checkpoint

src/pynwb/config/experimenter_termset.yaml → docs/gallery/general/experimenter_termset.yaml

@@ -10,10 +10,8 @@ default_range: string
 enums:
   Experimenters:
     permissible_values:
-      Oliver Rübel:
+      Bilbo Baggins:
         description: He who must not be named.
-        meaning: ORC:0000-0001-9902-1984
-      Ryan Ly:
-        description: The chosen one. 
-        meaning: ORC:0000-0001-9238-0642
-
+        meaning: ORC:111
+
+

docs/gallery/general/nwb_gallery_config.yaml

@@ -0,0 +1,13 @@
+namespaces:
+  core:
+    version: 2.7.0-alpha
+    data_types:
+      Subject:
+        species:
+          termset: nwb_subject_termset.yaml
+      NWBFile:
+        experimenter:
+          termset: experimenter_termset.yaml
+      # ElectrodeGroup: This will return when electrode table is redefined
+      #   location:
+      #     termset: location_termset.yaml

docs/gallery/general/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

docs/gallery/general/plot_configurator.py

@@ -29,7 +29,7 @@
 --------------------------------
 Before taking advantage of the all the wonders that comes with using a configuration file,
 the user needs to create one following some simple guidelines. To follow along with an example,
-please refer to ``nwb_config.yaml`` under ``src/config``. 
+please refer to ``nwb_config.yaml`` under ``src/config``.
 The configuration files is built on the foundation of the YAML syntax. The
 user will construct a series of nested dictioanries to encompass all the necessary information.
 
@@ -44,7 +44,14 @@
     import linkml_runtime  # noqa: F401
 except ImportError as e:
     raise ImportError("Please install linkml-runtime to run this example: pip install linkml-runtime") from e
-from hdmf.term_set import TermSet, TermSetWrapper
+
+from dateutil import tz
+from datetime import datetime
+from uuid import uuid4
+import os
+
+from pynwb import NWBFile, get_loaded_type_config, load_type_config, unload_type_config
+from pynwb.file import Subject
 
 # How to use a Configuration file
 # -------------------------------
@@ -53,12 +60,13 @@
 # It is important to remember that with the configuration loaded, the fields
 # are wrapped automatically, meaning the user should proceed with creating
 # the instances normally, i.e., without wrapping directly. In this example,
-# we load the the NWB curated configuration file that associates a
-# :py:class:`~hdmf.term_set.TermSet` for the species field in Subject.
-# The NWB configuration file is the default when you call
-# :py:func:`~pynwb.load_type_config`.
+# we load the a configuration file that associates a
+# :py:class:`~hdmf.term_set.TermSet` for the ``species`` field in
+# :py:class:`~pynwb.file.Subject`.
 
-load_type_config()
+dir_path = os.path.dirname(os.path.abspath(__file__))
+yaml_file = os.path.join(dir_path, 'nwb_gallery_config.yaml')
+load_type_config(config_path=yaml_file)
 
 session_start_time = datetime(2018, 4, 25, hour=2, minute=30, second=3, tzinfo=tz.gettz("US/Pacific"))
 
@@ -68,7 +76,7 @@
     session_start_time=session_start_time,  # required
     session_id="session_1234",  # optional
     experimenter=[
-        "Baggins, Bilbo",
+        "Bilbo Baggins",
     ],  # optional
     lab="Bag End Laboratory",  # optional
     institution="University of My Institution",  # optional

src/pynwb/config/nwb_config.yaml

@@ -5,9 +5,3 @@ namespaces:
       Subject:
         species:
           termset: nwb_subject_termset.yaml
-      NWBFile:
-        experimenter:
-          termset: experimenter_termset.yaml
-      # ElectrodeGroup: This will return when electrode table is redefined
-      #   location:
-      #     termset: location_termset.yaml

tests/unit/test_config.py

@@ -4,7 +4,7 @@
 
 from hdmf.term_set import TermSetWrapper
 
-from pynwb import NWBFile,get_loaded_type_config, load_type_config, unload_type_config
+from pynwb import NWBFile, get_loaded_type_config, load_type_config, unload_type_config
 from pynwb.file import Subject
 from pynwb.testing import TestCase
 
@@ -28,8 +28,7 @@ def test_get_loaded_type_config(self):
         config = get_loaded_type_config()
         self.assertEqual(config,
         {'namespaces': {'core': {'version': '2.7.0-alpha',
-        'data_types': {'Subject': {'species': {'termset': 'nwb_subject_termset.yaml'}},
-                       'NWBFile': {'experimenter': {'termset': 'experimenter_termset.yaml'}}}}}})
+        'data_types': {'Subject': {'species': {'termset': 'nwb_subject_termset.yaml'}}}}}})
 
     def test_default_config(self):
         session_start_time = datetime(2018, 4, 25, 2, 30, 3, tzinfo=tz.gettz("US/Pacific"))