Rmv MultiContainerInterface (#1260)

Co-authored-by: Ben Dichter <[email protected]>
Co-authored-by: Ryan Ly <[email protected]>

Author: bendichter

CHANGELOG.md

@@ -1,12 +1,13 @@
 # PyNWB Changelog
 
-## PyNWB 1.4.0 (August 10, 2020)
+## PyNWB 1.4.0 (August 11, 2020)
 
 ### Internal improvements:
-- Update requirements to use HDMF 2.0.1. @rly (#1256)
+- Update requirements to use HDMF 2.1.0. @rly (#1256)
 - Start FAQ section in documentation. @rly (#1249)
 - Improve deprecation warnings. @rly (#1261)
 - Update CI to test Python 3.8, update requirements. @rly (#1267, #1275)
+- Make use of `MultiContainerInterface` and `LabelledDict` that have been moved to HDMF. @bendichter @rly (#1260)
 
 ### Bug fixes:
 - For `ImageSeries`, add check if `external_file` is provided without `starting_frame` in `__init__`. @rly (#1264)

requirements-min.txt

@@ -1,6 +1,6 @@
 # these minimum requirements specify '==' for testing; setup.py replaces '==' with '>='
 h5py==2.9  # support for setting attrs to lists of utf-8 added in 2.9
-hdmf==2.0.1,<3
+hdmf==2.1.0,<3
 numpy==1.16
 pandas==0.23
 python-dateutil==2.7

requirements.txt

@@ -1,5 +1,5 @@
 h5py==2.10.0
-hdmf==2.0.1
+hdmf==2.1.0
 numpy==1.18.5
 pandas==0.25.3
 python-dateutil==2.8.1

src/pynwb/core.py

@@ -2,11 +2,12 @@
 import numpy as np
 import pandas as pd
 
-from hdmf.utils import docval, getargs, ExtenderMeta, call_docval_func, popargs, get_docval, fmt_docval_args
 from hdmf import Container, Data, DataRegion, get_region_slicer
-from hdmf.container import AbstractContainer
+from hdmf.container import AbstractContainer, MultiContainerInterface as hdmf_MultiContainerInterface
 from hdmf.common import DynamicTable, DynamicTableRegion  # noqa: F401
 from hdmf.common import VectorData, VectorIndex, ElementIdentifiers  # noqa: F401
+from hdmf.utils import docval, getargs, ExtenderMeta, call_docval_func, popargs
+from hdmf.utils import LabelledDict  # noqa: F401
 
 from . import CORE_NAMESPACE, register_class
 
@@ -39,28 +40,11 @@ class NWBContainer(NWBMixin, Container):
 
     __nwbfields__ = tuple()
 
-    @docval({'name': 'name', 'type': str, 'doc': 'the name of this container'})
-    def __init__(self, **kwargs):
-        call_docval_func(super(NWBContainer, self).__init__, kwargs)
-
-    def _to_dict(self, arg, label="NULL"):
-        return_dict = LabelledDict(label)
-        if arg is None:
-            return return_dict
-        else:
-            for i in arg:
-                assert i.name is not None  # If a container doesn't have a name, it gets lost!
-                assert i.name not in return_dict
-                return_dict[i.name] = i
-            return return_dict
-
 
 @register_class('NWBDataInterface', CORE_NAMESPACE)
 class NWBDataInterface(NWBContainer):
 
-    @docval(*get_docval(NWBContainer.__init__))
-    def __init__(self, **kwargs):
-        call_docval_func(super(NWBDataInterface, self).__init__, kwargs)
+    pass
 
 
 @register_class('NWBData', CORE_NAMESPACE)
@@ -332,309 +316,7 @@ def __getitem__(self, idx):
         return self.__regionslicer[idx]
 
 
-class MultiContainerInterface(NWBDataInterface):
-    '''
-    A class for dynamically defining a API classes that
-    represent NWBDataInterfaces that contain multiple Containers
-    of the same type
-
-    To use, extend this class, and create a dictionary as a class
-    attribute with the following keys:
-
-    * 'add' to name the method for adding Container instances
-
-    * 'create' to name the method fo creating Container instances
-
-    * 'get' to name the method for getting Container instances
-
-    * 'attr' to name the attribute that stores the Container instances
-
-    * 'type' to provide the Container object type
-
-    See LFP or Position for an example of how to use this.
-    '''
+class MultiContainerInterface(NWBDataInterface, hdmf_MultiContainerInterface):
+    """Defined in PyNWB for API backward compatibility. See HDMF MultiContainterInterface for details."""
 
