Package: gypsum 1.8.0

Aaron Lun

gypsum: Interface to the gypsum REST API

Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various adminstrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details.

Authors:Aaron Lun [aut, cre]

gypsum_1.8.0.tar.gz
gypsum_1.8.0.zip(r-4.7)gypsum_1.8.0.zip(r-4.6)gypsum_1.8.0.zip(r-4.5)
gypsum_1.8.0.tgz(r-4.6-any)gypsum_1.8.0.tgz(r-4.5-any)
gypsum_1.8.0.tar.gz(r-4.7-any)gypsum_1.8.0.tar.gz(r-4.6-any)
gypsum_1.8.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
gypsum/json (API)
NEWS

# Install 'gypsum' in R:
install.packages('gypsum', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/artifactdb/gypsum-r/issues

On BioConductor:gypsum-1.9.0(bioc 3.24)gypsum-1.8.0(bioc 3.23)

dataimport

4.78 score 1 stars 1 packages 20 scripts 47 exports 16 dependencies

Last updated from:35d37418ae (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING147
linux-devel-x86_64NOTE174
source / vignettesOK279
linux-release-x86_64NOTE159
macos-release-arm64NOTE112
macos-oldrel-arm64NOTE99
windows-develNOTE93
windows-releaseNOTE113
windows-oldrelNOTE98
wasm-releaseOK110

Exports:abortUploadaccessTokenapproveProbationcacheDirectorycloneVersioncompleteUploadcreateProjectdefineTextQueryfetchLatestfetchManifestfetchMetadataDatabasefetchMetadataSchemafetchPermissionsfetchQuotafetchSummaryfetchUsageformatObjectMetadatagsclistAssetslistFileslistProjectslistVersionsprepareDirectoryUploadpublicS3ConfigrefreshLatestrefreshUsagerejectProbationremoveAssetremoveProjectremoveVersionresolveLinksrestUrlsaveFilesaveVersionsearchMetadatasearchMetadataFiltersearchMetadataTextsearchMetadataTextFiltersetAccessTokensetPermissionssetQuotastartUploadtranslateTextQueryunlockProjectuploadDirectoryuploadFilesvalidateMetadata

Dependencies:askpassclicurlfilelockgluehttr2jsonlitelifecyclemagrittropensslR6rappdirsrlangsysvctrswithr

Interacting with the gypsum REST API

Aaron Lun

Rendered fromuserguide.Rmdusingknitr::rmarkdownon Jun 16 2026.

Last update: 2024-04-03
Started: 2023-12-06

Readme and manuals

Help Manual

Help pageTopics
Abort an uploadabortUpload
Get and set GitHub access tokensaccessToken setAccessToken
Approve a probational uploadapproveProbation
Cache directorycacheDirectory
Clone a version's directory structurecloneVersion
Complete an uploadcompleteUpload
Create a new projectcreateProject
Fetch the latest versionfetchLatest
Fetch version manifestfetchManifest
Fetch a metadata databasefetchMetadataDatabase
Fetch a metadata schemafetchMetadataSchema
Fetch project permissionsfetchPermissions
Fetch project quota detailsfetchQuota
Fetch version summaryfetchSummary
Fetch project usage detailsfetchUsage
Format object-related metadataformatObjectMetadata
List assetslistAssets
List files for a versionlistFiles
List all projectslistProjects
List asset versionslistVersions
Prepare to upload a directoryprepareDirectoryUpload
Public S3 configurationpublicS3Config
Refresh the latest versionrefreshLatest
Refresh the quota usagerefreshUsage
Reject a probational uploadrejectProbation
Remove an assetremoveAsset
Remove a projectremoveProject
Remove a version of an assetremoveVersion
Resolve links in the cache directoryresolveLinks
URL for the REST APIrestUrl
Save a file from a version of a project assetsaveFile
Save all files for a version of a project assetsaveVersion
Search the metadata databasedefineTextQuery gsc gypsum.search.clause Ops.gypsum.search.clause searchMetadata searchMetadataFilter searchMetadataText searchMetadataTextFilter
Set project permissionssetPermissions
Set project quotasetQuota
Start an uploadstartUpload
Translate a plain-text query to a gypsum.search.clausetranslateTextQuery
Unlock a projectunlockProject
Upload a directory to the gypsum backenduploadDirectory
Upload files for a versioned assetuploadFiles
Validate metadata against a JSON schemavalidateMetadata