all_steps = False bug

[jthermiz]

all_steps = False fails due to a linking issue.

python scripts/preprocess_folder ../nsds_lab_to_nwb/scripts/RVG21 Processing ../nsds_lab_to_nwb/scripts/RVG21/RVG21_B01.nwb Traceback (most recent call last): File "scripts/preprocess_folder", line 54, in all_steps=all_steps) File "/home/jhermiz/software/process_nwb/process_nwb/pipelines.py", line 106, in preprocess_block io.write(nwbfile) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 580, in func_call return func(args[0], *pargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/backends/hdf5/h5tools.py", line 404, in write call_docval_func(super().write, kwargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 423, in call_docval_func return func(fargs, fkwargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 580, in func_call return func(args[0], pargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/backends/io.py", line 49, in write f_builder = self.manager.build(container, source=self.source, root=True) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 580, in func_call return func(args[0], pargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/manager.py", line 181, in build export=export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 580, in func_call return func(args[0], pargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/manager.py", line 765, in build builder = obj_mapper.build(container, manager, builder=builder, source=source, spec_ext=spec_ext, export=export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 580, in func_call return func(args[0], pargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 699, in build self.add_groups(builder, self.__spec.groups, container, manager, source, export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 1023, in add_groups self.add_groups(sub_builder, spec.groups, container, build_manager, source, export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 1036, in add_groups self.add_containers(builder, spec, attr_value, build_manager, source, container, export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 1094, in add_containers self.add_containers(builder, spec, container, build_manager, source, parent_container, export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 1056, in add_containers new_builder = build_manager.build(value, source=source, spec_ext=spec, export=export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 580, in func_call return func(args[0], pargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/manager.py", line 171, in build result = self.type_map.build(container, self, source=source, spec_ext=spec_ext, export=export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 580, in func_call return func(args[0], pargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/manager.py", line 765, in build builder = obj_mapper.build(container, manager, builder=builder, source=source, spec_ext=spec_ext, export=export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 580, in func_call return func(args[0], pargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 699, in build self.add_groups(builder, self.spec.groups, container, manager, source, export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 1036, in __add_groups self.add_containers(builder, spec, attr_value, build_manager, source, container, export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 1094, in add_containers self.add_containers(builder, spec, container, build_manager, source, parent_container, export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 1056, in add_containers new_builder = build_manager.build(value, source=source, spec_ext=spec, export=export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 580, in func_call return func(args[0], **pargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/manager.py", line 171, in build result = self.type_map.build(container, self, source=source, spec_ext=spec_ext, export=export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 580, in func_call return func(args[0], pargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/manager.py", line 765, in build builder = obj_mapper.build(container, manager, builder=builder, source=source, spec_ext=spec_ext, export=export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/utils.py", line 580, in func_call return func(args[0], pargs) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 700, in build self.add_links(builder, self.__spec.links, container, manager, source, export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 956, in add_links self.add_containers(builder, spec, attr_value, build_manager, source, container, export) File "/home/jhermiz/anaconda3/envs/nsds_lab_to_nwb/lib/python3.7/site-packages/hdmf/build/objectmapper.py", line 1049, in add_containers raise OrphanContainerBuildError(builder, value) hdmf.build.errors.OrphanContainerBuildError: wvlt_amp_CAR_ln_downsampled_ECoG (wvlt_amp_CAR_ln_downsampled_ECoG): Linked ElectricalSeries 'CAR_ln_downsampled_ECoG' has no parent. Remove the link or ensure the linked container is added properly.