LoginSign Up
← Back to all sparks
I

ieugwasr

DEVOPS
Velocity0.0

Interface to the OpenGWAS Database API

github.com/MRCIEU/ieugwasr ↗

ieugwasr's release notes are a record of OpenGWAS tightening the tap.

gwasapi-clientrate-limitsbioinformaticsopengwas
◆Current state
ieugwasr is the R client for the OpenGWAS database of genome-wide association study summary statistics, and it also wraps plink for LD clumping and matrices. Every release in this window is about the client's relationship with the server: allowance depletion handling in 1.0.1, a new endpoint wrapper in 1.0.3, header bugs in 1.0.4, and new API limits on the associations endpoint in 1.1.0.
◆Where it's heading
The direction is set by the service, not the package. OpenGWAS has moved toward authenticated, quota-limited access, and each release absorbs another step — first detecting when an allowance is exhausted and erroring until it resets, later adapting to limits on a specific endpoint. Alongside that, the 1.0.4 rewrite of MR-Base references to OpenGWAS suggests the project is settling its identity after a rename.
◆Prediction
Expect further quota and authentication handling as OpenGWAS continues adjusting access policy, since that has driven the two most substantial releases here. Nothing in the entries points to new analysis capability.

◆Recent moves

  1. 1y ago

    ieugwasr 1.1.0 adapts to new associations endpoint limits

    The client absorbs new API limits on the associations endpoint, with better error handling and updated request headers. For users this decides whether large association queries fail cleanly or partway through, and it continues the quota arc that started with allowance checks in 1.0.1.

    View source ↗
  2. 1y ago

    ieugwasr 1.0.4 makes ld_clump find plink as documented

    ld_clump() and ld_matrix() now actually search for the plink binary the way the docs said they did — a gap between documentation and behavior that would have cost users real debugging time. The release also completes the MR-Base to OpenGWAS renaming and fixes an api_query() header bug.

    View source ↗
  3. 1y ago

    ieugwasr 1.0.3 adds gwasinfo_files() endpoint access

    A single function wrapping the /api/gwasinfo/files endpoint, giving users access to the underlying dataset files rather than only queried summaries. Small, and typical of how this client grows: one endpoint at a time as the server exposes it.

    View source ↗
  4. 2y ago

    ieugwasr 1.0.1 errors on depleted API allowance

    The client starts checking for allowance depletion and raising an error until the quota resets. This is the first entry in the arc that 1.1.0 continues, and it marks the point where OpenGWAS stopped behaving like an open endpoint.

    View source ↗