Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add keywords #620

Merged
merged 8 commits into from
Sep 18, 2018
Merged

Add keywords #620

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
4cfc235
fixes the yaml writer so that None is written as null
bendichter Sep 4, 2018
5063922
add null back to core
bendichter Sep 4, 2018
4a95e24
Merge branch 'dev' of https://github.com/NeurodataWithoutBorders/pynw…
bendichter Sep 12, 2018
04c8e1d
Merge branch 'fix_yaml_null' into dev
bendichter Sep 12, 2018
a1e1aa0
Merge branch 'dev' of https://github.com/NeurodataWithoutBorders/pynw…
bendichter Sep 13, 2018
e4c7ddb
add keywords: spec, constructor, test
bendichter Sep 17, 2018
d0d2689
Merge branch 'dev' into add_keywords
bendichter Sep 17, 2018
ad9acab
Iterable -> array_data
bendichter Sep 18, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions src/pynwb/data/nwb.file.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -166,6 +166,12 @@ groups:
dtype: text
doc: Institution(s) where experiment was performed
quantity: '?'
- name: keywords
dtype: text
doc: Terms to search over
quantity: '?'
shape:
- null
- name: lab
dtype: text
doc: Lab where experiment was performed
Expand Down
3 changes: 3 additions & 0 deletions src/pynwb/file.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -148,6 +148,7 @@ class NWBFile(MultiContainerInterface):
'description',
'experiment_description',
'session_id',
'keywords',
'lab',
'institution',
'notes',
Expand Down Expand Up @@ -180,6 +181,7 @@ class NWBFile(MultiContainerInterface):
{'name': 'session_id', 'type': str, 'doc': 'lab-specific ID for the session', 'default': None},
{'name': 'institution', 'type': str,
'doc': 'institution(s) where experiment is performed', 'default': None},
{'name': 'keywords', 'type': 'array_data', 'doc': 'Terms to search over', 'default': None},
{'name': 'notes', 'type': str,
'doc': 'Notes about the experiment.', 'default': None},
{'name': 'pharmacology', 'type': str,
Expand Down Expand Up @@ -259,6 +261,7 @@ def __init__(self, **kwargs):
self.acquisition = getargs('acquisition', kwargs)
self.stimulus = getargs('stimulus', kwargs)
self.stimulus_template = getargs('stimulus_template', kwargs)
self.keywords = getargs('keywords', kwargs)

self.modules = getargs('modules', kwargs)
epochs = getargs('epochs', kwargs)
Expand Down
4 changes: 3 additions & 1 deletion tests/unit/pynwb_tests/test_file.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,8 @@ def setUp(self):
source_script='noscript',
source_script_file_name='nofilename',
stimulus_notes='test stimulus notes',
data_collection='test data collection notes')
data_collection='test data collection notes',
keywords=('these', 'are', 'keywords'))

def test_constructor(self):
self.assertEqual(self.nwbfile.session_description, 'a test session description for a test NWBFile')
Expand All @@ -49,6 +50,7 @@ def test_constructor(self):
self.assertEqual(self.nwbfile.data_collection, 'test data collection notes')
self.assertEqual(self.nwbfile.source_script, 'noscript')
self.assertEqual(self.nwbfile.source_script_file_name, 'nofilename')
self.assertEqual(self.nwbfile.keywords, ('these', 'are', 'keywords'))

def test_create_electrode_group(self):
name = 'example_electrode_group'
Expand Down