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-any)gypsum_1.8.0.zip(r-4.6-any)gypsum_1.8.0.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
gypsum/json (API)

# 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

5.53 score 1 stars 1 packages 20 scripts 5.6k downloads 47 exports 16 dependencies

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

Target	Result	Time
bioc-checks	WARNING	168
linux-devel	NOTE	231
source / vignettes	OK	176
linux-release	NOTE	238
macos-release	NOTE	111
macos-oldrel	NOTE	128
windows-devel	NOTE	101
windows-release	NOTE	100
windows-oldrel	NOTE	85
wasm-release	OK	111

Exports:abortUpload accessToken approveProbation cacheDirectory cloneVersion completeUpload createProject defineTextQuery fetchLatest fetchManifest fetchMetadataDatabase fetchMetadataSchema fetchPermissions fetchQuota fetchSummary fetchUsage formatObjectMetadata gsc listAssets listFiles listProjects listVersions prepareDirectoryUpload publicS3Config refreshLatest refreshUsage rejectProbation removeAsset removeProject removeVersion resolveLinks restUrl saveFile saveVersion searchMetadata searchMetadataFilter searchMetadataText searchMetadataTextFilter setAccessToken setPermissions setQuota startUpload translateTextQuery unlockProject uploadDirectory uploadFiles validateMetadata

Dependencies:askpass cli curl filelock glue httr2 jsonlite lifecycle magrittr openssl R6 rappdirs rlang sys vctrs withr

Interacting with the gypsum REST API

Rendered fromuserguide.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Abort an upload	abortUpload
Get and set GitHub access tokens	accessToken setAccessToken
Approve a probational upload	approveProbation
Cache directory	cacheDirectory
Clone a version's directory structure	cloneVersion
Complete an upload	completeUpload
Create a new project	createProject
Fetch the latest version	fetchLatest
Fetch version manifest	fetchManifest
Fetch a metadata database	fetchMetadataDatabase
Fetch a metadata schema	fetchMetadataSchema
Fetch project permissions	fetchPermissions
Fetch project quota details	fetchQuota
Fetch version summary	fetchSummary
Fetch project usage details	fetchUsage
Format object-related metadata	formatObjectMetadata
List assets	listAssets
List files for a version	listFiles
List all projects	listProjects
List asset versions	listVersions
Prepare to upload a directory	prepareDirectoryUpload
Public S3 configuration	publicS3Config
Refresh the latest version	refreshLatest
Refresh the quota usage	refreshUsage
Reject a probational upload	rejectProbation
Remove an asset	removeAsset
Remove a project	removeProject
Remove a version of an asset	removeVersion
Resolve links in the cache directory	resolveLinks
URL for the REST API	restUrl
Save a file from a version of a project asset	saveFile
Save all files for a version of a project asset	saveVersion
Search the metadata database	defineTextQuery gsc gypsum.search.clause Ops.gypsum.search.clause searchMetadata searchMetadataFilter searchMetadataText searchMetadataTextFilter
Set project permissions	setPermissions
Set project quota	setQuota
Start an upload	startUpload
Translate a plain-text query to a gypsum.search.clause	translateTextQuery
Unlock a project	unlockProject
Upload a directory to the gypsum backend	uploadDirectory
Upload files for a versioned asset	uploadFiles
Validate metadata against a JSON schema	validateMetadata