Procedure API endpoint

Table of contents

1. Fields
2. Types of procedure
3. List view
4. Add
5. Detail
6. Change
7. Delete

Fields

Field	Description
id	UUID identificator formatted as a string
type	string [required]. See options below
notes	string [max length: 500]
subject	related subject ID formatted as a string [required]
date_time	string containing date and time (ISO 8601)
consumablestock	related consumable stock ID formatted as a string
equipment	list of related equipment IDs formatted as strings
brain_region	related brain region ID formatted as a string
details	JSON object mapped to the internal type_json field. See accepted schemas below
coordinates_system	string [required]. See options below
coordinates_details	JSON object mapped to the internal coordinates_json field. See accepted schemas below

Types of procedure

A detailed list of the available type options and accepted schemas for the details and coordinates_details fields can be found in the Procedure schemas documentation and Coordinates schemas documentation.

List view

• Allowed portals: public, private
• Request method: GET
• URL: https://www.brainstem.org/api/private/modules/procedure
• Data: None
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.load_model('procedure')

Response example

{'procedures': [
    {
        'id': 'f79d84c8-6bec-40e3-b18a-5b25e57f4a09',
        'type': 'SiliconProbeImplant',
        'notes': 'acute implant',
        'subject': '0f87c229-6769-4854-83a5-c71e154246b8',
        'date_time': '2024-03-12T09:00:00Z',
        'consumablestock': 'a5f29099-2758-4163-a8e4-e5e2898e57b2',
        'equipment': ['5b032f95-3f5b-4a27-9680-5f8f671dba22'],
        'details': {
            'probeId': 'SP-64A',
            'sterilizationMethod': 'Ethylene Oxide'
        },
        'brain_region': '15f9aef5-2d46-4ff2-a0db-ac6be759c05c',
        'coordinates_system': 'Stereotaxic_BregmaAbsolute',
        'coordinates_details': {
            'apCoordinate': -2.5,
            'mlCoordinate': 1.5,
            'dvCoordinate': -1.0,
            'apAngle': 0.0,
            'mlAngle': 10.0,
            'dvAngle': 0.0
        }
    },
    {
        'id': 'a18dd2b1-6393-468c-9424-1bc77b9e4976',
        'type': 'OpticFiberImplant',
        'notes': 'bilateral implant',
        'subject': '0f87c229-6769-4854-83a5-c71e154246b8',
        'date_time': None,
        'consumablestock': None,
        'equipment': [],
        'details': {
            'fiberTipShape': 'flat',
            'fiberId': 'OF-L-2024-07',
            'sterilizationMethod': 'Autoclave'
        },
        'brain_region': '15f9aef5-2d46-4ff2-a0db-ac6be759c05c',
        'coordinates_system': 'Stereotaxic_BregmaBrainSurface',
        'coordinates_details': {
            'apCoordinate': -2.8,
            'mlCoordinate': 1.2,
            'surfaceDepth': -0.5,
            'apAngle': 0.0,
            'mlAngle': 5.0
        }
    }
]}

Add

• Allowed portals: private
• Request method: POST
• URL: https://www.brainstem.org/api/private/modules/procedure
• Data: JSON dictionary containing at least the required fields.
• Responses: 201 OK; 400 Bad request; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.save_model(
    "procedure",
    data={
        "type": "OpticFiberImplant",
        "subject": "0f87c229-6769-4854-83a5-c71e154246b8",
        "consumablestock": "a5f29099-2758-4163-a8e4-e5e2898e57b2",
        "equipment": ["5b032f95-3f5b-4a27-9680-5f8f671dba22"],
        "notes": "bilateral implant",
        "details": {"fiberTipShape": "flat", "fiberId": "OF-L-2024-07", "sterilizationMethod": "Autoclave"},
        "coordinates_system": "Stereotaxic_BregmaAbsolute",
        "coordinates_details": {
            "apCoordinate": -2.8,
            "mlCoordinate": 1.2,
            "dvCoordinate": -2.5,
            "apAngle": 0.0,
            "mlAngle": 5.0,
            "dvAngle": 0.0
        }
    }
)

