import fnmatch
import os
import errno
+import urlparse
+import re
+import logging
+
+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 schema_salad.ref_resolver import DefaultFetcher
+
+logger = logging.getLogger('arvados.cwl-runner')
class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
"""Implement the cwltool FsAccess interface for Arvados Collections."""
self.collections = {}
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:]
+ sp = path.split("/", 1)
+ p = sp[0]
+ if p.startswith("keep:") and arvados.util.keep_locator_pattern.match(p[5:]):
+ pdh = p[5:]
if pdh not in self.collections:
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], sp[1] if len(sp) == 2 else None)
else:
return (None, path)
return path
else:
return os.path.realpath(path)
+
+class CollectionFetcher(DefaultFetcher):
+ def __init__(self, cache, session, api_client=None, keep_client=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.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("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)
+
+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 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)