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bendichter avatar codycbakerphd avatar saksham20 avatar

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ndx-ibl's Issues

A few changes to the spec

IblSessionData
session_data.subject - > Subject.subject_id
session_data.procedures -> NWBFile.session_description
session_data.number -> NWBFile.session_id
session_data.narrative -> NWBFile.notes
session_data.end_type needs to be a date time (Low priority)

IblSubject should keep the name=“subject” of the Subject class it inherited from
Subject.death_date should be a datetime (Low priority)

Using `None` instead of empty strings for missing attrs

subject_data = {'age': str(subject_table.get('age_weeks', '')),
                'subject_id' : subject_table.get('id', ''),
                'description': subject_table.get('description', ''),
                'genotype': ','.join(subject_table.get('genotype'), []),
                'sex': subject_table.get('sex', ''),
                'species': subject_table.get('species', ''),
                'weight': str(subject_table.get('reference_weight', '')),
                'date_of_birth': datetime.datetime.strptime(subject_table.get('birth_date'), format='%Y-%m-%d')
                'nickname': subject_table.get('nickname', ''),
                'url': subject_table.get('url', ''),
                "responsible_user": subject_table.get('responsible_user', ''),
                "death_date": subject_table.get('death_date', ''),
                "litter": subject_table.get('litter', ''),
                "strain": subject_table.get('strain', ''),
                "source": subject_table.get('source', ''),
                "line": subject_table.get('line', ''),
                "projects": subject_table.get('projects', ''),
                "session_projects": subject_table.get('session_projects', ''),
                "lab": subject_table.get('lab', ''),
                "alive": subject_table.get('alive', False),
                "last_water_restriction": subject_table.get('last_water_restriction', null),
                "expected_water": subject_table.get('expected_water', np.nan),
                "remaining_water": subject_table.get('remaining_water', np.nan),
                'weighings': [str(i) for i in subject_table['IBLSubject']['weighings']],
                'water_administrations': [str(i) for i in subject_table['water_administrations']]
                }

Don't use empty strings. use None instead.

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