X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/70f1b69fe1f0567483afc182e47fe717756b8bd1..33b9f9bd117931bae54f45566fb77e654dcbe263:/sdk/cwl/arvados_cwl/pathmapper.py diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py index 73c81ceb0f..3a0c69b08a 100644 --- a/sdk/cwl/arvados_cwl/pathmapper.py +++ b/sdk/cwl/arvados_cwl/pathmapper.py @@ -6,6 +6,8 @@ import os 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 @@ -28,33 +30,38 @@ class ArvPathMapper(PathMapper): 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") + 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 % src[5:], srcobj["class"], True) + + 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", + 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 % st.fn[5:], "File") + self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.fn[5:], "File", True) 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", True) 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") + + 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) @@ -67,21 +74,25 @@ class ArvPathMapper(PathMapper): for l in obj.get("secondaryFiles", []): self.addentry(l, c, path, subdirs) elif obj["class"] == "Directory": - for l in obj["listing"]: + 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 WorkflowException("Don't know what to do with '%s'" % obj["location"]) + 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() - for k,v in self.arvrunner.get_uploaded().iteritems(): - self._pathmap[k] = MapperEnt(v.resolved, self.collection_pattern % v.resolved[5:], "File") + 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", True) for srcobj in referenced_files: self.visit(srcobj, uploadfiles) @@ -96,17 +107,18 @@ class ArvPathMapper(PathMapper): project=self.arvrunner.project_uuid) for src, ab, st in uploadfiles: - self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.fn[5:], "File") + self._pathmap[src] = MapperEnt(st.fn, self.collection_pattern % st.keepref, + "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) - subdirs = [] - for l in srcobj["listing"]: + 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) @@ -114,17 +126,13 @@ class ArvPathMapper(PathMapper): 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") + 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 ) - 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) @@ -132,13 +140,18 @@ class ArvPathMapper(PathMapper): 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") + 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(ab, ab, "Directory") + 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(ab, ab, "Directory") + self._pathmap[loc] = MapperEnt("keep:%s/%s" % (c.portable_data_hash(), sub[2:]), + ab, "Directory", True) self.keepdir = None @@ -150,27 +163,31 @@ class ArvPathMapper(PathMapper): else: return super(ArvPathMapper, self).reversemap(target) -class InitialWorkDirPathMapper(PathMapper): +class StagingPathMapper(PathMapper): + _follow_dirs = True - def visit(self, obj, stagedir, basedir, copy=False): + 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(obj["location"], stagedir, "Directory") - self.visitlisting(obj.get("listing", []), stagedir, basedir) + 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 - tgt = os.path.join(stagedir, obj["basename"]) - if "contents" in obj and obj["location"].startswith("_:"): - self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile") + if "contents" in obj and loc.startswith("_:"): + self._pathmap[loc] = MapperEnt(obj["contents"], tgt, "CreateFile", staged) else: if copy: - self._pathmap[loc] = MapperEnt(obj["path"], tgt, "WritableFile") + self._pathmap[loc] = MapperEnt(loc, tgt, "WritableFile", staged) else: - self._pathmap[loc] = MapperEnt(obj["path"], tgt, "File") + 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 @@ -178,24 +195,13 @@ class InitialWorkDirPathMapper(PathMapper): # with any secondary files. self.visitlisting(referenced_files, self.stagedir, basedir) - for path, (ab, tgt, type) in self._pathmap.items(): + for path, (ab, tgt, type, staged) in self._pathmap.items(): if type in ("File", "Directory") and ab.startswith("keep:"): - self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type) - + self._pathmap[path] = MapperEnt("$(task.keep)/%s" % ab[5:], tgt, type, staged) -class FinalOutputPathMapper(PathMapper): - def visit(self, obj, stagedir, basedir, copy=False): - # type: (Dict[unicode, Any], unicode, unicode, bool) -> None - loc = obj["location"] - if obj["class"] == "Directory": - self._pathmap[loc] = MapperEnt(loc, stagedir, "Directory") - elif obj["class"] == "File": - if loc in self._pathmap: - return - tgt = os.path.join(stagedir, obj["basename"]) - self._pathmap[loc] = MapperEnt(loc, tgt, "File") - self.visitlisting(obj.get("secondaryFiles", []), stagedir, basedir) +class NoFollowPathMapper(StagingPathMapper): + _follow_dirs = False def setup(self, referenced_files, basedir): # type: (List[Any], unicode) -> None self.visitlisting(referenced_files, self.stagedir, basedir)