HERD name change (#933)

* HERD name change

* schema

* schema

* Update plot_external_resources.py

* Update docs/gallery/plot_external_resources.py

Co-authored-by: Oliver Ruebel <[email protected]>

* missed changes of externalresource to herd

---------

Co-authored-by: Oliver Ruebel <[email protected]>

Author: mavaylon1

docs/gallery/plot_external_resources.py

@@ -1,34 +1,34 @@
 """
-ExternalResources
-=================
+HERD: HDMF External Resources Data Structure
+==============================================
 
 This is a user guide to interacting with the
-:py:class:`~hdmf.common.resources.ExternalResources` class. The ExternalResources type
+:py:class:`~hdmf.common.resources.HERD` class. The HERD type
 is experimental and is subject to change in future releases. If you use this type,
 please provide feedback to the HDMF team so that we can improve the structure and
 access of data stored with this type for your use cases.
 
 Introduction
 -------------
-The :py:class:`~hdmf.common.resources.ExternalResources` class provides a way
+The :py:class:`~hdmf.common.resources.HERD` class provides a way
 to organize and map user terms from their data (keys) to multiple entities
 from the external resources. A typical use case for external resources is to link data
 stored in datasets or attributes to ontologies. For example, you may have a
 dataset ``country`` storing locations. Using
-:py:class:`~hdmf.common.resources.ExternalResources` allows us to link the
+:py:class:`~hdmf.common.resources.HERD` allows us to link the
 country names stored in the dataset to an ontology of all countries, enabling
 more rigid standardization of the data and facilitating data query and
 introspection.
 
 From a user's perspective, one can think of the
-:py:class:`~hdmf.common.resources.ExternalResources` as a simple table, in which each
+:py:class:`~hdmf.common.resources.HERD` as a simple table, in which each
 row associates a particular ``key`` stored in a particular ``object`` (i.e., Attribute
 or Dataset in a file) with a particular ``entity`` (i.e, a term of an online
 resource). That is, ``(object, key)`` refer to parts inside a
 file and ``entity`` refers to an external resource outside the file, and
-:py:class:`~hdmf.common.resources.ExternalResources` allows us to link the two. To
+:py:class:`~hdmf.common.resources.HERD` allows us to link the two. To
 reduce data redundancy and improve data integrity,
-:py:class:`~hdmf.common.resources.ExternalResources` stores this data internally in a
+:py:class:`~hdmf.common.resources.HERD` stores this data internally in a
 collection of interlinked tables.
 
 * :py:class:`~hdmf.common.resources.KeyTable` where each row describes a
@@ -45,21 +45,21 @@
   :py:class:`~hdmf.common.resources.ObjectKey` pair identifying which keys
   are used by which objects.
 
-The :py:class:`~hdmf.common.resources.ExternalResources` class then provides
+The :py:class:`~hdmf.common.resources.HERD` class then provides
 convenience functions to simplify interaction with these tables, allowing users
-to treat :py:class:`~hdmf.common.resources.ExternalResources` as a single large table as
+to treat :py:class:`~hdmf.common.resources.HERD` as a single large table as
 much as possible.
 
-Rules to ExternalResources
+Rules to HERD
 ---------------------------
-When using the :py:class:`~hdmf.common.resources.ExternalResources` class, there
+When using the :py:class:`~hdmf.common.resources.HERD` class, there
 are rules to how users store information in the interlinked tables.
 
