X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/b478b8a0b4263b0e54060e3fecaab9b6ecdcb085..d6cccb3ea4e5f076a436d9935e3835d4b620b859:/sdk/cwl/arvados_cwl/pathmapper.py diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py index d083b78f5a..7353d7239c 100644 --- a/sdk/cwl/arvados_cwl/pathmapper.py +++ b/sdk/cwl/arvados_cwl/pathmapper.py @@ -1,3 +1,7 @@ +from future import standard_library +standard_library.install_aliases() +from builtins import str +from past.builtins import basestring # Copyright (C) The Arvados Authors. All rights reserved. # # SPDX-License-Identifier: Apache-2.0 @@ -6,9 +10,9 @@ import re import logging import uuid import os -import urllib +import urllib.request, urllib.parse, urllib.error -from arvados_cwl.util import get_current_container, get_intermediate_collection_info +import arvados_cwl.util import arvados.commands.run import arvados.collection @@ -60,7 +64,7 @@ class ArvPathMapper(PathMapper): 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) + self._pathmap[src] = MapperEnt(src, self.collection_pattern % urllib.parse.unquote(src[5:]), srcobj["class"], True) debug = logger.isEnabledFor(logging.DEBUG) @@ -77,7 +81,7 @@ class ArvPathMapper(PathMapper): 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) + self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % urllib.parse.unquote(st.fn[5:]), "File", True) else: raise WorkflowException("Input file path '%s' is invalid" % st) elif src.startswith("_:"): @@ -119,6 +123,39 @@ class ArvPathMapper(PathMapper): else: raise SourceLine(obj, "location", WorkflowException).makeError("Don't know what to do with '%s'" % obj["location"]) + def needs_new_collection(self, srcobj, prefix=""): + """Check if files need to be staged into a new collection. + + If all the files are in the same collection and in the same + paths they would be staged to, return False. Otherwise, a new + collection is needed with files copied/created in the + appropriate places. + """ + + loc = srcobj["location"] + if loc.startswith("_:"): + return True + if prefix: + if loc != prefix+srcobj["basename"]: + return True + else: + i = loc.rfind("/") + if i > -1: + prefix = loc[:i+1] + else: + prefix = loc+"/" + if srcobj["class"] == "File" and loc not in self._pathmap: + return True + for s in srcobj.get("secondaryFiles", []): + if self.needs_new_collection(s, prefix): + return True + if srcobj.get("listing"): + prefix = "%s%s/" % (prefix, srcobj["basename"]) + for l in srcobj["listing"]: + if self.needs_new_collection(l, prefix): + return True + return False + def setup(self, referenced_files, basedir): # type: (List[Any], unicode) -> None uploadfiles = set() @@ -143,7 +180,7 @@ class ArvPathMapper(PathMapper): packed=False) for src, ab, st in uploadfiles: - self._pathmap[src] = MapperEnt(urllib.quote(st.fn, "/:+@"), self.collection_pattern % st.fn[5:], + self._pathmap[src] = MapperEnt(urllib.parse.quote(st.fn, "/:+@"), self.collection_pattern % st.fn[5:], "Directory" if os.path.isdir(ab) else "File", True) for srcobj in referenced_files: @@ -155,8 +192,8 @@ class ArvPathMapper(PathMapper): for l in srcobj.get("listing", []): self.addentry(l, c, ".", remap) - container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger) - info = get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl) + container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger) + info = arvados_cwl.util.get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl) c.save_new(name=info["name"], owner_uuid=self.arvrunner.project_uuid, @@ -169,13 +206,20 @@ class ArvPathMapper(PathMapper): elif srcobj["class"] == "File" and (srcobj.get("secondaryFiles") or (srcobj["location"].startswith("_:") and "contents" in srcobj)): + # If all secondary files/directories are located in + # the same collection as the primary file and the + # paths and names that are consistent with staging, + # don't create a new collection. + if not self.needs_new_collection(srcobj): + continue + 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, ".", remap) - container = get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger) - info = get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl) + container = arvados_cwl.util.get_current_container(self.arvrunner.api, self.arvrunner.num_retries, logger) + info = arvados_cwl.util.get_intermediate_collection_info(None, container, self.arvrunner.intermediate_output_ttl) c.save_new(name=info["name"], owner_uuid=self.arvrunner.project_uuid, @@ -188,7 +232,7 @@ class ArvPathMapper(PathMapper): 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) + self._pathmap["_:" + str(uuid.uuid4())] = MapperEnt("keep:"+c.portable_data_hash(), ab, "Directory", True) if remap: for loc, sub in remap: @@ -261,7 +305,7 @@ class VwdPathMapper(StagingPathMapper): # with any secondary files. self.visitlisting(referenced_files, self.stagedir, basedir) - for path, (ab, tgt, type, staged) in self._pathmap.items(): + for path, (ab, tgt, type, staged) in list(self._pathmap.items()): if type in ("File", "Directory") and ab.startswith("keep:"): self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type, staged)