- def arvExecutor(self, tool, job_order, **kwargs):
- self.debug = kwargs.get("debug")
+ def make_output_collection(self, name, outputObj):
+ outputObj = copy.deepcopy(outputObj)
+
+ files = []
+ def capture(fileobj):
+ files.append(fileobj)
+
+ adjustDirObjs(outputObj, capture)
+ adjustFileObjs(outputObj, capture)
+
+ generatemapper = FinalOutputPathMapper(files, "", "", separateDirs=False)
+
+ final = arvados.collection.Collection(api_client=self.api,
+ keep_client=self.keep_client,
+ num_retries=self.num_retries)
+
+ srccollections = {}
+ for k,v in generatemapper.items():
+ sp = k.split("/")
+ srccollection = sp[0][5:]
+ if srccollection not in srccollections:
+ srccollections[srccollection] = arvados.collection.CollectionReader(
+ srccollection,
+ api_client=self.api,
+ keep_client=self.keep_client,
+ num_retries=self.num_retries)
+ reader = srccollections[srccollection]
+ try:
+ srcpath = "/".join(sp[1:]) if len(sp) > 1 else "."
+ final.copy(srcpath, v.target, source_collection=reader, overwrite=False)
+ except IOError as e:
+ logger.warn("While preparing output collection: %s", e)