 1. Multiple :py:class:`~hdmf.common.resources.Key` objects can have the same name.
    They are disambiguated by the :py:class:`~hdmf.common.resources.Object` associated
    with each, meaning we may have keys with the same name in different objects, but for a particular object
    all keys must be unique.
-2. In order to query specific records, the :py:class:`~hdmf.common.resources.ExternalResources` class
+2. In order to query specific records, the :py:class:`~hdmf.common.resources.HERD` class
    uses '(file, object_id, relative_path, field, key)' as the unique identifier.
 3. :py:class:`~hdmf.common.resources.Object` can have multiple :py:class:`~hdmf.common.resources.Key`
    objects.
@@ -74,7 +74,7 @@
    Use the format provided by the resource. For example, Identifiers.org uses the ID ``ncbigene:22353``
    but the NCBI Gene uses the ID ``22353`` for the same term.
 8. In a majority of cases, :py:class:`~hdmf.common.resources.Object` objects will have an empty string
-   for 'field'. The :py:class:`~hdmf.common.resources.ExternalResources` class supports compound data_types.
+   for 'field'. The :py:class:`~hdmf.common.resources.HERD` class supports compound data_types.
    In that case, 'field' would be the field of the compound data_type that has an external reference.
 9. In some cases, the attribute that needs an external reference is not a object with a 'data_type'.
    The user must then use the nearest object that has a data type to be used as the parent object. When
@@ -85,41 +85,41 @@
     has :py:class:`~hdmf.common.resources.File` along the parent hierarchy.
 """
 ######################################################
-# Creating an instance of the ExternalResources class
+# Creating an instance of the HERD class
 # ----------------------------------------------------
 
 # sphinx_gallery_thumbnail_path = 'figures/gallery_thumbnail_externalresources.png'
-from hdmf.common import ExternalResources
+from hdmf.common import HERD
 from hdmf.common import DynamicTable, VectorData
-from hdmf import Container, ExternalResourcesManager
+from hdmf import Container, HERDManager
 from hdmf import Data
 import numpy as np
 import os
 # Ignore experimental feature warnings in the tutorial to improve rendering
 import warnings
-warnings.filterwarnings("ignore", category=UserWarning, message="ExternalResources is experimental*")
+warnings.filterwarnings("ignore", category=UserWarning, message="HERD is experimental*")
 
 
 # Class to represent a file
-class ExternalResourcesManagerContainer(Container, ExternalResourcesManager):
+class HERDManagerContainer(Container, HERDManager):
     def __init__(self, **kwargs):
-        kwargs['name'] = 'ExternalResourcesManagerContainer'
+        kwargs['name'] = 'HERDManagerContainer'
         super().__init__(**kwargs)
 
 
-er = ExternalResources()
-file = ExternalResourcesManagerContainer(name='file')
+er = HERD()
+file = HERDManagerContainer(name='file')
 
 
 ###############################################################################
 # Using the add_ref method
 # ------------------------------------------------------
-# :py:func:`~hdmf.common.resources.ExternalResources.add_ref`
+# :py:func:`~hdmf.common.resources.HERD.add_ref`
 # is a wrapper function provided by the
-# :py:class:`~hdmf.common.resources.ExternalResources` class that simplifies adding
-# data. Using :py:func:`~hdmf.common.resources.ExternalResources.add_ref` allows us to
+# :py:class:`~hdmf.common.resources.HERD` class that simplifies adding
+# data. Using :py:func:`~hdmf.common.resources.HERD.add_ref` allows us to
 # treat new entries similar to adding a new row to a flat table, with
-# :py:func:`~hdmf.common.resources.ExternalResources.add_ref` taking care of populating
+# :py:func:`~hdmf.common.resources.HERD.add_ref` taking care of populating
 # the underlying data structures accordingly.
 
 data = Data(name="species", data=['Homo sapiens', 'Mus musculus'])
@@ -165,7 +165,7 @@ def __init__(self, **kwargs):
     entity_uri='http://www.informatics.jax.org/marker/MGI:1343464'
 )
 
-# Note: :py:func:`~hdmf.common.resources.ExternalResources.add_ref` internally resolves the object
+# Note: :py:func:`~hdmf.common.resources.HERD.add_ref` internally resolves the object
 # to the closest parent, so that ``er.add_ref(container=genotypes, attribute='genotype_name')`` and
 # ``er.add_ref(container=genotypes.genotype_name, attribute=None)`` will ultimately both use the ``object_id``
 # of the ``genotypes.genotype_name`` :py:class:`~hdmf.common.table.VectorData` column and
@@ -197,12 +197,12 @@ def __init__(self, **kwargs):
 )
 
 ###############################################################################
-# Visualize ExternalResources
+# Visualize HERD
 # ------------------------------------------------------
-# Users can visualize `~hdmf.common.resources.ExternalResources` as a flattened table or
+# Users can visualize `~hdmf.common.resources.HERD` as a flattened table or
 # as separate tables.
 
