import errno
import urlparse
import re
+import logging
+import threading
+
+import ruamel.yaml as yaml
import cwltool.stdfsaccess
from cwltool.pathmapper import abspath
import arvados.util
import arvados.collection
import arvados.arvfile
+import arvados.errors
from schema_salad.ref_resolver import DefaultFetcher
-class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
- """Implement the cwltool FsAccess interface for Arvados Collections."""
+logger = logging.getLogger('arvados.cwl-runner')
- def __init__(self, basedir, api_client=None, keep_client=None):
- super(CollectionFsAccess, self).__init__(basedir)
+class CollectionCache(object):
+ def __init__(self, api_client, keep_client, num_retries):
self.api_client = api_client
self.keep_client = keep_client
self.collections = {}
+ self.lock = threading.Lock()
- 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:]
+ def get(self, pdh):
+ with self.lock:
if pdh not in self.collections:
+ logger.debug("Creating collection reader for %s", pdh)
self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client,
keep_client=self.keep_client)
- return (self.collections[pdh], "/".join(p[1:]))
+ return self.collections[pdh]
+
+
+class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
+ """Implement the cwltool FsAccess interface for Arvados Collections."""
+
+ def __init__(self, basedir, collection_cache=None):
+ super(CollectionFsAccess, self).__init__(basedir)
+ self.collection_cache = collection_cache
+
+ def get_collection(self, path):
+ 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), sp[1] if len(sp) == 2 else None)
else:
return (None, path)
def exists(self, fn):
collection, rest = self.get_collection(fn)
if collection:
- return collection.exists(rest)
+ if rest:
+ return collection.exists(rest)
+ else:
+ return True
else:
return super(CollectionFsAccess, self).exists(fn)
return os.path.realpath(path)
class CollectionFetcher(DefaultFetcher):
- def __init__(self, cache, session, api_client=None, keep_client=None):
+ 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 = CollectionFsAccess("", api_client=api_client, keep_client=keep_client)
+ self.fsaccess = fs_access
+ self.num_retries = num_retries
def fetch_text(self, url):
if url.startswith("keep:"):
- with self.fsaccess.open(url) as f:
+ with self.fsaccess.open(url, "r") as f:
return f.read()
- if url.startswith("arv:"):
- return self.api_client.workflows().get(uuid=url[4:]).execute()["definition"]
+ 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):
- if url.startswith("keep:"):
- return self.fsaccess.exists(url)
- if url.startswith("arv:"):
- if self.fetch_text(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):
return url
basesp = urlparse.urlsplit(base_url)
- if basesp.scheme == "keep":
+ if basesp.scheme in ("keep", "arvwf"):
if not basesp.path:
raise IOError(errno.EINVAL, "Invalid Keep locator", base_url)
pdh = baseparts.pop(0)
- if not arvados.util.keep_locator_pattern.match(pdh):
+ 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.pop()
path = "/".join([pdh] + baseparts + urlparts)
- return urlparse.urlunsplit(("keep", "", path, "", urlsp.fragment))
+ return urlparse.urlunsplit((basesp.scheme, "", path, "", urlsp.fragment))
return super(CollectionFetcher, self).urljoin(base_url, url)
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):
+def collectionResolver(api_client, document_loader, uri, num_retries=4):
if workflow_uuid_pattern.match(uri):
- return "arv:%s" % 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:" + uri
+ return "keep:%s" % (uri)
if arvados.util.collection_uuid_pattern.match(p[0]):
- return "keep:%s%s" % (self.api_client.collections().
- get(uuid=uri).execute()["portable_data_hash"],
+ 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)
projects / arvados.git / blobdiff