import re
+import logging
+import uuid
+import os
import arvados.commands.run
import arvados.collection
-from cwltool.pathmapper import PathMapper, MapperEnt, abspath
+
+from schema_salad.sourceline import SourceLine
+
+from cwltool.pathmapper import PathMapper, MapperEnt, abspath, adjustFileObjs, adjustDirObjs
+from cwltool.workflow import WorkflowException
+
+logger = logging.getLogger('arvados.cwl-runner')
class ArvPathMapper(PathMapper):
"""Convert container-local paths to and from Keep collection ids."""
- pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+')
+ pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+$')
+ pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.+)?$')
def __init__(self, arvrunner, referenced_files, input_basedir,
collection_pattern, file_pattern, name=None, **kwargs):
self.name = name
super(ArvPathMapper, self).__init__(referenced_files, input_basedir, None)
+ def visit(self, srcobj, uploadfiles):
+ src = srcobj["location"]
+ if srcobj["class"] == "File":
+ if "#" in src:
+ src = src[:src.index("#")]
+ if isinstance(src, basestring) and ArvPathMapper.pdh_path.match(src):
+ self._pathmap[src] = MapperEnt(src, self.collection_pattern % src[5:], "File")
+ if src not in self._pathmap:
+ # Local FS ref, may need to be uploaded or may be on keep
+ # mount.
+ ab = abspath(src, self.input_basedir)
+ st = arvados.commands.run.statfile("", ab, fnPattern="keep:%s/%s")
+ with SourceLine(srcobj, "location", WorkflowException):
+ if isinstance(st, arvados.commands.run.UploadFile):
+ uploadfiles.add((src, ab, st))
+ elif isinstance(st, arvados.commands.run.ArvFile):
+ self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.fn[5:], "File")
+ elif src.startswith("_:"):
+ if "contents" in srcobj:
+ pass
+ else:
+ raise WorkflowException("File literal '%s' is missing contents" % src)
+ elif src.startswith("arvwf:"):
+ self._pathmap[src] = MapperEnt(src, src, "File")
+ else:
+ raise WorkflowException("Input file path '%s' is invalid" % st)
+ if "secondaryFiles" in srcobj:
+ for l in srcobj["secondaryFiles"]:
+ self.visit(l, uploadfiles)
+ elif srcobj["class"] == "Directory":
+ if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src):
+ self._pathmap[src] = MapperEnt(src, self.collection_pattern % src[5:], "Directory")
+ for l in srcobj.get("listing", []):
+ self.visit(l, uploadfiles)
+
+ def addentry(self, obj, c, path, subdirs):
+ if obj["location"] in self._pathmap:
+ src, srcpath = self.arvrunner.fs_access.get_collection(self._pathmap[obj["location"]].resolved)
+ if srcpath == "":
+ srcpath = "."
+ c.copy(srcpath, path + "/" + obj["basename"], source_collection=src, overwrite=True)
+ for l in obj.get("secondaryFiles", []):
+ self.addentry(l, c, path, subdirs)
+ elif obj["class"] == "Directory":
+ for l in obj["listing"]:
+ self.addentry(l, c, path + "/" + obj["basename"], subdirs)
+ subdirs.append((obj["location"], path + "/" + obj["basename"]))
+ elif obj["location"].startswith("_:") and "contents" in obj:
+ with c.open(path + "/" + obj["basename"], "w") as f:
+ f.write(obj["contents"].encode("utf-8"))
+ else:
+ raise SourceLine(obj, "location", WorkflowException).makeError("Don't know what to do with '%s'" % obj["location"])
+
def setup(self, referenced_files, basedir):
# type: (List[Any], unicode) -> None
- self._pathmap = self.arvrunner.get_uploaded()
uploadfiles = set()
+ already_uploaded = self.arvrunner.get_uploaded()
+ for k in referenced_files:
+ loc = k["location"]
+ if loc in already_uploaded:
+ v = already_uploaded[loc]
+ self._pathmap[loc] = MapperEnt(v.resolved, self.collection_pattern % v.resolved[5:], "File")
+
for srcobj in referenced_files:
- if srcobj["class"] == "File":
- src = srcobj["location"]
- if "#" in src:
- src = src[:src.index("#")]
- if isinstance(src, basestring) and ArvPathMapper.pdh_path.match(src):
- self._pathmap[src] = MapperEnt(src, self.collection_pattern % src[5:], "File")
- if src not in self._pathmap:
- # Local FS ref, may need to be uploaded or may be on keep
- # mount.
