import re import logging import uuid import os import urllib import arvados.commands.run import arvados.collection 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+/.+$') pdh_dirpath = re.compile(r'^keep:[0-9a-f]{32}\+\d+(/.*)?$') def __init__(self, arvrunner, referenced_files, input_basedir, collection_pattern, file_pattern, name=None, **kwargs): self.arvrunner = arvrunner self.input_basedir = input_basedir self.collection_pattern = collection_pattern self.file_pattern = file_pattern self.name = name super(ArvPathMapper, self).__init__(referenced_files, input_basedir, None) def visit(self, srcobj, uploadfiles): src = srcobj["location"] if "#" in src: src = src[:src.index("#")] if isinstance(src, basestring) and ArvPathMapper.pdh_dirpath.match(src): self._pathmap[src] = MapperEnt(src, self.collection_pattern % urllib.unquote(src[5:]), srcobj["class"], True) if src not in self._pathmap: if src.startswith("file:"): # 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", dirPattern="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 % urllib.unquote(st.fn[5:]), "File", True) else: raise WorkflowException("Input file path '%s' is invalid" % st) elif src.startswith("_:"): if srcobj["class"] == "File" and "contents" not in srcobj: raise WorkflowException("File literal '%s' is missing `contents`" % src) if srcobj["class"] == "Directory" and "listing" not in srcobj: raise WorkflowException("Directory literal '%s' is missing `listing`" % src) else: self._pathmap[src] = MapperEnt(src, src, srcobj["class"], True) with SourceLine(srcobj, "secondaryFiles", WorkflowException): for l in srcobj.get("secondaryFiles", []): self.visit(l, uploadfiles) with SourceLine(srcobj, "listing", WorkflowException): 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.get("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 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 % urllib.unquote(v.resolved[5:]), "File", True) for srcobj in referenced_files: self.visit(srcobj, uploadfiles) if uploadfiles: arvados.commands.run.uploadfiles([u[2] for u in uploadfiles], self.arvrunner.api, dry_run=False, 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(urllib.quote(st.fn, "/:+@"), self.collection_pattern % st.fn[5:], "Directory" if os.path.isdir(ab) else "File", True) self.arvrunner.add_uploaded(src, self._pathmap[src]) for srcobj in referenced_files: subdirs = [] 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) for l in srcobj.get("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("keep:"+c.portable_data_hash(), ab, "Directory", True) 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 ) 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("keep:%s/%s" % (c.portable_data_hash(), srcobj["basename"]), ab, "File", True) if srcobj.get("secondaryFiles"): ab = self.collection_pattern % c.portable_data_hash() self._pathmap["_:" + unicode(uuid.uuid4())] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True) if subdirs: for loc, sub in subdirs: # subdirs will all start with "./", strip it off ab = self.file_pattern % (c.portable_data_hash(), sub[2:]) self._pathmap[loc] = MapperEnt("keep:%s/%s" % (c.portable_data_hash(), sub[2:]), ab, "Directory", True) self.keepdir = None def reversemap(self, target): if target.startswith("keep:"): return (target, target) elif self.keepdir and target.startswith(self.keepdir): 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, staged=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", staged) 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", staged) else: if copy: self._pathmap[loc] = MapperEnt(loc, tgt, "WritableFile", staged) else: self._pathmap[loc] = MapperEnt(loc, tgt, "File", staged) 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, staged) in self._pathmap.items(): if type in ("File", "Directory") and ab.startswith("keep:"): self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type, staged) class NoFollowPathMapper(StagingPathMapper): _follow_dirs = False def setup(self, referenced_files, basedir): # type: (List[Any], unicode) -> None self.visitlisting(referenced_files, self.stagedir, basedir)