#! /usr/bin/env python # arv-copy [--recursive] [--no-recursive] object-uuid src dst # # Copies an object from Arvados instance src to instance dst. # # By default, arv-copy recursively copies any dependent objects # necessary to make the object functional in the new instance # (e.g. for a pipeline instance, arv-copy copies the pipeline # template, input collection, docker images, git repositories). If # --no-recursive is given, arv-copy copies only the single record # identified by object-uuid. # # The user must have files $HOME/.config/arvados/{src}.conf and # $HOME/.config/arvados/{dst}.conf with valid login credentials for # instances src and dst. If either of these files is not found, # arv-copy will issue an error. import argparse import os import re import sets import sys import logging import tempfile import arvados import arvados.config import arvados.keep logger = logging.getLogger('arvados.arv-copy') def main(): logger.setLevel(logging.DEBUG) parser = argparse.ArgumentParser( description='Copy a pipeline instance from one Arvados instance to another.') parser.add_argument( '--recursive', dest='recursive', action='store_true', help='Recursively copy any dependencies for this object. (default)') parser.add_argument( '--no-recursive', dest='recursive', action='store_false', help='Do not copy any dependencies. NOTE: if this option is given, the copied object will need to be updated manually in order to be functional.') parser.add_argument( '--dst-git-repo', dest='dst_git_repo', help='The name of the destination git repository.') parser.add_argument( '--project_uuid', dest='project_uuid', help='The UUID of the project at the destination to which the pipeline should be copied.') parser.add_argument( 'object_uuid', help='The UUID of the object to be copied.') parser.add_argument( 'source_arvados', help='The name of the source Arvados instance.') parser.add_argument( 'destination_arvados', help='The name of the destination Arvados instance.') parser.set_defaults(recursive=True) args = parser.parse_args() # Create API clients for the source and destination instances src_arv = api_for_instance(args.source_arvados) dst_arv = api_for_instance(args.destination_arvados) # Identify the kind of object we have been given, and begin copying. t = uuid_type(src_arv, args.object_uuid) if t == 'Collection': result = copy_collection(args.object_uuid, src=src_arv, dst=dst_arv) elif t == 'PipelineInstance': result = copy_pipeline_instance(args.object_uuid, dst_git_repo=args.dst_git_repo, dst_project=args.project_uuid, recursive=args.recursive, src=src_arv, dst=dst_arv) elif t == 'PipelineTemplate': result = copy_pipeline_template(args.object_uuid, recursive=args.recursive, src=src_arv, dst=dst_arv) else: abort("cannot copy object {} of type {}".format(args.object_uuid, t)) print result exit(0) # api_for_instance(instance_name) # # Creates an API client for the Arvados instance identified by # instance_name. Credentials must be stored in # $HOME/.config/arvados/instance_name.conf # def api_for_instance(instance_name): if '/' in instance_name: abort('illegal instance name {}'.format(instance_name)) config_file = os.path.join(os.environ['HOME'], '.config', 'arvados', "{}.conf".format(instance_name)) cfg = arvados.config.load(config_file) if 'ARVADOS_API_HOST' in cfg and 'ARVADOS_API_TOKEN' in cfg: api_is_insecure = ( cfg.get('ARVADOS_API_HOST_INSECURE', '').lower() in set( ['1', 't', 'true', 'y', 'yes'])) client = arvados.api('v1', host=cfg['ARVADOS_API_HOST'], token=cfg['ARVADOS_API_TOKEN'], insecure=api_is_insecure, cache=False) else: abort('need ARVADOS_API_HOST and ARVADOS_API_TOKEN for {}'.format(instance_name)) return client # copy_pipeline_instance(pi_uuid, dst_git_repo, dst_project, recursive, src, dst) # # Copies a pipeline instance identified by pi_uuid from src to dst. # # If the 'recursive' option evaluates to True: # 1. Copies all input collections # * For each component in the pipeline, include all collections # listed as job dependencies for that component) # 2. Copy docker images # 3. Copy git repositories # 4. Copy the pipeline template # # The only