gypsum

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 1.8.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: httr2, jsonlite, filelock, rappdirs
• Imports: httr2, jsonlite, filelock, rappdirs
• Install: BiocManager::install("gypsum")

When to Use

• Programmatically downloading files, manifests, and summaries from the gypsum bucket using saveFile, saveVersion, fetchManifest, and fetchSummary.
• Uploading files to the gypsum backend using the upload sequence: startUpload, uploadFiles, and completeUpload.
• Creating new versions of existing assets efficiently by deduplicating redundant files using cloneVersion and prepareDirectoryUpload.
• Validating metadata against the Bioconductor JSON schema prior to upload using validateMetadata.
• Managing project permissions, probational uploads, and quotas using setPermissions, approveProbation, and setQuota.

When NOT to Use

• For general-purpose cloud storage interactions (like raw Google Cloud Storage buckets) without an ArtifactDB backend, use packages like googleCloudStorageR instead.
• For downloading standard Bioconductor package source files or annotation resources, use BiocManager or AnnotationHub instead.
• For local-only file management and caching without a REST API backend, use BiocFileCache instead.

Data Requirements

• Input format: File paths, directory structures, or metadata lists formatted according to the ArtifactDB JSON schema.
• Authentication: Requires a GitHub OAuth token for write operations (uploads, deletions, permission changes), set via setAccessToken. Read operations are public.
• Network: Requires an active internet connection to communicate with the gypsum REST API endpoint.