-# `~hdmf.common.resources.ExternalResources` as a flattened table
+# `~hdmf.common.resources.HERD` as a flattened table
 er.to_dataframe()
 
 # The individual interlinked tables:
@@ -216,13 +216,13 @@ def __init__(self, **kwargs):
 ###############################################################################
 # Using the get_key method
 # ------------------------------------------------------
-# The :py:func:`~hdmf.common.resources.ExternalResources.get_key`
+# The :py:func:`~hdmf.common.resources.HERD.get_key`
 # method will return a :py:class:`~hdmf.common.resources.Key` object. In the current version of
-# :py:class:`~hdmf.common.resources.ExternalResources`, duplicate keys are allowed; however, each key needs a unique
+# :py:class:`~hdmf.common.resources.HERD`, duplicate keys are allowed; however, each key needs a unique
 # linking Object. In other words, each combination of (file, container, relative_path, field, key)
-# can exist only once in :py:class:`~hdmf.common.resources.ExternalResources`.
+# can exist only once in :py:class:`~hdmf.common.resources.HERD`.
 
-# The :py:func:`~hdmf.common.resources.ExternalResources.get_key` method will be able to return the
+# The :py:func:`~hdmf.common.resources.HERD.get_key` method will be able to return the
 # :py:class:`~hdmf.common.resources.Key` object if the :py:class:`~hdmf.common.resources.Key` object is unique.
 genotype_key_object = er.get_key(key_name='Rorb')
 
@@ -232,18 +232,18 @@ def __init__(self, **kwargs):
                                 container=species['Species_Data'],
                                 key_name='Ursus arctos horribilis')
 
-# The :py:func:`~hdmf.common.resources.ExternalResources.get_key` also will check the
+# The :py:func:`~hdmf.common.resources.HERD.get_key` also will check the
 # :py:class:`~hdmf.common.resources.Object` for a :py:class:`~hdmf.common.resources.File` along the parent hierarchy
-# if the file is not provided as in :py:func:`~hdmf.common.resources.ExternalResources.add_ref`
+# if the file is not provided as in :py:func:`~hdmf.common.resources.HERD.add_ref`
 
 ###############################################################################
 # Using the add_ref method with a key_object
 # ------------------------------------------------------
 # Multiple :py:class:`~hdmf.common.resources.Object` objects can use the same
 # :py:class:`~hdmf.common.resources.Key`. To use an existing key when adding
-# new entries into :py:class:`~hdmf.common.resources.ExternalResources`, pass the
+# new entries into :py:class:`~hdmf.common.resources.HERD`, pass the
 # :py:class:`~hdmf.common.resources.Key` object instead of the 'key_name' to the
-# :py:func:`~hdmf.common.resources.ExternalResources.add_ref` method. If a 'key_name'
+# :py:func:`~hdmf.common.resources.HERD.add_ref` method. If a 'key_name'
 # is used, a new :py:class:`~hdmf.common.resources.Key` will be created.
 
 er.add_ref(
@@ -258,7 +258,7 @@ def __init__(self, **kwargs):
 ###############################################################################
 # Using the get_object_entities
 # ------------------------------------------------------
-# The :py:class:`~hdmf.common.resources.ExternalResources.get_object_entities` method
+# The :py:class:`~hdmf.common.resources.HERD.get_object_entities` method
 # allows the user to retrieve all entities and key information associated with an `Object` in
 # the form of a pandas DataFrame.
 
@@ -269,7 +269,7 @@ def __init__(self, **kwargs):
 ###############################################################################
 # Using the get_object_type
 # ------------------------------------------------------
-# The :py:class:`~hdmf.common.resources.ExternalResources.get_object_entities` method
+# The :py:class:`~hdmf.common.resources.HERD.get_object_entities` method
 # allows the user to retrieve all entities and key information associated with an `Object` in
 # the form of a pandas DataFrame.
 
@@ -285,9 +285,9 @@ def __init__(self, **kwargs):
 # column/field is associated with different ontologies, then use field='x' to denote that
 # 'x' is using the external reference.
 