changes made to the copied pipeline instance are: # 1. The original pipeline instance UUID is preserved in # the 'properties' hash as 'copied_from_pipeline_instance_uuid'. # 2. The pipeline_template_uuid is changed to the new template uuid. # 3. The owner_uuid of the instance is changed to the user who # copied it. # def copy_pipeline_instance(pi_uuid, dst_git_repo=None, dst_project=None, recursive=True, src=None, dst=None): # Fetch the pipeline instance record. pi = src.pipeline_instances().get(uuid=pi_uuid).execute() pi['properties']['copied_from_pipeline_instance_uuid'] = pi_uuid if recursive: # Copy the pipeline template and save the copied template. pt = copy_pipeline_template(pi['pipeline_template_uuid'], recursive=True, src=src, dst=dst) # Copy input collections, docker images and git repos. pi = copy_collections(pi, src, dst) copy_git_repos(pi, dst_git_repo, src, dst) # Update the fields of the pipeline instance with the copied # pipeline template. pi['pipeline_template_uuid'] = pt['uuid'] if dst_project: pi['owner_uuid'] = dst_project else: del pi['owner_uuid'] else: # not recursive print >>sys.stderr, "Copying only pipeline instance {}.".format(pi_uuid) print >>sys.stderr, "You are responsible for making sure all pipeline dependencies have been updated." # Create the new pipeline instance at the destination Arvados. new_pi = dst.pipeline_instances().create(pipeline_instance=pi).execute() return new_pi # copy_pipeline_template(pt_uuid, recursive, src, dst) # # Copies a pipeline template identified by pt_uuid from src to dst. # # If the 'recursive' option evaluates to true, also copy any collections, # docker images and git repositories that this template references. # # The owner_uuid of the new template is changed to that of the user # who copied the template. # # Returns the copied pipeline template object. # def copy_pipeline_template(pt_uuid, recursive=True, src=None, dst=None): # fetch the pipeline template from the source instance pt = src.pipeline_templates().get(uuid=pt_uuid).execute() if recursive: # Copy input collections, docker images and git repos. pt = copy_collections(pt, src, dst) copy_git_repos(pt, dst_git_repo, src, dst) pt['name'] = pt['name'] + ' copy' del pt['uuid'] del pt['owner_uuid'] return dst.pipeline_templates().create(body=pt).execute() # copy_collections(obj, src, dst) # # Recursively copies all collections referenced by 'obj' from src # to dst. # # Returns a copy of obj with any old collection uuids replaced by # the new ones. # def copy_collections(obj, src, dst): if type(obj) in [str, unicode]: if uuid_type(src, obj) == 'Collection': newc = copy_collection(obj, src, dst) if obj != newc['uuid'] and obj != newc['portable_data_hash']: return newc['uuid'] return obj elif type(obj) == dict: return {v: copy_collections(obj[v], src, dst) for v in obj} elif type(obj) == list: return [copy_collections(v, src, dst) for v in obj] return obj # copy_git_repos(p, dst_repo, src, dst) # # Copies all git repositories referenced by pipeline instance or # template 'p' from src to dst. # # Git repository dependencies are identified by: # * p['components'][c]['repository'] # * p['components'][c]['job']['repository'] # for each component c in the pipeline. # # The pipeline object is updated in place with the new repository # names. The return value is undefined. # def copy_git_repos(p, dst_repo, src=None, dst=None): copied = set() for c in p['components']: component = p['components'][c] if 'repository' in component: repo = component['repository'] if repo not in copied: copy_git_repo(repo, dst_repo, src, dst) copied.add(repo) component['repository'] = dst_repo if 'job' in component and 'repository' in component['job']: repo = component['job']['repository'] if repo not in copied: copy_git_repo(repo, dst_repo, src, dst) copied.add(repo) component['job']['repository'] = dst_repo # copy_collection(obj_uuid, src, dst) # # Copies the collection identified by obj_uuid from src to dst. # Returns the collection object created at dst. # # For this application, it is critical to preserve the # collection's manifest hash, which is not guaranteed