X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c1ac820b37938e3b9a533d93b55eb12a0808cf0d..eb58fd945645f5a670c761f7046b10885941167e:/sdk/cwl/arvados_cwl/fsaccess.py diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py index ae4532bec8..5981268128 100644 --- a/sdk/cwl/arvados_cwl/fsaccess.py +++ b/sdk/cwl/arvados_cwl/fsaccess.py @@ -1,29 +1,89 @@ +# Copyright (C) The Arvados Authors. All rights reserved. +# +# SPDX-License-Identifier: Apache-2.0 + import fnmatch import os import errno +import urlparse +import re +import logging +import threading +from collections import OrderedDict + +import ruamel.yaml as yaml import cwltool.stdfsaccess from cwltool.pathmapper import abspath +import cwltool.resolver import arvados.util import arvados.collection import arvados.arvfile +import arvados.errors + +from googleapiclient.errors import HttpError + +from schema_salad.ref_resolver import DefaultFetcher + +logger = logging.getLogger('arvados.cwl-runner') + +class CollectionCache(object): + def __init__(self, api_client, keep_client, num_retries, + cap=256*1024*1024, + min_entries=2): + self.api_client = api_client + self.keep_client = keep_client + self.num_retries = num_retries + self.collections = OrderedDict() + self.lock = threading.Lock() + self.total = 0 + self.cap = cap + self.min_entries = min_entries + + def cap_cache(self): + if self.total > self.cap: + # ordered list iterates from oldest to newest + for pdh, v in self.collections.items(): + if self.total < self.cap or len(self.collections) < self.min_entries: + break + # cut it loose + logger.debug("Evicting collection reader %s from cache", pdh) + del self.collections[pdh] + self.total -= v[1] + + def get(self, pdh): + with self.lock: + if pdh not in self.collections: + logger.debug("Creating collection reader for %s", pdh) + cr = arvados.collection.CollectionReader(pdh, api_client=self.api_client, + keep_client=self.keep_client, + num_retries=self.num_retries) + sz = len(cr.manifest_text()) * 128 + self.collections[pdh] = (cr, sz) + self.total += sz + self.cap_cache() + else: + cr, sz = self.collections[pdh] + # bump it to the back + del self.collections[pdh] + self.collections[pdh] = (cr, sz) + return cr + class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess): """Implement the cwltool FsAccess interface for Arvados Collections.""" - def __init__(self, basedir, api_client=None): + def __init__(self, basedir, collection_cache=None): super(CollectionFsAccess, self).__init__(basedir) - self.api_client = api_client - self.collections = {} + self.collection_cache = collection_cache def get_collection(self, path): - p = path.split("/") - if p[0].startswith("keep:") and arvados.util.keep_locator_pattern.match(p[0][5:]): - pdh = p[0][5:] - if pdh not in self.collections: - self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client) - return (self.collections[pdh], "/".join(p[1:])) + sp = path.split("/", 1) + p = sp[0] + if p.startswith("keep:") and arvados.util.keep_locator_pattern.match(p[5:]): + pdh = p[5:] + return (self.collection_cache.get(pdh), urlparse.unquote(sp[1]) if len(sp) == 2 else None) else: return (None, path) @@ -51,28 +111,48 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess): def glob(self, pattern): collection, rest = self.get_collection(pattern) - if collection and not rest: + if collection is not None and not rest: return [pattern] patternsegments = rest.split("/") - return self._match(collection, patternsegments, "keep:" + collection.manifest_locator()) + return sorted(self._match(collection, patternsegments, "keep:" + collection.manifest_locator())) def open(self, fn, mode): collection, rest = self.get_collection(fn) - if collection: + if collection is not None: return collection.open(rest, mode) else: return super(CollectionFsAccess, self).open(self._abs(fn), mode) def exists(self, fn): - collection, rest = self.get_collection(fn) - if collection: - return collection.exists(rest) + try: + collection, rest = self.get_collection(fn) + except HttpError as err: + if err.resp.status == 404: + return False + else: + raise + if collection is not None: + if rest: + return collection.exists(rest) + else: + return True else: return super(CollectionFsAccess, self).exists(fn) + def size(self, fn): # type: (unicode) -> bool + collection, rest = self.get_collection(fn) + if collection is not None: + if rest: + arvfile = collection.find(rest) + if isinstance(arvfile, arvados.arvfile.ArvadosFile): + return arvfile.size() + raise IOError(errno.EINVAL, "Not a path to a file %s" % (fn)) + else: + return super(CollectionFsAccess, self).size(fn) + def isfile(self, fn): # type: (unicode) -> bool collection, rest = self.get_collection(fn) - if collection: + if collection is not None: if rest: return isinstance(collection.find(rest), arvados.arvfile.ArvadosFile) else: @@ -82,9 +162,9 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess): def isdir(self, fn): # type: (unicode) -> bool collection, rest = self.get_collection(fn) - if collection: + if collection is not None: if rest: - return isinstance(collection.find(rest), arvados.collection.Collection) + return isinstance(collection.find(rest), arvados.collection.RichCollectionBase) else: return True else: @@ -92,14 +172,14 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess): def listdir(self, fn): # type: (unicode) -> List[unicode] collection, rest = self.get_collection(fn) - if collection: + if collection is not None: if rest: dir = collection.find(rest) else: dir = collection if dir is None: raise IOError(errno.ENOENT, "Directory '%s' in '%s' not found" % (rest, collection.portable_data_hash())) - if not isinstance(dir, arvados.collection.Collection): + if not isinstance(dir, arvados.collection.RichCollectionBase): raise IOError(errno.ENOENT, "Path '%s' in '%s' is not a Directory" % (rest, collection.portable_data_hash())) return [abspath(l, fn) for l in dir.keys()] else: @@ -114,7 +194,104 @@ class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess): if path.startswith("$(task.tmpdir)") or path.startswith("$(task.outdir)"): return path collection, rest = self.get_collection(path) - if collection: + if collection is not None: return path else: return os.path.realpath(path) + +class CollectionFetcher(DefaultFetcher): + def __init__(self, cache, session, api_client=None, fs_access=None, num_retries=4): + super(CollectionFetcher, self).__init__(cache, session) + self.api_client = api_client + self.fsaccess = fs_access + self.num_retries = num_retries + + def fetch_text(self, url): + if url.startswith("keep:"): + with self.fsaccess.open(url, "r") as f: + return f.read() + if url.startswith("arvwf:"): + record = self.api_client.workflows().get(uuid=url[6:]).execute(num_retries=self.num_retries) + definition = record["definition"] + ('\nlabel: "%s"\n' % record["name"].replace('"', '\\"')) + return definition + return super(CollectionFetcher, self).fetch_text(url) + + def check_exists(self, url): + try: + if url.startswith("http://arvados.org/cwl"): + return True + if url.startswith("keep:"): + return self.fsaccess.exists(url) + if url.startswith("arvwf:"): + if self.fetch_text(url): + return True + except arvados.errors.NotFoundError: + return False + except: + logger.exception("Got unexpected exception checking if file exists:") + return False + return super(CollectionFetcher, self).check_exists(url) + + def urljoin(self, base_url, url): + if not url: + return base_url + + urlsp = urlparse.urlsplit(url) + if urlsp.scheme or not base_url: + return url + + basesp = urlparse.urlsplit(base_url) + if basesp.scheme in ("keep", "arvwf"): + if not basesp.path: + raise IOError(errno.EINVAL, "Invalid Keep locator", base_url) + + baseparts = basesp.path.split("/") + urlparts = urlsp.path.split("/") if urlsp.path else [] + + pdh = baseparts.pop(0) + + if basesp.scheme == "keep" and not arvados.util.keep_locator_pattern.match(pdh): + raise IOError(errno.EINVAL, "Invalid Keep locator", base_url) + + if urlsp.path.startswith("/"): + baseparts = [] + urlparts.pop(0) + + if baseparts and urlsp.path: + baseparts.pop() + + path = "/".join([pdh] + baseparts + urlparts) + return urlparse.urlunsplit((basesp.scheme, "", path, "", urlsp.fragment)) + + return super(CollectionFetcher, self).urljoin(base_url, url) + + schemes = [u"file", u"http", u"https", u"mailto", u"keep", u"arvwf"] + + def supported_schemes(self): # type: () -> List[Text] + return self.schemes + + +workflow_uuid_pattern = re.compile(r'[a-z0-9]{5}-7fd4e-[a-z0-9]{15}') +pipeline_template_uuid_pattern = re.compile(r'[a-z0-9]{5}-p5p6p-[a-z0-9]{15}') + +def collectionResolver(api_client, document_loader, uri, num_retries=4): + if uri.startswith("keep:") or uri.startswith("arvwf:"): + return uri + + if workflow_uuid_pattern.match(uri): + return "arvwf:%s#main" % (uri) + + if pipeline_template_uuid_pattern.match(uri): + pt = api_client.pipeline_templates().get(uuid=uri).execute(num_retries=num_retries) + return "keep:" + pt["components"].values()[0]["script_parameters"]["cwl:tool"] + + p = uri.split("/") + if arvados.util.keep_locator_pattern.match(p[0]): + return "keep:%s" % (uri) + + if arvados.util.collection_uuid_pattern.match(p[0]): + return "keep:%s%s" % (api_client.collections(). + get(uuid=p[0]).execute()["portable_data_hash"], + uri[len(p[0]):]) + + return cwltool.resolver.tool_resolver(document_loader, uri)