- ab = abspath(src, self.input_basedir)
- st = arvados.commands.run.statfile("", ab, fnPattern=self.file_pattern)
- if isinstance(st, arvados.commands.run.UploadFile):
- uploadfiles.add((src, ab, st))
- elif isinstance(st, arvados.commands.run.ArvFile):
- self._pathmap[src] = MapperEnt(ab, st.fn, "File")
- else:
- raise cwltool.workflow.WorkflowException("Input file path '%s' is invalid" % st)
+ self.visit(srcobj, uploadfiles)
if uploadfiles:
arvados.commands.run.uploadfiles([u[2] for u in uploadfiles],
self.arvrunner.api,
dry_run=False,
- num_retries=3,
- fnPattern=self.file_pattern,
+ num_retries=self.arvrunner.num_retries,
+ fnPattern="keep:%s/%s",
name=self.name,
project=self.arvrunner.project_uuid)
for src, ab, st in uploadfiles:
- self._pathmap[src] = MapperEnt(ab, st.fn, "File")
+ self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.fn[5:], "File")
self.arvrunner.add_uploaded(src, self._pathmap[src])
+ for srcobj in referenced_files:
+ if srcobj["class"] == "Directory":
+ if srcobj["location"] not in self._pathmap:
+ c = arvados.collection.Collection(api_client=self.arvrunner.api,
+ keep_client=self.arvrunner.keep_client,
+ num_retries=self.arvrunner.num_retries)
+ subdirs = []
+ for l in srcobj["listing"]:
+ self.addentry(l, c, ".", subdirs)
+
+ check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
+ if not check["items"]:
+ c.save_new(owner_uuid=self.arvrunner.project_uuid)
+
+ ab = self.collection_pattern % c.portable_data_hash()
+ self._pathmap[srcobj["location"]] = MapperEnt(ab, ab, "Directory")
+ for loc, sub in subdirs:
+ ab = self.file_pattern % (c.portable_data_hash(), sub[2:])
+ self._pathmap[loc] = MapperEnt(ab, ab, "Directory")
+ elif srcobj["class"] == "File" and (srcobj.get("secondaryFiles") or
+ (srcobj["location"].startswith("_:") and "contents" in srcobj)):
+
+ c = arvados.collection.Collection(api_client=self.arvrunner.api,
+ keep_client=self.arvrunner.keep_client,
+ num_retries=self.arvrunner.num_retries )
+ subdirs = []
+ self.addentry(srcobj, c, ".", subdirs)
+
+ check = self.arvrunner.api.collections().list(filters=[["portable_data_hash", "=", c.portable_data_hash()]], limit=1).execute(num_retries=self.arvrunner.num_retries)
+ if not check["items"]:
+ c.save_new(owner_uuid=self.arvrunner.project_uuid)
+
+ ab = self.file_pattern % (c.portable_data_hash(), srcobj["basename"])
+ self._pathmap[srcobj["location"]] = MapperEnt(ab, ab, "File")
+ if srcobj.get("secondaryFiles"):
+ ab = self.collection_pattern % c.portable_data_hash()
+ self._pathmap["_:" + unicode(uuid.uuid4())] = MapperEnt(ab, ab, "Directory")
+ for loc, sub in subdirs:
+ ab = self.file_pattern % (c.portable_data_hash(), sub[2:])
+ self._pathmap[loc] = MapperEnt(ab, ab, "Directory")
+
self.keepdir = None
def reversemap(self, target):
return (target, "keep:" + target[len(self.keepdir)+1:])
else:
return super(ArvPathMapper, self).reversemap(target)
+
+class StagingPathMapper(PathMapper):
+ _follow_dirs = True
+
+ def visit(self, obj, stagedir, basedir, copy=False):
+ # type: (Dict[unicode, Any], unicode, unicode, bool) -> None
+ loc = obj["location"]
+ tgt = os.path.join(stagedir, obj["basename"])
+ if obj["class"] == "Directory":
+ self._pathmap[loc] = MapperEnt(loc, tgt, "Directory")
+ if loc.startswith("_:") or self._follow_dirs:
+ self.visitlisting(obj.get("listing", []), tgt, basedir)
+ elif obj["class"] == "File":
+ if loc in self._pathmap:
+ return
+ if "contents" in obj and loc.startswith("_:"):
+ self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile")
+ else:
+ if copy:
+ self._pathmap[loc] = MapperEnt(loc, tgt, "WritableFile")
+ else:
+ self._pathmap[loc] = MapperEnt(loc, tgt, "File")
+ self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir)
+
+
+class VwdPathMapper(StagingPathMapper):
+ def setup(self, referenced_files, basedir):
+ # type: (List[Any], unicode) -> None
+
+ # Go through each file and set the target to its own directory along
+ # with any secondary files.
+ self.visitlisting(referenced_files, self.stagedir, basedir)
+
+ for path, (ab, tgt, type) in self._pathmap.items():
+ if type in ("File", "Directory") and ab.startswith("keep:"):
+ self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type)
+
+
+class NoFollowPathMapper(StagingPathMapper):
+ _follow_dirs = False
+ def setup(self, referenced_files, basedir):
+ # type: (List[Any], unicode) -> None
+ self.visitlisting(referenced_files, self.stagedir, basedir)
projects / arvados.git / blobdiff