jobs
Find jobs
Lists jobs on the instance.
Jobs can be filtered by their current state by providing desired states as
query parameters.
Archived jobs are not currently returned from the API.
Errors
| Status | Description |
|---|---|
| 400 | Invalid query |
Request
get
/jobs
Response
{
"status": "200"
}Update archived field
Sets the archived field on job documents.
Parameters
| Name | Type | Required | Description |
|---|---|---|---|
| updates | array | true |
Errors
| Status | Description |
|---|---|
| 400 | Invalid archived field |
Request
patch
/jobs
Response
{
"status": "200"
}Get a job
Fetches the details for a job.
Errors
| Status | Description |
|---|---|
| 404 | Not found |
Request
get
/jobs/{job_id}
Response
{
"example": {
"acquired": true,
"archived": false,
"args": {
"analysis_id": "rr8iryfy",
"index_id": "u3lm1rk8",
"ref_id": "d19exr83",
"sample_id": "4eynwmic",
"sample_name": "21BP088",
"subtractions": [
"0nhpi36p"
]
},
"created_at": "2022-07-08T18:37:44.936000Z",
"id": "splu0pq3",
"progress": 100,
"rights": {
"analyses": {
"modify": [
"rr8iryfy"
],
"read": [
"rr8iryfy"
],
"remove": [
"rr8iryfy"
]
},
"indexes": {
"read": [
"u3lm1rk8"
]
},
"references": {
"read": [
"d19exr83"
]
},
"samples": {
"read": [
"4eynwmic"
]
},
"subtractions": {
"read": [
"0nhpi36p"
]
}
},
"stage": "",
"state": "complete",
"status": [
{
"error": null,
"progress": 0,
"stage": null,
"state": "waiting",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T18:37:44.936000Z"
},
{
"error": null,
"progress": 3,
"stage": null,
"state": "preparing",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T18:41:20.647000Z"
},
{
"error": null,
"progress": 16,
"stage": "eliminate_otus",
"state": "running",
"step_description": "Map sample reads to reference OTUs and discard.",
"step_name": "Eliminate Otus",
"timestamp": "2022-07-08T18:48:11.287000Z"
},
{
"error": null,
"progress": 33,
"stage": "eliminate_subtraction",
"state": "running",
"step_description": "Map remaining reads to the subtraction and discard.",
"step_name": "Eliminate Subtraction",
"timestamp": "2022-07-08T19:00:24.291000Z"
},
{
"error": null,
"progress": 50,
"stage": "reunite_pairs",
"state": "running",
"step_description": "Reunite paired reads after elimination.",
"step_name": "Reunite Pairs",
"timestamp": "2022-07-08T19:02:53.618000Z"
},
{
"error": null,
"progress": 66,
"stage": "assemble",
"state": "running",
"step_description": "Assemble reads using SPAdes.",
"step_name": "Assemble",
"timestamp": "2022-07-08T19:02:53.644000Z"
},
{
"error": null,
"progress": 83,
"stage": "process_fasta",
"state": "running",
"step_description": "Find ORFs in the assembled contigs.",
"step_name": "Process Fasta",
"timestamp": "2022-07-08T19:07:22.352000Z"
},
{
"error": null,
"progress": 100,
"stage": "vfam",
"state": "running",
"step_description": "Search for viral motifs in ORF translations.",
"step_name": "Vfam",
"timestamp": "2022-07-08T19:07:44.531000Z"
},
{
"error": null,
"progress": 100,
"stage": "",
"state": "complete",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T19:13:04.293000Z"
}
],
"user": {
"administrator": false,
"handle": "jonathan",
"id": "88yksx67"
},
"workflow": "nuvs"
},
"status": "200"
}Cancel a job
Cancels a job using its 'job id'.
Errors
| Status | Description |
|---|---|
| 403 | Not permitted |
| 404 | Not found |
| 409 | Not cancellable |
Request
put
/jobs/{job_id}/cancel
Response
{
"example": {
"acquired": true,
"archived": false,
"args": {
"analysis_id": "rr8iryfy",
"index_id": "u3lm1rk8",
"ref_id": "d19exr83",
"sample_id": "4eynwmic",
"sample_name": "21BP088",
"subtractions": [
"0nhpi36p"
]
},
"created_at": "2022-07-08T18:37:44.936000Z",
"id": "splu0pq3",
"progress": 100,
"rights": {
"analyses": {
"modify": [
"rr8iryfy"
],
"read": [
"rr8iryfy"
],
"remove": [
"rr8iryfy"
]
},
"indexes": {
"read": [
"u3lm1rk8"
]
},
"references": {
"read": [
"d19exr83"
]
},
"samples": {
"read": [
"4eynwmic"
]
},
"subtractions": {
"read": [
"0nhpi36p"
]
}
},
"stage": "",
"state": "complete",
"status": [
{
"error": null,
"progress": 0,
"stage": null,
"state": "waiting",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T18:37:44.936000Z"
},
{
"error": null,
"progress": 3,
"stage": null,
"state": "preparing",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T18:41:20.647000Z"
},
{
"error": null,
"progress": 16,
"stage": "eliminate_otus",
"state": "running",
"step_description": "Map sample reads to reference OTUs and discard.",
"step_name": "Eliminate Otus",
"timestamp": "2022-07-08T18:48:11.287000Z"
},
{
"error": null,
"progress": 33,
"stage": "eliminate_subtraction",
"state": "running",
"step_description": "Map remaining reads to the subtraction and discard.",
"step_name": "Eliminate Subtraction",
"timestamp": "2022-07-08T19:00:24.291000Z"
},
{
"error": null,
"progress": 50,
"stage": "reunite_pairs",
"state": "running",
"step_description": "Reunite paired reads after elimination.",
"step_name": "Reunite Pairs",
"timestamp": "2022-07-08T19:02:53.618000Z"
},
{
"error": null,
"progress": 66,
"stage": "assemble",
"state": "running",
"step_description": "Assemble reads using SPAdes.",
"step_name": "Assemble",
"timestamp": "2022-07-08T19:02:53.644000Z"
},
{
"error": null,
"progress": 83,
"stage": "process_fasta",
"state": "running",
"step_description": "Find ORFs in the assembled contigs.",
"step_name": "Process Fasta",
"timestamp": "2022-07-08T19:07:22.352000Z"
},
{
"error": null,
"progress": 100,
"stage": "vfam",
"state": "running",
"step_description": "Search for viral motifs in ORF translations.",
"step_name": "Vfam",
"timestamp": "2022-07-08T19:07:44.531000Z"
},
{
"error": null,
"progress": 100,
"stage": "",
"state": "complete",
"step_description": null,
"step_name": null,
"timestamp": "2022-07-08T19:13:04.293000Z"
}
],
"user": {
"administrator": false,
"handle": "jonathan",
"id": "88yksx67"
},
"workflow": "nuvs"
},
"status": "200"
}