with the # arvados.CollectionReader and arvados.CollectionWriter classes. # Copying each block in the collection manually, followed by # the manifest block, ensures that the collection's manifest # hash will not change. # def copy_collection(obj_uuid, src=None, dst=None): c = src.collections().get(uuid=obj_uuid).execute() # Check whether a collection with this hash already exists # at the destination. If so, just return that collection. if 'portable_data_hash' in c: colhash = c['portable_data_hash'] else: colhash = c['uuid'] dstcol = dst.collections().list( filters=[['portable_data_hash', '=', colhash]] ).execute() if dstcol['items_available'] > 0: return dstcol['items'][0] # Fetch the collection's manifest. manifest = c['manifest_text'] logging.debug('copying collection %s', obj_uuid) logging.debug('manifest_text = %s', manifest) # Enumerate the block locators found in the manifest. collection_blocks = sets.Set() src_keep = arvados.keep.KeepClient(src) for line in manifest.splitlines(): try: block_hash = line.split()[1] collection_blocks.add(block_hash) except ValueError: abort('bad manifest line in collection {}: {}'.format(obj_uuid, f)) # Copy each block from src_keep to dst_keep. dst_keep = arvados.keep.KeepClient(dst) for locator in collection_blocks: data = src_keep.get(locator) logger.debug('copying block %s', locator) logger.info("Retrieved %d bytes", len(data)) dst_keep.put(data) # Copy the manifest and save the collection. logger.debug('saving {} manifest: {}'.format(obj_uuid, manifest)) dst_keep.put(manifest) return dst.collections().create(body={"manifest_text": manifest}).execute() # copy_git_repo(src_git_repo, dst_git_repo, src, dst) # # Copies commits from git repository 'src_git_repo' on Arvados # instance 'src' to 'dst_git_repo' on 'dst'. Both src_git_repo # and dst_git_repo are repository names, not UUIDs (i.e. "arvados" # or "jsmith") # # All commits will be copied to a destination branch named for the # source repository URL. # # Because users cannot create their own repositories, the # destination repository must already exist. # # The user running this command must be authenticated # to both repositories. # def copy_git_repo(src_git_repo, dst_git_repo, src=None, dst=None): # Identify the fetch and push URLs for the git repositories. r = src.repositories().list( filters=[['name', '=', src_git_repo]]).execute() if r['items_available'] != 1: raise Exception('cannot identify source repo {}; {} repos found' .format(src_git_repo, r['items_available'])) src_git_url = r['items'][0]['fetch_url'] logger.debug('src_git_url: {}'.format(src_git_url)) r = dst.repositories().list( filters=[['name', '=', dst_git_repo]]).execute() if r['items_available'] != 1: raise Exception('cannot identify source repo {}; {} repos found' .format(dst_git_repo, r['items_available'])) dst_git_push_url = r['items'][0]['push_url'] logger.debug('dst_git_push_url: {}'.format(dst_git_push_url)) tmprepo = tempfile.mkdtemp() dst_branch = re.sub(r'\W+', '_', src_git_url) arvados.util.run_command( ["git", "clone", src_git_url, tmprepo], cwd=os.path.dirname(tmprepo)) arvados.util.run_command( ["git", "checkout", "-b", dst_branch], cwd=tmprepo) arvados.util.run_command(["git", "remote", "add", "dst", dst_git_push_url], cwd=tmprepo) arvados.util.run_command(["git", "push", "dst", dst_branch], cwd=tmprepo) # uuid_type(api, object_uuid) # # Returns the name of the class that object_uuid belongs to, based on # the second field of the uuid. This function consults the api's # schema to identify the object class. # # It returns a string such as 'Collection', 'PipelineInstance', etc. # # Special case: if handed a Keep locator hash, return 'Collection'. # def uuid_type(api, object_uuid): if re.match(r'^[a-f0-9]{32}\+[0-9]+(\+[A-Za-z0-9+-]+)?$', object_uuid): return 'Collection' p = object_uuid.split('-') if len(p) == 3: type_prefix = p[1] for k in api._schema.schemas: obj_class = api._schema.schemas[k].get('uuidPrefix', None) if type_prefix == obj_class: return k return None def abort(msg, code=1): print >>sys.stderr, "arv-copy:", msg exit(code) if __name__ == '__main__': main()