspec, src, dst, dst_repo, args): # names. The return value is undefined. # def copy_git_repos(p, src, dst, dst_repo, args): - for component in p['components'].itervalues(): + for component in p['components'].values(): migrate_jobspec(component, src, dst, dst_repo, args) if 'job' in component: migrate_jobspec(component['job'], src, dst, dst_repo, args) @@ -760,8 +782,8 @@ def select_git_url(api, repo_name, retries, allow_insecure_http, allow_insecure_ git_url = None for url in priority: if url.startswith("http"): - u = urlparse.urlsplit(url) - baseurl = urlparse.urlunsplit((u.scheme, u.netloc, "", "", "")) + u = urllib.parse.urlsplit(url) + baseurl = urllib.parse.urlunsplit((u.scheme, u.netloc, "", "", "")) git_config = ["-c", "credential.%s/.username=none" % baseurl, "-c", "credential.%s/.helper=!cred(){ cat >/dev/null; if [ \"$1\" = get ]; then echo password=$ARVADOS_API_TOKEN; fi; };cred" % baseurl] else: @@ -785,7 +807,7 @@ def select_git_url(api, repo_name, retries, allow_insecure_http, allow_insecure_ if git_url.startswith("http:"): if allow_insecure_http: - logger.warn("Using insecure git url %s but will allow this because %s", git_url, allow_insecure_http_opt) + logger.warning("Using insecure git url %s but will allow this because %s", git_url, allow_insecure_http_opt) else: raise Exception("Refusing to use insecure git url %s, use %s if you really want this." % (git_url, allow_insecure_http_opt)) @@ -845,7 +867,7 @@ def copy_docker_images(pipeline, src, dst, args): runtime_constraints field from src to dst.""" logger.debug('copy_docker_images: {}'.format(pipeline['uuid'])) - for c_name, c_info in pipeline['components'].iteritems(): + for c_name, c_info in pipeline['components'].items(): if ('runtime_constraints' in c_info and 'docker_image' in c_info['runtime_constraints']): copy_docker_image(