-    @docval(*get_docval(NWBDataInterface.__init__))
-    def __init__(self, **kwargs):
-        call_docval_func(super(MultiContainerInterface, self).__init__, kwargs)
-        if isinstance(self.__clsconf__, dict):
-            attr_name = self.__clsconf__['attr']
-            self.fields[attr_name] = LabelledDict(attr_name)
-        else:
-            for d in self.__clsconf__:
-                attr_name = d['attr']
-                self.fields[attr_name] = LabelledDict(attr_name)
-
-    @staticmethod
-    def __add_article(noun):
-        if isinstance(noun, tuple):
-            noun = noun[0]
-        if isinstance(noun, type):
-            noun = noun.__name__
-        if noun[0] in ('aeiouAEIOU'):
-            return 'an %s' % noun
-        return 'a %s' % noun
-
-    @staticmethod
-    def __join(argtype):
-        def tostr(x):
-            return x.__name__ if isinstance(x, type) else x
-        if isinstance(argtype, (list, tuple)):
-            args = [tostr(x) for x in argtype]
-            if len(args) == 1:
-                return args[0].__name__
-            else:
-                ", ".join(tostr(x) for x in args[:-1]) + ' or ' + args[-1]
-        else:
-            return tostr(argtype)
-
-    @classmethod
-    def __make_get(cls, func_name, attr_name, container_type):
-        doc = "Get %s from this %s" % (cls.__add_article(container_type), cls.__name__)
-
-        @docval({'name': 'name', 'type': str, 'doc': 'the name of the %s' % cls.__join(container_type),
-                 'default': None},
-                rtype=container_type, returns='the %s with the given name' % cls.__join(container_type),
-                func_name=func_name, doc=doc)
-        def _func(self, **kwargs):
-            name = getargs('name', kwargs)
-            d = getattr(self, attr_name)
-            ret = None
-            if name is None:
-                if len(d) > 1:
-                    msg = "more than one element in %s of %s '%s' -- must specify a name" % \
-                          (attr_name, cls.__name__, self.name)
-                    raise ValueError(msg)
-                elif len(d) == 0:
-                    msg = "%s of %s '%s' is empty" % (attr_name, cls.__name__, self.name)
-                    raise ValueError(msg)
-                elif len(d) == 1:
-                    for v in d.values():
-                        ret = v
-            else:
-                ret = d.get(name)
-                if ret is None:
-                    msg = "'%s' not found in %s of %s '%s'" % (name, attr_name, cls.__name__, self.name)
-                    raise KeyError(msg)
-            return ret
-
-        return _func
-
-    @classmethod
-    def __make_add(cls, func_name, attr_name, container_type):
-        doc = "Add %s to this %s" % (cls.__add_article(container_type), cls.__name__)
-
-        @docval({'name': attr_name, 'type': (list, tuple, dict, container_type),
-                 'doc': 'the %s to add' % cls.__join(container_type)},
-                func_name=func_name, doc=doc)
-        def _func(self, **kwargs):
-            container = getargs(attr_name, kwargs)
-            if isinstance(container, container_type):
-                containers = [container]
-            elif isinstance(container, dict):
-                containers = container.values()
-            else:
-                containers = container
-            d = getattr(self, attr_name)
-            for tmp in containers:
-                if not isinstance(tmp.parent, Container):
-                    tmp.parent = self
-                # else, the ObjectMapper will create a link from self (parent) to tmp (child with existing parent)
-                if tmp.name in d:
-                    msg = "'%s' already exists in '%s'" % (tmp.name, self.name)
-                    raise ValueError(msg)
-                d[tmp.name] = tmp
-            return container
-        return _func
-
-    @classmethod
-    def __make_create(cls, func_name, add_name, container_type):
-        doc = "Create %s and add it to this %s" % (cls.__add_article(container_type), cls.__name__)
