Specimen log API endpoint

Records followed over time for a specimen set, such as temperature, pH or slice health.

Table of contents

1. Endpoints
2. Fields
3. List
4. Add
5. Detail
6. Change
7. Delete
8. Data model

Endpoints

• Private portal: https://www.brainstem.org/api/private/modules/specimenlog/ (needs a token; one record: append <id>/)
• Public portal: https://www.brainstem.org/api/public/modules/specimenlog/ (read-only, public projects, no token)
• Response keys: specimenlog (detail, create, update), specimenlogs (list)
• Permissions: inherited through specimen_set → projects (from project)
• Entry schemas: type selects a SpecimenLog type; each log entry is validated against it.

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]
type	one of the SpecimenLog types [required]
specimen_set	specimenset id [required]
target_specimens	list of specimen ids. Specific specimens within the specimen set targeted by this log. Leave empty when the log applies to the whole specimen set.
description	string; max 500 characters; nullable
protocol	protocol id; nullable
updated_at	datetime [read-only]
created_at	datetime [read-only]; nullable

List

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

Use example (Python API tool)

resp = client.load('specimenlog', load_all=True)
records = resp['specimenlogs']

Use example (MATLAB API tool)

resp = client.load('specimenlog', 'load_all', true);
records = resp.specimenlogs;

Response example

{
    "specimenlogs": [
        {
            "id": "<id>",
            "type": "BathSolution",
            "specimen_set": "<specimenset-id>",
            "target_specimens": [
                "<specimen-id>"
            ],
            "description": "",
            "protocol": "<protocol-id>",
            "updated_at": "2024-03-22T10:30:00Z",
            "created_at": "2024-03-22T10:30:00Z"
        }
    ],
    "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/modules/specimenlog/
• 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('specimenlog', data={"type": "BathSolution", "specimen_set": "<specimenset-id>"})
record = resp.json()['specimenlog']

Use example (MATLAB API tool)

created = client.save(struct('type', 'BathSolution', 'specimen_set', '<specimenset-id>'), 'specimenlog');
record = created.specimenlog;

Detail

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

Use example (Python API tool)

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

Use example (MATLAB API tool)

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

Response example

{
    "specimenlog": {
        "id": "<id>",
        "type": "BathSolution",
        "specimen_set": "<specimenset-id>",
        "target_specimens": [
            "<specimen-id>"
        ],
        "description": "",
        "protocol": "<protocol-id>",
        "updated_at": "2024-03-22T10:30:00Z",
        "created_at": "2024-03-22T10:30:00Z"
    }
}

Change

• Allowed portals: private
• Request method: PATCH
• URL: https://www.brainstem.org/api/private/modules/specimenlog/<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('specimenlog', id='<id>', data={"description": "new value"})

Use example (MATLAB API tool)

client.save(struct('id', '<id>', 'description', 'new value'), 'specimenlog', 'method', 'patch');

Delete

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

Use example (Python API tool)

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

Use example (MATLAB API tool)

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

Data model

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