nwb-linkml/docs/notes/pynwb.md

PyNWB notes

How does pynwb use the schema?

• nwb-schema is included as a git submodule within pynwb
• __get_resources encodes the location of the directory
• __TYPE_MAP eventually contains the schema information
• on import, load_namespaces populates __TYPE_MAP
• register_class decorator is used on all pynwb classes to register with __TYPE_MAP
  • Unclear how the schema is used if the containers contain the same information
• the register_container_type method in hdmf's TypeMap class seems to overwrite the loaded schema???
  • __NS_CATALOG seems to actually hold references to the schema but it doesn't seem to be used anywhere except within __TYPE_MAP ?
• NWBHDF5IO uses TypeMap to greate a BuildManager
  • Parent class HDF5IO then reimplements a lot of basic functionality from elsehwere
  • Parent-parent metaclass HDMFIO appears to be the final writing class?
  • BuildManager.build then calls TypeMap.build ???
• TypeMap.build ...
  • gets the ObjectMapper which does god knows what
  • Calls the ObjectMapper.build method
  • Which seems to ultimately create a DatasetBuilder object
• The DatasetBuilder is returned to the BuildManager which seems to just store it?
• HDMFIO.write then calls write_builder to use the builder, which is unimplemented in the metaclass
  • HDF5IO.write_builder implements it for HDF5, which then calls write_group, write_dataset, write_link, depending on the builder types, each of which are extremely heavy methods!
  • eg. write_dataset is basically unreadable to me, but seems to implement every type of dataset writing in a single method.
• At this point it is entirely unclear how the schema is involved, but the file is written.