Subtraction Updated May 3, 2022

Find

Find profile subtractions by id (name) or nickname.

GET /api/subtraction

Parameters

Name Type Default Description
find string null subtraction name to filter by
page integer 1 page number of results to return
per_page integer 15 number of documents to return per page

Example

GET /api/hmms?find=Arab&per_page=1

Response

Status: 200 OK

{
	"documents": [
		{
			"ready": true,
			"file": {
				"id": "vlekszor-ATgenomeTAIR9.171",
				"name": "ATgenomeTAIR9.171"
			},
			"job": {
				"id": "ritpnbst"
			},
			"id": "Arabidopsis"
		}
	],
	"total_count": 1,
	"found_count": 1,
	"page_count": 1,
	"per_page": 1,
	"page": 1,
	"host_count": 1,
	"ready_host_count": 1
}

Errors

None

Get

Get the complete representation of a given subtraction.

GET /api/subtraction/:id

Example

GET /api/subtraction/Arabidopsis

Response

Status: 200 OK

{
	"ready": true,
	"is_host": true,
	"file": {
		"id": "vlekszor-ATgenomeTAIR9.171",
		"name": "ATgenomeTAIR9.171"
	},
	"user": {
		"id": "igboyes"
	},
	"job": {
		"id": "ritpnbst"
	},
	"count": 7,
	"gc": {
		"a": 0.319,
		"t": 0.319,
		"g": 0.18,
		"c": 0.18,
		"n": 0.002
	},
	"linked_samples": [
		{
			"name": "Test 1",
			"id": "htosefxu"
		}
	],
	"id": "Arabidopsis"
}

Errors

Status Message Reason
404 Not found sample_id in URL does not exist

Create

Permission modify_subtraction

Create a new subtraction from a file that has previously been uploaded into the file manager.

POST /api/subtraction

Input

Name Type Required Description
subtraction_id string true a unique name for the host (eg. Arabidopsis)
nickname string false a nickname for the host
file_id string true the unique id of the host FASTA file

Example

POST /api/subtraction 
{
	"subtraction_id": "Test 1",
	"nickname": "Foobar",
	"file_id": "djbxvhmy-ATgenomeTAIR9.171"
}

Response

Status: 201 Created

{
	"ready": false,
	"is_host": true,
	"file": {
		"id": "djbxvhmy-ATgenomeTAIR9.171",
		"name": "ATgenomeTAIR9.171"
	},
	"user": {
		"id": "igboyes"
	},
	"job": {
		"id": "rjbszwmm"
	},
	"nickname": "Foobar",
	"id": "Test 1"
}

Errors

Status Message Reason
400 File does not exist file identified by file_id does not exist
400 Subtraction id already exists id is already in use by an existing subtraction
403 Not permitted client does not have the ‘modify_subtraction` permission
422 Invalid input JSON request body is invalid

Edit

Permission modify_subtraction

Change the nickname of an existing subtraction.

PATCH /api/subtraction/:id

Input

Name Type Required Description
nickname string false a nickname for the host

Example

PATCH /api/subtraction/Arabdidopsis 
{
	"nickname": "Thale cress"
}

Response

Status: 200 OK

{
	"ready": true,
	"is_host": true,
	"file": {
		"id": "vlekszor-ATgenomeTAIR9.171",
		"name": "ATgenomeTAIR9.171"
	},
	"user": {
		"id": "igboyes"
	},
	"job": {
		"id": "ritpnbst"
	},
	"count": 7,
	"gc": {
		"a": 0.319,
		"t": 0.319,
		"g": 0.18,
		"c": 0.18,
		"n": 0.002
	},
	"nickname": "Thale cress",
	"id": "Arabidopsis"
}

Errors

Status Message Reason
403 Not permitted client does not have the ‘modify_subtraction` permission
404 Not found subtraction does not exist
422 Invalid input JSON request body is invalid

Remove

Permission modify_subtraction

Remove an existing subtraction

DELETE /api/subtraction/:id

Example

DELETE /api/subtraction/Test%201

Response

Status: 204 No content

Errors

Status Message Reason
403 Not permitted client does not have the ‘modify_subtraction` permission
404 Not found subtraction does not exist
409 Has linked samples subtraction is in use by one or more sample and cannot be removed
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