Response example

{'procedure': {
    'id': 'd37c9255-d5ae-47d9-b6e1-4ec760c200fb',
    'type': 'OpticFiberImplant',
    'notes': 'bilateral implant',
    'subject': '0f87c229-6769-4854-83a5-c71e154246b8',
    'date_time': None,
    'consumablestock': 'a5f29099-2758-4163-a8e4-e5e2898e57b2',
    'equipment': ['5b032f95-3f5b-4a27-9680-5f8f671dba22'],
    'details': {'fiberTipShape': 'flat', 'fiberId': 'OF-L-2024-07', 'sterilizationMethod': 'Autoclave'},
    'brain_region': None,
    'coordinates_system': 'Stereotaxic_BregmaAbsolute',
    'coordinates_details': {
        "apCoordinate": -2.8,
        "mlCoordinate": 1.2,
        "dvCoordinate": -2.5,
        "apAngle": 0.0,
        "mlAngle": 5.0,
        "dvAngle": 0.0
    }
}}

Detail

• Allowed portals: public, private
• Request method: GET
• URL: https://www.brainstem.org/api/private/modules/procedure/<id>/
• Data: None
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.load_model('procedure', id='d37c9255-d5ae-47d9-b6e1-4ec760c200fb')

Response example

{'procedure': {
    'id': 'd37c9255-d5ae-47d9-b6e1-4ec760c200fb',
    'type': 'OpticFiberImplant',
    'notes': 'bilateral implant',
    'subject': '0f87c229-6769-4854-83a5-c71e154246b8',
    'date_time': None,
    'consumablestock': 'a5f29099-2758-4163-a8e4-e5e2898e57b2',
    'equipment': ['5b032f95-3f5b-4a27-9680-5f8f671dba22'],
    'details': {'fiberTipShape': 'flat', 'fiberId': 'OF-L-2024-07', 'sterilizationMethod': 'Autoclave'},
    'brain_region': None,
    'coordinates_system': 'Stereotaxic_BregmaAbsolute',
    'coordinates_details': {
        "apCoordinate": -2.8,
        "mlCoordinate": 1.2,
        "dvCoordinate": -2.5,
        "apAngle": 0.0,
        "mlAngle": 5.0,
        "dvAngle": 0.0
    }
}}

Change

• Allowed portals: private
• Request method: PATCH
• URL: https://www.brainstem.org/api/private/modules/procedure/<id>/
• Data: dictionary containing the fields to be updated
• Responses: 200 OK; 400 Bad request; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.save_model(
    "procedure",
    id="d37c9255-d5ae-47d9-b6e1-4ec760c200fb",
    data={"notes": "implant tightened"}
)

Response example

{'procedure': {
    'id': 'd37c9255-d5ae-47d9-b6e1-4ec760c200fb',
    'type': 'OpticFiberImplant',
    'notes': 'implant tightened',
    'subject': '0f87c229-6769-4854-83a5-c71e154246b8',
    'date_time': None,
    'consumablestock': 'a5f29099-2758-4163-a8e4-e5e2898e57b2',
    'equipment': ['5b032f95-3f5b-4a27-9680-5f8f671dba22'],
    'details': {'fiberTipShape': 'flat', 'fiberId': 'OF-L-2024-07', 'sterilizationMethod': 'Autoclave'},
    'brain_region': None,
    'coordinates_system': 'Stereotaxic_BregmaAbsolute',
    'coordinates_details': {
        "apCoordinate": -2.8,
        "mlCoordinate": 1.2,
        "dvCoordinate": -2.5,
        "apAngle": 0.0,
        "mlAngle": 5.0,
        "dvAngle": 0.0
    }
}}

Delete

• Allowed portals: private
• Request method: DELETE
• URL: https://www.brainstem.org/api/private/modules/procedure/<id>/
• Data: None
• Responses: 204 OK; 403 Not allowed; 404 Not found

Use example (using Python API)

resp = client.delete_model("procedure", id="d37c9255-d5ae-47d9-b6e1-4ec760c200fb")