-
-        @docval(*filter(_not_parent, get_docval(container_type.__init__)), func_name=func_name, doc=doc,
-                returns="the %s object that was created" % cls.__join(container_type), rtype=container_type)
-        def _func(self, **kwargs):
-            cargs, ckwargs = fmt_docval_args(container_type.__init__, kwargs)
-            ret = container_type(*cargs, **ckwargs)
-            getattr(self, add_name)(ret)
-            return ret
-        return _func
-
-    @classmethod
-    def __make_constructor(cls, clsconf):
-        args = list()
-        for conf in clsconf:
-            attr_name = conf['attr']
-            container_type = conf['type']
-            args.append({'name': attr_name, 'type': (list, tuple, dict, container_type),
-                         'doc': '%s to store in this interface' % cls.__join(container_type), 'default': dict()})
-
-        args.append({'name': 'name', 'type': str, 'doc': 'the name of this container', 'default': cls.__name__})
-
-        @docval(*args, func_name='__init__')
-        def _func(self, **kwargs):
-            call_docval_func(super(cls, self).__init__, kwargs)
-            for conf in clsconf:
-                attr_name = conf['attr']
-                add_name = conf['add']
-                container = popargs(attr_name, kwargs)
-                add = getattr(self, add_name)
-                add(container)
-        return _func
-
-    @classmethod
-    def __make_getitem(cls, attr_name, container_type):
-        doc = "Get %s from this %s" % (cls.__add_article(container_type), cls.__name__)
-
-        @docval({'name': 'name', 'type': str, 'doc': 'the name of the %s' % cls.__join(container_type),
-                 'default': None},
-                rtype=container_type, returns='the %s with the given name' % cls.__join(container_type),
-                func_name='__getitem__', doc=doc)
-        def _func(self, **kwargs):
-            name = getargs('name', kwargs)
-            d = getattr(self, attr_name)
-            if len(d) == 0:
-                msg = "%s '%s' is empty" % (cls.__name__, self.name)
-                raise ValueError(msg)
-            if len(d) > 1 and name is None:
-                msg = "more than one %s in this %s -- must specify a name" % cls.__join(container_type), cls.__name__
-                raise ValueError(msg)
-            ret = None
-            if len(d) == 1:
-                for v in d.values():
-                    ret = v
-            else:
-                ret = d.get(name)
-                if ret is None:
-                    msg = "'%s' not found in %s '%s'" % (name, cls.__name__, self.name)
-                    raise KeyError(msg)
-            return ret
-
-        return _func
-
-    @classmethod
-    def __make_setter(cls, nwbfield, add_name):
-
-        @docval({'name': 'val', 'type': (list, tuple, dict), 'doc': 'the sub items to add', 'default': None})
-        def nwbbt_setter(self, **kwargs):
-            val = getargs('val', kwargs)
-            if val is None:
-                return
-            getattr(self, add_name)(val)
-
-        return nwbbt_setter
-
-    @ExtenderMeta.pre_init
-    def __build_class(cls, name, bases, classdict):
-        '''
-        This classmethod will be called during class declaration in the metaclass to automatically
-        create setters and getters for NWB fields that need to be exported
-        '''
-        if not hasattr(cls, '__clsconf__'):
-            return
-        multi = False
-        if isinstance(cls.__clsconf__, dict):
-            clsconf = [cls.__clsconf__]
-        elif isinstance(cls.__clsconf__, list):
-            multi = True
-            clsconf = cls.__clsconf__
-        else:
-            raise TypeError("'__clsconf__' must be a dict or a list of dicts")
-
-        for i, d in enumerate(clsconf):
-            # get add method name
-            add = d.get('add')
-            if add is None:
-                msg = "MultiContainerInterface subclass '%s' is missing 'add' key in __clsconf__" % cls.__name__
-                if multi:
