Protocol API endpoint

A written method the lab reuses, such as a standard operating procedure.

Table of contents

1. Endpoints
2. Fields
3. List
4. Add
5. Detail
6. Change
7. Delete
8. Custom actions
9. Data model
10. Usage notes

Endpoints

• Private portal: https://www.brainstem.org/api/private/personal_attributes/protocol/ (needs a token; one record: append <id>/)
• Public portal: https://www.brainstem.org/api/public/personal_attributes/protocol/ (read-only, public projects, no token)
• Response keys: protocol (detail, create, update), protocols (list)
• Permissions: object permissions on the record itself (member / manager / owner roles)
• Deleting: also deletes the linked protocolgroupmembershipinvitation, protocolmembershipinvitation records; refused (400) while procedure, procedureepisode, procedureepisodetemplate, proceduretemplate, subjectlog records point to it; clears the link on specimenlog, specimenprocedure, specimenproceduretemplate records

Fields

[required] fields must be sent on create; [read-only] fields are returned but cannot be set. A nestable relation can be traversed in filters (filter{field.other}) and sideloaded with include[]=field.*; other relations can only be compared with ids (filter{field}=<id>). See the query syntax.

Field	Description
id	UUID string [read-only]
name	string [required]; max 255 characters
description	string; nullable
url	string; max 200 characters
protocol_type	one of breeding, procedure, specimen_procedure, subject_log, specimen_log [required]
subtypes	list of strings
subtype_display	computed [read-only]
licenses	list of license ids; nestable. Licenses that authorize this protocol
attachment	string; max 100 characters
is_public	boolean. Designates if the protocol is publicly available
procedures	list of procedure ids [read-only]; nullable; nestable
subjectlogs	list of subjectlog ids [read-only]; nullable; nestable
users	computed [read-only]
groups	computed [read-only]

List

• Allowed portals: private, public
• Request method: GET
• URL: https://www.brainstem.org/api/private/personal_attributes/protocol/
• Responses: 200 OK; 401 Not authenticated; 403 Not allowed

Use example (Python API tool)

resp = client.load('protocol', load_all=True)
records = resp['protocols']

Use example (MATLAB API tool)

resp = client.load('protocol', 'load_all', true);
records = resp.protocols;

Response example

{
    "protocols": [
        {
            "id": "<id>",
            "name": "Protocol 1",
            "description": "",
            "url": "",
            "protocol_type": "breeding",
            "subtypes": [],
            "subtype_display": null,
            "licenses": [
                "<license-id>"
            ],
            "attachment": "",
            "is_public": true,
            "procedures": [
                "<procedure-id>"
            ],
            "subjectlogs": [
                "<subjectlog-id>"
            ],
            "users": null,
            "groups": null
        }
    ],
    "meta": {
        "page": 1,
        "per_page": 100,
        "total_results": 1,
        "total_pages": 1
    }
}

Add

• Allowed portals: private
• Request method: POST
• URL: https://www.brainstem.org/api/private/personal_attributes/protocol/
• Data: JSON object with at least the required fields
• Responses: 201 Created; 400 Bad request (validation errors per field); 403 Not allowed

Use example (Python API tool)

resp = client.save('protocol', data={"name": "Protocol 1", "protocol_type": "breeding"})
record = resp.json()['protocol']

Use example (MATLAB API tool)

created = client.save(struct('name', 'Protocol 1', 'protocol_type', 'breeding'), 'protocol');
record = created.protocol;

Detail

• Allowed portals: private, public
• Request method: GET
• URL: https://www.brainstem.org/api/private/personal_attributes/protocol/<id>/
• Responses: 200 OK; 403 Not allowed; 404 Not found

Use example (Python API tool)

resp = client.load('protocol', id='<id>')
record = resp.json()['protocol']

Use example (MATLAB API tool)

out = client.load('protocol', 'id', '<id>');
record = out.protocol;

Response example

{
    "protocol": {
        "id": "<id>",
        "name": "Protocol 1",
        "description": "",
        "url": "",
        "protocol_type": "breeding",
        "subtypes": [],
        "subtype_display": null,
        "licenses": [
            "<license-id>"
        ],
        "attachment": "",
        "is_public": true,
        "procedures": [
            "<procedure-id>"
        ],
        "subjectlogs": [
            "<subjectlog-id>"
        ],
        "users": null,
        "groups": null
    }
}

Change

• Allowed portals: private
• Request method: PATCH
• URL: https://www.brainstem.org/api/private/personal_attributes/protocol/<id>/
• Data: JSON object with the fields to change. Lists (projects, tags, …) and JSON payloads (details, coordinates) are replaced as a whole: read the record first and send the full list or object.
• Responses: 200 OK; 400 Bad request; 403 Not allowed; 404 Not found

Use example (Python API tool)

resp = client.save('protocol', id='<id>', data={"name": "Protocol 1 (renamed)"})

Use example (MATLAB API tool)

client.save(struct('id', '<id>', 'name', 'Protocol 1 (renamed)'), 'protocol', 'method', 'patch');

Delete

• Allowed portals: private
• Request method: DELETE
• URL: https://www.brainstem.org/api/private/personal_attributes/protocol/<id>/
• Responses: 204 Deleted; 400 Still referenced by other records; 403 Not allowed; 404 Not found

Use example (Python API tool)

resp = client.delete('protocol', id='<id>')

Use example (MATLAB API tool)

client.delete('<id>', 'protocol');

Custom actions

Action	Request
leave	POST /api/private/personal_attributes/protocol/<id>/leave/

Data model

The fields are described for the web forms on the Protocol data model page.

Usage notes

• attachment is a file, not text: upload it as multipart form data (PDF, DOCX, XLSX, PPTX, ODT, CSV, Markdown or plain text, up to 15 MB). Responses return a signed download URL.
• subtypes are type codes of the selected protocol_type: procedure types for procedure, specimen procedure types for specimen_procedure, subject log types for subject_log and specimen log types for specimen_log. Codes are case-sensitive. An empty list makes the protocol apply to every type; when you change protocol_type, send matching subtypes (or []) in the same request.