Specimen procedure template API endpoint

A reusable template that prefills a new specimen procedure.

Table of contents

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

Endpoints

• Private portal: https://www.brainstem.org/api/private/modules/specimenproceduretemplate/ (needs a token; one record: append <id>/)
• Public portal: https://www.brainstem.org/api/public/modules/specimenproceduretemplate/ (read-only, public projects, no token)
• Response keys: specimenproceduretemplate (detail, create, update), specimenproceduretemplates (list)
• Permissions: inherited through projects (from project)
• Schema payload: type selects a SpecimenProcedure type; send its fields in details. type_schema_version is set by the server; do not send it.
• Deleting: also deletes the linked materialusagetemplate 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. Descriptive name for this specimen procedure template
projects	list of project ids
type	one of the SpecimenProcedure types [required]
type_display	computed [read-only]
notes	string; max 500 characters; nullable
date_time	datetime; nullable
target_regions	list of anatomicalregion ids
target_regions_display	computed [read-only]
equipment	list of equipment ids
protocol	protocol id; nullable
licenses	list of license ids
details	JSON object
type_schema_version	string [set by the server]. Schema version for type_json field
updated_at	datetime [read-only]
created_at	datetime [read-only]; nullable
user	user id [read-only]
user_display	computed [read-only]
summary	computed [read-only]
materials	computed [read-only]
stages	computed [read-only]

List

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

Use example (Python API tool)

resp = client.load('specimenproceduretemplate', load_all=True)
records = resp['specimenproceduretemplates']

Use example (MATLAB API tool)

resp = client.load('specimenproceduretemplate', 'load_all', true);
records = resp.specimenproceduretemplates;

Response example

{
    "specimenproceduretemplates": [
        {
            "id": "<id>",
            "name": "Specimen procedure template 1",
            "projects": [
                "<project-id>"
            ],
            "type": "Dissection",
            "type_display": null,
            "notes": "",
            "date_time": "2024-03-22T10:30:00Z",
            "target_regions": [
                "<anatomicalregion-id>"
            ],
            "target_regions_display": null,
            "equipment": [
                "<equipment-id>"
            ],
            "protocol": "<protocol-id>",
            "licenses": [
                "<license-id>"
            ],
            "details": {
                "...": "see the schema of the selected type"
            },
            "type_schema_version": "set by the server",
            "updated_at": "2024-03-22T10:30:00Z",
            "created_at": "2024-03-22T10:30:00Z",
            "user": "<user-id>",
            "user_display": null,
            "summary": null,
            "materials": null,
            "stages": 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/modules/specimenproceduretemplate/
• 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('specimenproceduretemplate', data={"name": "Specimen procedure template 1", "type": "AntigenRetrieval", "details": {"...": "see the schema of the selected type"}})
record = resp.json()['specimenproceduretemplate']

Use example (MATLAB API tool)

created = client.save(struct('name', 'Specimen procedure template 1', 'type', 'AntigenRetrieval', 'details', struct()), 'specimenproceduretemplate');  % struct() stands for the fields of the selected type
record = created.specimenproceduretemplate;

Detail

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

Use example (Python API tool)

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

Use example (MATLAB API tool)

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

Response example

{
    "specimenproceduretemplate": {
        "id": "<id>",
        "name": "Specimen procedure template 1",
        "projects": [
            "<project-id>"
        ],
        "type": "Dissection",
        "type_display": null,
        "notes": "",
        "date_time": "2024-03-22T10:30:00Z",
        "target_regions": [
            "<anatomicalregion-id>"
        ],
        "target_regions_display": null,
        "equipment": [
            "<equipment-id>"
        ],
        "protocol": "<protocol-id>",
        "licenses": [
            "<license-id>"
        ],
        "details": {
            "...": "see the schema of the selected type"
        },
        "type_schema_version": "set by the server",
        "updated_at": "2024-03-22T10:30:00Z",
        "created_at": "2024-03-22T10:30:00Z",
        "user": "<user-id>",
        "user_display": null,
        "summary": null,
        "materials": null,
        "stages": null
    }
}

Change

• Allowed portals: private
• Request method: PATCH
• URL: https://www.brainstem.org/api/private/modules/specimenproceduretemplate/<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('specimenproceduretemplate', id='<id>', data={"name": "Specimen procedure template 1 (renamed)"})

Use example (MATLAB API tool)

client.save(struct('id', '<id>', 'name', 'Specimen procedure template 1 (renamed)'), 'specimenproceduretemplate', 'method', 'patch');

Delete

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

Use example (Python API tool)

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

Use example (MATLAB API tool)

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