-                    msg += " at element %d" % i
-                raise ValueError(msg)
-
-            # get container attribute name
-            attr = d.get('attr')
-            if attr is None:
-                msg = "MultiContainerInterface subclass '%s' is missing 'attr' key in __clsconf__" % cls.__name__
-                if multi:
-                    msg += " at element %d" % i
-                raise ValueError(msg)
-
-            # get container type
-            container_type = d.get('type')
-            if container_type is None:
-                msg = "MultiContainerInterface subclass '%s' is missing 'type' key in __clsconf__" % cls.__name__
-                if multi:
-                    msg += " at element %d" % i
-                raise ValueError(msg)
-
-            # create property with the name given in 'attr'
-            if not hasattr(cls, attr):
-                aconf = cls._check_field_spec(attr)
-                getter = cls._getter(aconf)
-                doc = "a dictionary containing the %s in this %s container" % \
-                      (cls.__join(container_type), cls.__name__)
-                setattr(cls, attr, property(getter, cls.__make_setter(aconf, add), None, doc))
-
-            # create the add method
-            setattr(cls, add, cls.__make_add(add, attr, container_type))
-
-            # get create method name
-            create = d.get('create')
-            if create is not None:
-                setattr(cls, create, cls.__make_create(create, add, container_type))
-
-            get = d.get('get')
-            if get is not None:
-                setattr(cls, get, cls.__make_get(get, attr, container_type))
-
-        if len(clsconf) == 1:
-            setattr(cls, '__getitem__', cls.__make_getitem(attr, container_type))
-
-        # create the constructor, only if it has not been overridden
-        # i.e. it is the same method as the parent class constructor
-        if cls.__init__ == MultiContainerInterface.__init__:
-            setattr(cls, '__init__', cls.__make_constructor(clsconf))
-
-
-class LabelledDict(dict):
-    '''
-    A dict wrapper class for aggregating Timeseries
-    from the standard locations
-    '''
-
-    @docval({'name': 'label', 'type': str, 'doc': 'the label on this dictionary'},
-            {'name': 'def_key_name', 'type': str, 'doc': 'the default key name', 'default': 'name'})
-    def __init__(self, **kwargs):
-        label, def_key_name = getargs('label', 'def_key_name', kwargs)
-        self.__label = label
-        self.__defkey = def_key_name
-
-    @property
-    def label(self):
-        return self.__label
-
-    def __getitem__(self, args):
-        key = args
-        if '==' in args:
-            key, val = args.split("==")
-            key = key.strip()
-            val = val.strip()
-            if key != self.__defkey:
-                ret = list()
-                for item in self.values():
-                    if getattr(item, key, None) == val:
-                        ret.append(item)
-                return ret if len(ret) else None
-            key = val
-        return super(LabelledDict, self).__getitem__(key)
-
-    @docval({'name': 'container', 'type': (NWBData, NWBContainer), 'doc': 'the container to add to this LabelledDict'})
-    def add(self, **kwargs):
-        '''
-        Add a container to this LabelledDict
-        '''
-        container = getargs('container', kwargs)
-        key = getattr(container, self.__defkey, None)
-        if key is None:
-            msg = "container '%s' does not have attribute '%s'" % (container.name, self.__defkey)
-            raise ValueError(msg)
-        self[key] = container
+    pass

src/pynwb/file.py

@@ -380,7 +380,7 @@ def __init__(self, **kwargs):
     def all_children(self):
         stack = [self]
         ret = list()
-        self.__obj = LabelledDict(label='all_objects', def_key_name='object_id')
+        self.__obj = LabelledDict(label='all_objects', key_attr='object_id')
         while len(stack):
             n = stack.pop()
             ret.append(n)