-# Let's create a new instance of :py:class:`~hdmf.common.resources.ExternalResources`.
-er = ExternalResources()
-file = ExternalResourcesManagerContainer(name='file')
+# Let's create a new instance of :py:class:`~hdmf.common.resources.HERD`.
+er = HERD()
+file = HERDManagerContainer(name='file')
 
 data = Data(
     name='data_name',
@@ -307,28 +307,28 @@ def __init__(self, **kwargs):
 )
 
 ###############################################################################
-# Write ExternalResources
+# Write HERD
 # ------------------------------------------------------
-# :py:class:`~hdmf.common.resources.ExternalResources` is written as a zip file of
+# :py:class:`~hdmf.common.resources.HERD` is written as a zip file of
 # the individual tables written to tsv.
 # The user provides the path, which contains the name of the directory.
 
 er.to_norm_tsv(path='./')
 
 ###############################################################################
-# Read ExternalResources
+# Read HERD
 # ------------------------------------------------------
-# Users can read :py:class:`~hdmf.common.resources.ExternalResources` from the tsv format
+# Users can read :py:class:`~hdmf.common.resources.HERD` from the tsv format
 # by providing the path to the directory.
 
-er_read = ExternalResources.from_norm_tsv(path='./')
+er_read = HERD.from_norm_tsv(path='./')
 os.remove('./er.zip')
 
 ###############################################################################
-# Using TermSet with ExternalResources
+# Using TermSet with HERD
 # ------------------------------------------------
 # :py:class:`~hdmf.term_set.TermSet` allows for an easier way to add references to
-# :py:class:`~hdmf.common.resources.ExternalResources`. These enumerations take place of the
+# :py:class:`~hdmf.common.resources.HERD`. These enumerations take place of the
 # entity_id and entity_uri parameters. :py:class:`~hdmf.common.resources.Key` values will have
 # to match the name of the term in the :py:class:`~hdmf.term_set.TermSet`.
 from hdmf.term_set import TermSet

src/hdmf/__init__.py

@@ -1,6 +1,6 @@
 from . import query
 from .backends.hdf5.h5_utils import H5Dataset, H5RegionSlicer
-from .container import Container, Data, DataRegion, ExternalResourcesManager
+from .container import Container, Data, DataRegion, HERDManager
 from .region import ListSlicer
 from .utils import docval, getargs
 from .term_set import TermSet

src/hdmf/backends/hdf5/h5tools.py

@@ -61,15 +61,15 @@ def can_read(path):
              'doc': 'the MPI communicator to use for parallel I/O', 'default': None},
             {'name': 'file', 'type': [File, "S3File"], 'doc': 'a pre-existing h5py.File object', 'default': None},
             {'name': 'driver', 'type': str, 'doc': 'driver for h5py to use when opening HDF5 file', 'default': None},
-            {'name': 'external_resources_path', 'type': str,
-             'doc': 'The path to the ExternalResources', 'default': None},)
+            {'name': 'herd_path', 'type': str,
+             'doc': 'The path to the HERD', 'default': None},)
     def __init__(self, **kwargs):
         """Open an HDF5 file for IO.
         """
         self.logger = logging.getLogger('%s.%s' % (self.__class__.__module__, self.__class__.__qualname__))
-        path, manager, mode, comm, file_obj, driver, external_resources_path = popargs('path', 'manager', 'mode',
+        path, manager, mode, comm, file_obj, driver, herd_path = popargs('path', 'manager', 'mode',
                                                                                        'comm', 'file', 'driver',
-                                                                                       'external_resources_path',
+                                                                                       'herd_path',
                                                                                        kwargs)
 
         self.__open_links = []  # keep track of other files opened from links in this file
@@ -93,7 +93,7 @@ def __init__(self, **kwargs):
         self.__comm = comm
         self.__mode = mode
         self.__file = file_obj
-        super().__init__(manager, source=path, external_resources_path=external_resources_path)
+        super().__init__(manager, source=path, herd_path=herd_path)
         # NOTE: source is not set if path is None and file_obj is passed
         self.__built = dict() # keep track of each builder for each dataset/group/link for each file
         self.__read = dict() # keep track of which files have been read. Key is the filename value is the builder