Strain approval API endpoint

A request to add or change a shared strain, reviewed before it takes effect.

Table of contents

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

Endpoints

• Private portal: https://www.brainstem.org/api/private/taxonomies/strainapproval/ (needs a token; one record: append <id>/)
• Public portal: not available
• Response keys: strain_approval (detail, create, update), strain_approvals (list)
• Permissions: see the permissions page

Form-only inputs (sent on create or update, not returned in responses):

• merge_to_id [required].
• breeding [required]. Choices: I, O, W, U.

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 100 characters
popular_name	string; max 100 characters
description	string; max 2000 characters
species	species id [required]
rrid	string; max 100 characters; nullable. Research Resource Identifier (RRID) for tracking standardized research resources
external_identifiers	JSON object; nullable. External identifiers and their source URLs from various databases (NCBI, JAX, DOI, etc.)
comments	string; nullable
instance_id	UUID string [required]; nullable
action	one of Add, Change [required]
reviewer	user id [required]; nullable
status	one of Pending, Accepted, Rejected, Cancelled, HoldForRejection, HoldForMerge, Merged, ChangesRequired [required]

List

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

Use example (Python API tool)

resp = client.load('strainapproval', load_all=True)
records = resp['strain_approvals']

Use example (MATLAB API tool)

resp = client.load('strainapproval', 'load_all', true);
records = resp.strain_approvals;

Response example

{
    "strain_approvals": [
        {
            "id": "<id>",
            "name": "Strain approval 1",
            "popular_name": "",
            "description": "",
            "species": "<species-id>",
            "rrid": "",
            "external_identifiers": {},
            "comments": "",
            "instance_id": "<id>",
            "action": "Add",
            "reviewer": "<user-id>",
            "status": "Pending"
        }
    ],
    "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/taxonomies/strainapproval/
• 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('strainapproval', data={"name": "Strain approval 1", "species": "<species-id>", "instance_id": "<id>", "action": "Add", "reviewer": "<user-id>", "status": "Pending", "merge_to_id": "<merge_to_id>", "breeding": "I"})
record = resp.json()['strain_approval']

Use example (MATLAB API tool)

created = client.save(struct('name', 'Strain approval 1', 'species', '<species-id>', 'instance_id', '<id>', 'action', 'Add', 'reviewer', '<user-id>', 'status', 'Pending', 'merge_to_id', '<merge_to_id>', 'breeding', 'I'), 'strainapproval');
record = created.strain_approval;

Detail

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

Use example (Python API tool)

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

Use example (MATLAB API tool)

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

Response example

{
    "strain_approval": {
        "id": "<id>",
        "name": "Strain approval 1",
        "popular_name": "",
        "description": "",
        "species": "<species-id>",
        "rrid": "",
        "external_identifiers": {},
        "comments": "",
        "instance_id": "<id>",
        "action": "Add",
        "reviewer": "<user-id>",
        "status": "Pending"
    }
}

Change

• Allowed portals: private
• Request method: PATCH
• URL: https://www.brainstem.org/api/private/taxonomies/strainapproval/<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('strainapproval', id='<id>', data={"name": "Strain approval 1 (renamed)"})

Use example (MATLAB API tool)

client.save(struct('id', '<id>', 'name', 'Strain approval 1 (renamed)'), 'strainapproval', 'method', 'patch');

Delete

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

Use example (Python API tool)

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

Use example (MATLAB API tool)

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

Custom actions

Action	Request
accept_approval	PATCH, POST /api/private/taxonomies/strainapproval/<id>/accept/
cancel_approval	PATCH, POST /api/private/taxonomies/strainapproval/<id>/cancel/
hold_for_merge_approval	PATCH, POST /api/private/taxonomies/strainapproval/<id>/hold_for_merge/
hold_for_rejection_approval	PATCH, POST /api/private/taxonomies/strainapproval/<id>/hold_for_rejection/
merge_approval	PATCH, POST /api/private/taxonomies/strainapproval/<id>/merge/
reject_approval	PATCH, POST /api/private/taxonomies/strainapproval/<id>/reject/
changes_required_approval	PATCH, POST /api/private/taxonomies/strainapproval/<id>/require_changes/

Approval requests are reviewed by the admin team of the taxonomy or resource. The actions move a request through its lifecycle: accept, reject, require_changes, hold_for_merge, merge (merge into an existing record given by merge_to_id) and cancel (by the submitter).