Paolo Di Tommaso

Fix console "Plugin manager not initialised" warn

1

This PR fixed the warning reported by the Console when running a script more then one time > WARN: Plugin manager not initialised -- Using built-in executors

NGS toolkit should provide an API to set cache configuration options

1

Currently when accessing read collections by using the NGS API download reads are cached in the path `$HOME/ncbi/public` for open-access data, and the path $HOME/ncbi/dbGaP-xxxx for other. There's no way...

Use buildkit for container image builds

4

Wave uses [Kaniko](https://github.com/GoogleContainerTools/kaniko) to build container images. However this can be some compatibility and security issues. The goal of this task is to replace it with [Buildkit](https://github.com/moby/buildkit) which provides a...

When requesting the metrics for `pulls`,`fusion`, and `build` and providing the date parameter, the breakdown per org should be included in the response, in addition to the total per day.

This PR adds an interceptor class able to trace the elapsed time required to carry out the execution of the method(s) to which the `@TraceElapsedTime` annotation is applied.

### Context When a build request is submitted the build status is stored via the persistent service [here](https://github.com/seqeralabs/wave/blob/71188e687866873255f88f2c974de0579e1340d1/src/main/groovy/io/seqera/wave/service/builder/ContainerBuildServiceImpl.groovy#L241-L241) and later update [here](https://github.com/seqeralabs/wave/blob/71188e687866873255f88f2c974de0579e1340d1/src/main/groovy/io/seqera/wave/service/persistence/PersistenceService.groovy#L39-L39). This record is used to check build [status](https://github.com/seqeralabs/wave/blob/71188e687866873255f88f2c974de0579e1340d1/src/main/groovy/io/seqera/wave/controller/BuildController.groovy#L76-L76)...

Cleanup of complete blob upload jobs

5

The blob cache uses Kubernetes pods (and [job in the future](https://github.com/seqeralabs/wave/issues/475)) to upload them in the cache storage. Those jobs should be deleted when the upload is completed successfully. It...

Delete potential corrupted uploads

1

The [BlobCacheService](https://github.com/seqeralabs/wave/blob/1c3d08d198d05acd72a0b28c4aa798067da46215/src/main/groovy/io/seqera/wave/service/blob/BlobCacheService.groovy#L30-L30) uploads container image blobs to a cache (S3 bucket) in certain conditions. In the case the upload process is interrupted or fails for unexpected errors, a partially (corrupted)...

The goal of this issue is to include in this repo and the documentation the TypeSpec specification of the Wave endpoints and corresponding model objects. See [TypeSpec](https://typespec.io/) docs for further...

The [BlobCacheService](https://github.com/seqeralabs/wave/blob/1c3d08d198d05acd72a0b28c4aa798067da46215/src/main/groovy/io/seqera/wave/service/blob/BlobCacheService.groovy#L30-L30) uploads container image blobs to a cache (S3 bucket) in certain condition. The upload is made a via K8s pod, see [here](https://github.com/seqeralabs/wave/blob/1c3d08d198d05acd72a0b28c4aa798067da46215/src/main/groovy/io/seqera/wave/service/blob/impl/KubeTransferStrategy.groovy#L49-L58). This issue aims to use instead...