import fnmatch
import os
+import errno
+import urlparse
+import re
-import cwltool.process
+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
+
+from schema_salad.ref_resolver import DefaultFetcher
-class CollectionFsAccess(cwltool.process.StdFsAccess):
+class CollectionFsAccess(cwltool.stdfsaccess.StdFsAccess):
"""Implement the cwltool FsAccess interface for Arvados Collections."""
- def __init__(self, basedir):
+ def __init__(self, basedir, api_client=None, keep_client=None):
super(CollectionFsAccess, self).__init__(basedir)
+ self.api_client = api_client
+ self.keep_client = keep_client
self.collections = {}
def get_collection(self, path):
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)
+ self.collections[pdh] = arvados.collection.CollectionReader(pdh, api_client=self.api_client,
+ keep_client=self.keep_client)
return (self.collections[pdh], "/".join(p[1:]))
else:
return (None, path)
def glob(self, pattern):
collection, rest = self.get_collection(pattern)
+ if collection and not rest:
+ return [pattern]
patternsegments = rest.split("/")
return self._match(collection, patternsegments, "keep:" + collection.manifest_locator())
if collection:
return collection.open(rest, mode)
else:
- return open(self._abs(fn), mode)
+ 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)
else:
- return os.path.exists(self._abs(fn))
+ return super(CollectionFsAccess, self).exists(fn)
+
+ def isfile(self, fn): # type: (unicode) -> bool
+ collection, rest = self.get_collection(fn)
+ if collection:
+ if rest:
+ return isinstance(collection.find(rest), arvados.arvfile.ArvadosFile)
+ else:
+ return False
+ else:
+ return super(CollectionFsAccess, self).isfile(fn)
+
+ def isdir(self, fn): # type: (unicode) -> bool
+ collection, rest = self.get_collection(fn)
+ if collection:
+ if rest:
+ return isinstance(collection.find(rest), arvados.collection.RichCollectionBase)
+ else:
+ return True
+ else:
+ return super(CollectionFsAccess, self).isdir(fn)
+
+ def listdir(self, fn): # type: (unicode) -> List[unicode]
+ collection, rest = self.get_collection(fn)
+ if collection:
+ 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.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:
+ return super(CollectionFsAccess, self).listdir(fn)
+
+ def join(self, path, *paths): # type: (unicode, *unicode) -> unicode
+ if paths and paths[-1].startswith("keep:") and arvados.util.keep_locator_pattern.match(paths[-1][5:]):
+ return paths[-1]
+ return os.path.join(path, *paths)
+
+ def realpath(self, path):
+ if path.startswith("$(task.tmpdir)") or path.startswith("$(task.outdir)"):
+ return path
+ collection, rest = self.get_collection(path)
+ if collection:
+ return path
+ else:
+ return os.path.realpath(path)
+
+class CollectionFetcher(DefaultFetcher):
+ def __init__(self, cache, session, api_client=None, keep_client=None):
+ super(CollectionFetcher, self).__init__(cache, session)
+ self.api_client = api_client
+ self.fsaccess = CollectionFsAccess("", api_client=api_client, keep_client=keep_client)
+
+ def fetch_text(self, url):
+ if url.startswith("keep:"):
+ with self.fsaccess.open(url, "r") as f:
+ return f.read()
+ if url.startswith("arvwf:"):
+ return self.api_client.workflows().get(uuid=url[6:]).execute()["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("arvwf:"):
+ if self.fetch_text(url):
+ return True
+ 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):
+ 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()
+ 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)