API overview¶
Warning
The OmicsDM API is using version 2 of the OpenAPI specification. For the purpose of this documentation, the swagger file is converted to version 3 using editor-next.swagger.io.
API 1.0¶
Servers¶
| Description | URL |
|---|---|
analysis¶
POST /api/analysis/¶
create a new project in Opal via Jenkins
Response 200 OK¶
POST /api/analysis/abort¶
abort an analysis
Response 200 OK¶
POST /api/analysis/data¶
create a new project in Opal via Jenkins
Response 200 OK¶
POST /api/analysis/files¶
create a new project in Opal via Jenkins
Response 200 OK¶
POST /api/analysis/results¶
create a new project in Opal via Jenkins
Response 200 OK¶
POST /api/analysis/run¶
create a new project in Opal via Jenkins
Response 200 OK¶
POST /api/analysis/start¶
Add a new analysis to the database
Response 200 OK¶
POST /api/analysis/status¶
get analysis status
Response 200 OK¶
POST /api/analysis/submissiondata¶
create a new project in Opal via Jenkins
Response 200 OK¶
POST /api/analysis/template/query¶
create a new project in Opal via Jenkins
Response 200 OK¶
POST /api/analysis/template/save¶
create a new project in Opal via Jenkins
Response 200 OK¶
POST /api/analysis/types¶
get possible analysis types based on the files
Response 200 OK¶
GET /api/analysis/viewcols¶
Get datasets view fields
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
test¶
GET /api/curltest¶
To test curl access
Response 200 OK¶
GET /api/tokentest¶
Response 200 OK¶
datasets¶
PUT /api/datasets/¶
update a Dataset of a certain userid
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
POST /api/datasets/admin/update¶
Update dataset(s)
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
POST /api/datasets/admin/view¶
Get all the dataset data
Response 200 OK¶
POST /api/datasets/adminviewcols¶
Get datasets admin columns
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
POST /api/datasets/all¶
Get all the datasets data by keycloak group
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Request body
application/json
This example has been generated automatically from the schema and it is not accurate. Refer to the schema for more information.Schema of the request body
{
"type": "object",
"properties": {
"pageSize": {
"type": "integer",
"description": "Number of datasets per page"
},
"page": {
"type": "integer",
"description": "Page number"
},
"sorted": {
"type": "string",
"description": "Sorted by"
},
"filtered": {
"type": "string",
"description": "Filtered by"
}
}
}
Response 200 OK¶
Response 500 Internal Server Error¶
POST /api/datasets/clinical/uploadfinish¶
create a presigned url for the clinical data upload
Description and store it in the database
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
POST /api/datasets/create¶
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
POST /api/datasets/list¶
Get all datasets by keycloak group and filtered by project_id
Description Returns list of all dataset IDs of the user's kc group; can be filtered by dataset id
(additionally it can be filtered by the dataset_id)
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
POST /api/datasets/policy/uploadfinish¶
create a presigned url for the dataset policy upload
Description and store it in the database
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
POST /api/datasets/submissioncols¶
Get the columnn specification for the dataset submission
Description Modify the columns for dataset submission
from the project table
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
POST /api/datasets/validate¶
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
GET /api/datasets/viewcols¶
Get datasets view fields
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
files¶
GET /api/files/¶
sign request
Description github.com/TTLabs/EvaporateJS/blob/master/example/signing_example.py
Response 200 OK¶
POST /api/files/admin/update¶
Update file(s)
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
POST /api/files/admin/view¶
Get all the file data
Response 200 OK¶
POST /api/files/adminviewcols¶
Get datasets view fields
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
POST /api/files/all¶
Response 200 OK¶
POST /api/files/cellxgene¶
Response 200 OK¶
POST /api/files/disable¶
Response 200 OK¶
POST /api/files/donwnload¶
Response 200 OK¶
POST /api/files/download¶
Response 200 OK¶
POST /api/files/finishupload¶
Response 200 OK¶
POST /api/files/startupload¶
Response 200 OK¶
GET /api/files/submissioncols¶
Get file submission fields
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
POST /api/files/viewcols¶
Get datasets view fields
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
projects¶
POST /api/projects/¶
Update a project
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
POST /api/projects/admin/update¶
Update a project
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
POST /api/projects/admin/view¶
Get all the project data
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
POST /api/projects/adminviewcols¶
Get project submission fields
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
POST /api/projects/all¶
Get all the projects data by keycloak group
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
POST /api/projects/create¶
Create a new project
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
GET /api/projects/submissioncols¶
Get project submission fields
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
POST /api/projects/validate¶
Description Returns...
Input parameters
| Parameter | In | Type | Default | Nullable | Description |
|---|---|---|---|---|---|
| Authorization | header | string | No |
Response 200 OK¶
Response 500 Internal Server Error¶
template¶
GET /api/template/¶
get the template
Response 200 OK¶
Schemas¶
All_DATASETS_GET_RESPONSE¶
| Name | Type |
|---|---|
| filtered | string |
| page | integer |
| pageSize | integer |
| sorted | string |
Common responses¶
This section describes common responses that are reused across operations.
ParseError¶
When a mask can't be parsed
MaskError¶
When any error occurs on mask
ApiException¶
Return custom JSON when APIException is raised
Tags¶
| Name | Description |
|---|---|
| test | test related operations |
| template | template related operations |
| projects | projects related operations |
| datasets | datasets related operations |
| files | files related operations |
| analysis | analysis related operations |