https://github.com/bhklab/snakemake-kubernetes-api
Flask API to be used as the new data processing layer of ORCESTRA.
https://github.com/bhklab/snakemake-kubernetes-api
Last synced: about 2 months ago
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Flask API to be used as the new data processing layer of ORCESTRA.
- Host: GitHub
- URL: https://github.com/bhklab/snakemake-kubernetes-api
- Owner: bhklab
- Created: 2022-02-18T22:11:07.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2023-04-13T22:04:05.000Z (about 2 years ago)
- Last Synced: 2025-03-27T14:03:58.313Z (2 months ago)
- Language: Python
- Homepage:
- Size: 115 KB
- Stars: 2
- Watchers: 3
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# snakemake-kubernetes-api
Flask API used as the new data processing layer of ORCESTRA.
Refer to [this wiki page](https://github.com/bhklab/snakemake-kubernetes-api/wiki/Set-up-on-Compute-Canada-VM) for setting up and configuring the application.
## API End-points
**GET /api/pipeline/list**
Lists all pipelines.
Example:
```
curl http://Host_URL/api/pipeline/list
```
**POST /api/pipeline/create**
Creates a pipeline based on json object.
Example:
```
curl -X POST http://Host_URL/api/pipeline/create \
-H "Content-Type: application/json" \
-H "Authorization: AUTHORIZATION_TOKEN" \
-d SEE EXAMPLE JSON FILE (examples/create_pipeline_example.json)
```
**POST /api/pipeline/run**
Triggers a data object curation pipeline run.
Example:
```
curl -X POST http://Host_URL/api/pipeline/run \
-H "Content-Type: application/json" \
-H "Authorization: AUTHORIZATION_TOKEN" \
-d SEE EXAMPLE JSON FILE (examples/run_pipeline_example.json)
```
**GET /api/data_object/list**
Lists data objects.
Accepted parameters:
```
status (optional, by default it returns 'complete' and 'uploaded' data objects): processing, complete or uploaded
pipeline_name (optional): string value for pipeline name
latest (optional, defaults to 'false'): boolean, if true, returns the latest pipeline run filtered with other parameters.
```
Example:
```
curl http://Host_URL/api/data_object/list
```
**GET /api/data_object/download**
Downloads a data object to local storage.
Example:
```
curl 'http://Host_URL/api/data_object/download?data_obj_id=Data_Object_ID' --output File_Name
```
**POST /api/data_object/upload**
Uploads a data object to Zenodo.
Example:
```
curl -X POST http://Host_URL/api/data_object/upload \
-H "Content-Type: application/json" \
-H "Authorization: AUTHORIZATION_TOKEN" \
-d '{"data_obj_id": Data_Object_ID, 'deposition_id': Zenodo_Deposition_ID}'
```
```deposition_id``` is an optional parameter used to upload a data object as a new version of an already-existing object on Zenodo.
***Desposition id is the last 7 digits of the DOI of an existing data object in Zenodo.***
**GET /api/log/list**
Returns a list of log files for a pipeline.
Example:
```
curl http://Host_URL/api/logs?pipeline=Pipeline_Name
```
**GET /api/log/download**
Downloads a specified log file for a pipeline.
Example:
```
curl http://Host_URL/api/log/download?pipeline=Pipeline_Name&filename=Log_File_Name --output Log_File_Name
```
**GET /api/k8/error_pods**
If there is an error, Kubernetes pod will not be deleted. This API route gets a list of pods in error status.
Example:
```
curl http://Host_URL/api/k8/error_pods
```
**GET /api/k8/pod_log**
Returns Kubernetes log of a specified pod.
Example:
```
curl http://Host_URL/api/k8/pod_log?podname=Pod_Name_From_Snakemake_Log_Or_List_Of_K8_Error_Pods
```