X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/5c4d9d38dcee73a7ffb6221c80f707c3924da64f..ae92d144610446849eb568247a44f02ae985c281:/sdk/cwl/arvados_cwl/pathmapper.py diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py index 9a76f81da5..64fdfa0d04 100644 --- a/sdk/cwl/arvados_cwl/pathmapper.py +++ b/sdk/cwl/arvados_cwl/pathmapper.py @@ -2,20 +2,28 @@ # # SPDX-License-Identifier: Apache-2.0 +from future import standard_library +standard_library.install_aliases() +from builtins import str +from past.builtins import basestring +from future.utils import viewitems + import re import logging import uuid import os -import urllib -import datetime +import urllib.request, urllib.parse, urllib.error +import arvados_cwl.util import arvados.commands.run import arvados.collection from schema_salad.sourceline import SourceLine from arvados.errors import ApiError -from cwltool.pathmapper import PathMapper, MapperEnt, abspath, adjustFileObjs, adjustDirObjs +from cwltool.pathmapper import PathMapper, MapperEnt +from cwltool.utils import adjustFileObjs, adjustDirObjs +from cwltool.stdfsaccess import abspath from cwltool.workflow import WorkflowException from .http import http_to_keep @@ -36,15 +44,16 @@ def trim_listing(obj): if obj.get("location", "").startswith("keep:") and "listing" in obj: del obj["listing"] +collection_pdh_path = re.compile(r'^keep:[0-9a-f]{32}\+\d+/.+$') +collection_pdh_pattern = re.compile(r'^keep:([0-9a-f]{32}\+\d+)(/.*)?') +collection_uuid_pattern = re.compile(r'^keep:([a-z0-9]{5}-4zz18-[a-z0-9]{15})(/.*)?$') 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, single_collection=False): + collection_pattern, file_pattern, name=None, single_collection=False, + optional_deps=None): self.arvrunner = arvrunner self.input_basedir = input_basedir self.collection_pattern = collection_pattern @@ -52,6 +61,8 @@ class ArvPathMapper(PathMapper): self.name = name self.referenced_files = [r["location"] for r in referenced_files] self.single_collection = single_collection + self.pdh_to_uuid = {} + self.optional_deps = optional_deps or [] super(ArvPathMapper, self).__init__(referenced_files, input_basedir, None) def visit(self, srcobj, uploadfiles): @@ -59,11 +70,18 @@ class ArvPathMapper(PathMapper): 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) - debug = logger.isEnabledFor(logging.DEBUG) + if isinstance(src, basestring) and src.startswith("keep:"): + if collection_pdh_pattern.match(src): + self._pathmap[src] = MapperEnt(src, self.collection_pattern % urllib.parse.unquote(src[5:]), srcobj["class"], True) + + if arvados_cwl.util.collectionUUID in srcobj: + self.pdh_to_uuid[src.split("/", 1)[0][5:]] = srcobj[arvados_cwl.util.collectionUUID] + elif not collection_uuid_pattern.match(src): + with SourceLine(srcobj, "location", WorkflowException, debug): + raise WorkflowException("Invalid keep reference '%s'" % src) + if src not in self._pathmap: if src.startswith("file:"): # Local FS ref, may need to be uploaded or may be on keep @@ -77,7 +95,7 @@ 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("_:"): @@ -86,9 +104,12 @@ class ArvPathMapper(PathMapper): if srcobj["class"] == "Directory" and "listing" not in srcobj: raise WorkflowException("Directory literal '%s' is missing `listing`" % src) elif src.startswith("http:") or src.startswith("https:"): - keepref = http_to_keep(self.arvrunner.api, self.arvrunner.project_uuid, src) - logger.info("%s is %s", src, keepref) - self._pathmap[src] = MapperEnt(keepref, keepref, srcobj["class"], True) + try: + keepref = http_to_keep(self.arvrunner.api, self.arvrunner.project_uuid, src) + logger.info("%s is %s", src, keepref) + self._pathmap[src] = MapperEnt(keepref, keepref, srcobj["class"], True) + except Exception as e: + logger.warning(str(e)) else: self._pathmap[src] = MapperEnt(src, src, srcobj["class"], True) @@ -114,11 +135,58 @@ class ArvPathMapper(PathMapper): remap.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")) + f.write(obj["contents"]) remap.append((obj["location"], path + "/" + obj["basename"])) else: + for opt in self.optional_deps: + if obj["location"] == opt["location"]: + return 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 + + i = loc.rfind("/") + if i > -1: + loc_prefix = loc[:i+1] + if not prefix: + prefix = loc_prefix + # quote/unquote to ensure consistent quoting + suffix = urllib.parse.quote(urllib.parse.unquote(loc[i+1:]), "/+@") + else: + # no '/' found + loc_prefix = loc+"/" + prefix = loc+"/" + suffix = "" + + if prefix != loc_prefix: + return True + + if "basename" in srcobj and suffix != urllib.parse.quote(srcobj["basename"], "/+@"): + return True + + 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, urllib.parse.quote(srcobj.get("basename", suffix), "/+@")) + 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 +211,7 @@ 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, "/:+@"), urllib.parse.quote(self.collection_pattern % st.fn[5:], "/:+@"), "Directory" if os.path.isdir(ab) else "File", True) for srcobj in referenced_files: @@ -155,7 +223,8 @@ class ArvPathMapper(PathMapper): for l in srcobj.get("listing", []): self.addentry(l, c, ".", remap) - info = self._get_intermediate_collection_info() + 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, @@ -165,15 +234,14 @@ class ArvPathMapper(PathMapper): 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)): - + elif srcobj["class"] == "File" and self.needs_new_collection(srcobj): c = arvados.collection.Collection(api_client=self.arvrunner.api, keep_client=self.arvrunner.keep_client, - num_retries=self.arvrunner.num_retries ) + num_retries=self.arvrunner.num_retries) self.addentry(srcobj, c, ".", remap) - info = self._get_intermediate_collection_info() + 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, @@ -186,7 +254,7 @@ 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: @@ -212,28 +280,15 @@ class ArvPathMapper(PathMapper): else: return None - def _get_intermediate_collection_info(self): - trash_time = None - if self.arvrunner.intermediate_output_ttl > 0: - trash_time = datetime.datetime.now() + datetime.timedelta(seconds=self.arvrunner.intermediate_output_ttl) - - current_container_uuid = None - try: - current_container = self.arvrunner.api.containers().current().execute(num_retries=self.arvrunner.num_retries) - current_container_uuid = current_container['uuid'] - except ApiError as e: - # Status code 404 just means we're not running in a container. - if e.resp.status != 404: - logger.info("Getting current container: %s", e) - props = {"type": "Intermediate", - "container": current_container_uuid} - - return {"name" : "Intermediate collection", - "trash_at" : trash_time, - "properties" : props} - class StagingPathMapper(PathMapper): + # Note that StagingPathMapper internally maps files from target to source. + # Specifically, the 'self._pathmap' dict keys are the target location and the + # values are 'MapperEnt' named tuples from which we use the 'resolved' attribute + # as the file identifier. This makes it possible to map an input file to multiple + # target directories. The exception is for file literals, which store the contents of + # the file in 'MapperEnt.resolved' and are therefore still mapped from source to target. + _follow_dirs = True def __init__(self, referenced_files, basedir, stagedir, separateDirs=True): @@ -243,33 +298,54 @@ class StagingPathMapper(PathMapper): def visit(self, obj, stagedir, basedir, copy=False, staged=False): # type: (Dict[unicode, Any], unicode, unicode, bool) -> None loc = obj["location"] + stagedir = obj.get("dirname") or stagedir tgt = os.path.join(stagedir, obj["basename"]) basetgt, baseext = os.path.splitext(tgt) + + def targetExists(): + return tgt in self.targets and ("contents" not in obj) and (self._pathmap[tgt].resolved != loc) + def literalTargetExists(): + return tgt in self.targets and "contents" in obj + n = 1 - if tgt in self.targets and (self.reversemap(tgt)[0] != loc): + if targetExists() or literalTargetExists(): while tgt in self.targets: n += 1 tgt = "%s_%i%s" % (basetgt, n, baseext) self.targets.add(tgt) if obj["class"] == "Directory": if obj.get("writable"): - self._pathmap[loc] = MapperEnt(loc, tgt, "WritableDirectory", staged) + self._pathmap[tgt] = MapperEnt(loc, tgt, "WritableDirectory", staged) else: - self._pathmap[loc] = MapperEnt(loc, tgt, "Directory", staged) + self._pathmap[tgt] = 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: + if tgt in self._pathmap: return if "contents" in obj and loc.startswith("_:"): self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile", staged) else: if copy or obj.get("writable"): - self._pathmap[loc] = MapperEnt(loc, tgt, "WritableFile", staged) + self._pathmap[tgt] = MapperEnt(loc, tgt, "WritableFile", staged) else: - self._pathmap[loc] = MapperEnt(loc, tgt, "File", staged) + self._pathmap[tgt] = MapperEnt(loc, tgt, "File", staged) self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir) + def mapper(self, src): # type: (Text) -> MapperEnt. + # Overridden to maintain the use case of mapping by source (identifier) to + # target regardless of how the map is structured interally. + def getMapperEnt(src): + for k,v in viewitems(self._pathmap): + if (v.type != "CreateFile" and v.resolved == src) or (v.type == "CreateFile" and k == src): + return v + + if u"#" in src: + i = src.index(u"#") + v = getMapperEnt(src[i:]) + return MapperEnt(v.resolved, v.target + src[i:], v.type, v.staged) + return getMapperEnt(src) + class VwdPathMapper(StagingPathMapper): def setup(self, referenced_files, basedir): @@ -279,7 +355,7 @@ 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 viewitems(self._pathmap): if type in ("File", "Directory") and ab.startswith("keep:"): self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type, staged)