integration

docs/gallery/general/plot_configurator.py

@@ -0,0 +1,39 @@
+from pynwb import nwb_config
+from datetime import datetime
+from uuid import uuid4
+
+import numpy as np
+from dateutil import tz
+
+from pynwb import NWBHDF5IO, NWBFile, TimeSeries
+from pynwb.behavior import Position, SpatialSeries
+from pynwb.epoch import TimeIntervals
+from pynwb.file import Subject
+
+session_start_time = datetime(2018, 4, 25, 2, 30, 3, tzinfo=tz.gettz("US/Pacific"))
+
+nwbfile = NWBFile(
+    session_description="Mouse exploring an open field",  # required
+    identifier=str(uuid4()),  # required
+    session_start_time=session_start_time,  # required
+    session_id="session_1234",  # optional
+    experimenter=[
+        "Baggins, Bilbo",
+    ],  # optional
+    lab="Bag End Laboratory",  # optional
+    institution="University of My Institution",  # optional
+    experiment_description="I went on an adventure to reclaim vast treasures.",  # optional
+    related_publications="DOI:10.1016/j.neuron.2016.12.011",  # optional
+)
+
+
+subject = Subject(
+    subject_id="001",
+    age="P90D",
+    description="mouse 5",
+    species="Mus musculus",
+    sex="M",
+)
+
+nwbfile.subject = subject
+breakpoint()

src/pynwb/__init__.py

@@ -18,6 +18,35 @@
 from .spec import NWBDatasetSpec, NWBGroupSpec, NWBNamespace  # noqa E402
 from .validate import validate  # noqa: F401, E402
 
+from .termset_config import NWBTermSetConfigurator
+
+
+nwb_config = NWBTermSetConfigurator(path='src/pynwb/config/nwb_config.yaml')
+
+@docval({'name': 'config_path', 'type': str, 'doc': 'Path to the configuartion file.',
+         'default': None})
+def load_termset_config(config_path: str):
+    """
+    If a user does not provide a config_path, then this method will unload any present configuration
+    and load the default curated configuration.
+
+    If a user provides a config_path, then this method will:
+    - Search the current configuation for data_types that are already present. These data_types will be
+    replaced with the new configuration.
+    - If the data_type is not present, then they will be loaded alongside the default curated configuration.
+    """
+    if config_path is None:
+        nwb_config.unload_termset_config()
+        nwb_config.load_termset_config()
+    else:
+        nwb_config.load_termset_config(config_path)
+
+def unload_termset_config():
+    """
+    Remove validation.
+    """
+    return nwb_config.unload_termset_config()
+
 
 def __get_resources():
     try:

src/pynwb/config/nwb_config.yaml

@@ -0,0 +1,6 @@
+Subject:
+    namespace:
+    namespace_version:
+    fields:
+      species: src/pynwb/config/nwb_subject_termset.yaml
+      # field2: ...

src/pynwb/config/nwb_subject_termset.yaml

@@ -0,0 +1,27 @@
+id: termset/species_example
+name: Species
+version: 0.0.1
+prefixes:
+  NCBI_TAXON: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=
+imports:
+  - linkml:types
+default_range: string
+
+enums:
+  Species:
+    permissible_values:
+      Homo sapiens:
+        description: the species is human
+        meaning: NCBI_TAXON:9606
+      Mus musculus:
+        description: the species is a house mouse
+        meaning: NCBI_TAXON:10090
+      Ursus arctos horribilis:
+        description: the species is a grizzly bear
+        meaning: NCBI_TAXON:116960
+      Myrmecophaga tridactyla:
+        description: the species is an anteater
+        meaning: NCBI_TAXON:71006
+      Ailuropoda melanoleuca:
+        description: the species is a panda
+        meaning: NCBI_TAXON:9646

src/pynwb/core.py

@@ -46,6 +46,15 @@ def _error_on_new_warn_on_construct(self, error_msg: str):
             raise ValueError(error_msg)
         warn(error_msg)
 
+    def get_config(self):
+        from . import nwb_config #update path
+        return nwb_config
+
+    def get_type_map(self):
+        from . import get_type_map
+        tm = get_type_map()
+        return tm
+
 
 @register_class('NWBContainer', CORE_NAMESPACE)
 class NWBContainer(NWBMixin, Container):

src/pynwb/file.py

@@ -109,6 +109,7 @@ class Subject(NWBContainer):
         {'name': 'strain', 'type': str, 'doc': 'The strain of the subject, e.g., "C57BL/6J"', 'default': None},
     )
     def __init__(self, **kwargs):
+        self.init_validation(constructor_args=kwargs)
         keys_to_set = (
             "age",
             "age__reference",

src/pynwb/termset_config.py

@@ -0,0 +1,12 @@
+from hdmf.term_set import TermSetConfigurator as hdmf_TermSetConfigurator
+from hdmf.utils import docval
+
+
+class NWBTermSetConfigurator(hdmf_TermSetConfigurator):
+    """
+
+    """
+    @docval({'name': 'path', 'type': str, 'doc': 'Path to the configuartion file.',
+             'default': 'src/pynwb/config/nwb_config.yaml'})
+    def __init__(self,**kwargs):
+        super().__init__(**kwargs)

tests/unit/test_config.py

@@ -0,0 +1,2 @@
+from pynwb import nwb_config
+breakpoint()