Check existence of NWBDataInterfaces

[afonsobspinto]

Hello everyone.
I'm designing a declarative way to specify requirements on an NWB 2.x file for a given plot.
The requirements are NWBDataInterfaces provided by your API:
"requirements": ["DfOverT", "processing.<ProcessingModule>.DfOverF"]
As you can see, they can be simple objects or a full path requirement.
My goal is to be able to verify if those requirements are met given any NWB 2.x, and to do that I'm trying the following:

nwb_map_id_api = {'acquisition': 'acquisition',
                      'analysis': 'analysis',
                      'epochs': 'epochs',
                      'processing': 'modules',  # this dictionary is needed mainly because of this
                      'stimulus': 'stimulus',
}

def has_all_requirements(self, requirements):
        """Given a list of requirements verifies if all are meet ."""
        return all(self._check_requirement(requirement)[0] for requirement in requirements)

def _check_requirement(self, requirement):
        list_string = requirement.split('.')
        return self._check_requirement_full_path(list_string) if len(list_string) > 1 else self._check_requirement_data_interfaces(requirement)

def _check_requirement_full_path(self, path_list):
        """Given a full_path requirement gets the initial group and expands it blindly in search of the last path
        element """
        group = NWBUtils.nwb_map_id_api.get(path_list[0])
        if group is not None:
            nodes = [getattr(self.nwbfile, group)]
            for index, remaining_path in enumerate(path_list[1:]):
                for node in nodes:
                    if index == len(path_list) - 2:
                        if isinstance(node, dict):
                            for value in list(node.values()):
                                if value.neurodata_type == remaining_path:
                                    return True, value
                        else:
                            for child in node.children:
                                if child.neurodata_type == remaining_path:
                                    return True, child
                    else:
                        nodes = list(node.values()) if isinstance(node, dict) else node.children
return False, None

def _check_requirement_data_interfaces(self, requirement):
        """Given a requirement looks for a match in all the nwb_data_interfaces of the nwb file """
        for data_interfaces in self.nwb_data_interfaces_list:
            if data_interfaces.neurodata_type == requirement:
                return True, data_interfaces
return False, None

As my previous issue, I would like to get your opinion on this.
I wasn't able to find this feature in your API. Do you think it has any value? Would you do this any other way?

[bendichter]

Hi @afonsobspinto, thanks for working on this stuff, and thanks for communicating what you are working on. I think this may overlap with the validation module. Check it out and see if that suits your needs.

[afonsobspinto]

Hey @bendichter. Thanks for the quick reply. I took a look into it and if I understood correctly I should define an extension with the attributes I require and use the validation module to check if the nwb file meets them, correct?
But besides verifying if those fields exist I will also need to access them. What would you recommend for that?