Package 'gypsum' reference manual

Title:	Interface to the gypsum REST API
Description:	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]
Maintainer:	Aaron Lun <[email protected]>
License:	MIT + file LICENSE
Version:	1.1.6
Built:	2024-09-19 03:13:30 UTC
Source:	https://github.com/bioc/gypsum

Abort an upload

Description

Abort an upload session, usually after an irrecoverable error.

Usage

abortUpload(init, url = restUrl())
abortUpload(init, url = restUrl())

Arguments

`init`	List containing `abort_url` and `session_token`. This is typically the return value from `startUpload`.
`url`	String containing the URL of the gypsum REST API.

Value

NULL is invisibly returned on successful abort.

Author(s)

Aaron Lun

Examples

tmp <- tempfile()
dir.create(tmp)
write(file=file.path(tmp, "blah.txt"), LETTERS)
dir.create(file.path(tmp, "foo"))
write(file=file.path(tmp, "foo", "bar.txt"), 1:10)

if (interactive()) {
    init <- startUpload(
        project="test-R", 
        asset="upload-abort-check", 
        version="v1", 
        files=list.files(tmp, recursive=TRUE),
        probation=TRUE,
        directory=tmp
    )

    # Aborting the upload.
    abortUpload(init) 
}

tmp <- tempfile()
dir.create(tmp)
write(file=file.path(tmp, "blah.txt"), LETTERS)
dir.create(file.path(tmp, "foo"))
write(file=file.path(tmp, "foo", "bar.txt"), 1:10)

if (interactive()) {
    init <- startUpload(
        project="test-R", 
        asset="upload-abort-check", 
        version="v1", 
        files=list.files(tmp, recursive=TRUE),
        probation=TRUE,
        directory=tmp
    )

    # Aborting the upload.
    abortUpload(init) 
}

Get and set GitHub access tokens

Description

Get and set GitHub access tokens for authentication to the gypsum API's endpoints.

Usage

accessToken(full = FALSE, request = TRUE, cache = cacheDirectory())

setAccessToken(
  token,
  app.url = restUrl(),
  app.key = NULL,
  app.secret = NULL,
  github.url = "https://api.github.com",
  user.agent = NULL,
  cache = cacheDirectory()
)
accessToken(full = FALSE, request = TRUE, cache = cacheDirectory())

setAccessToken(
  token,
  app.url = restUrl(),
  app.key = NULL,
  app.secret = NULL,
  github.url = "https://api.github.com",
  user.agent = NULL,
  cache = cacheDirectory()
)

Arguments

`full`	Logical scalar indicating whether to return the full token details.
`request`	Logical scalar indicating whether to request a new token if no cached token is available or if the current token has expired.
`cache`	String containing a path to the cache directory, to store the token across R sessions. If `NULL`, the token is not cached to (or read from) disk, which improves security on shared filesystems.
`token`	String containing a GitHub personal access token. This should have the `"read:org"` and `"read:user"` scopes. If missing, the user will be prompted to use GitHub's Oauth web application flow to acquire a token. If `NULL`, any existing tokens are cleared from cache.
`app.url`	String containing a URL of the gypsum REST API. This is used to obtain `app.key` and `app.secret` if either are `NULL`.
`app.key`	String containing the key for a GitHub Oauth app.
`app.secret`	String containing the secret for a GitHub Oauth app.
`github.url`	String containing the URL for the GitHub API. This is used to acquire more information about the token.
`user.agent`	String specifying the user agent for queries to various endpoints.

Value

setAccessToken sets the access token and invisibly returns a list containing:

token, a string containing the token.
name, the name of the GitHub user authenticated by the token.
expires, the Unix time at which the token expires.

If full=TRUE, accessToken returns the same list, typically retrieved from one of the caches. If no token was cached or the cached token has expired, it will call setAccessToken with default arguments to obtain one if request=TRUE; otherwise if request=FALSE, NULL is returned.

If full=FALSE, accessToken will return a string containing a token (or NULL, if no token is available and request=FALSE).

Author(s)

Aaron Lun

Examples

if (interactive()) {
    accessToken()
}
if (interactive()) {
    accessToken()
}

Approve a probational upload

Description

Pretty much as it says: approve a probational upload of a version of a project's asset. This removes the on_probation tag from the uploaded version.

Usage

approveProbation(
  project,
  asset,
  version,
  url = restUrl(),
  token = accessToken()
)
approveProbation(
  project,
  asset,
  version,
  url = restUrl(),
  token = accessToken()
)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`version`	String containing the version name.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to an owner of `project`.

Value

NULL is invisibly returned upon successful approval.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    # Mocking up a versioned asset.
    init <- startUpload(
        project="test-R", 
        asset="probation-approve", 
        version="v1", 
        files=character(0),
        probation=TRUE
    )
    completeUpload(init) 

    # Approving the probation:
    approveProbation("test-R", "probation-approve", "v1")

    # Just cleaning up after we're done.
    removeProjectAsset("test-R", "probation-approve")
}

if (interactive()) {
    # Mocking up a versioned asset.
    init <- startUpload(
        project="test-R", 
        asset="probation-approve", 
        version="v1", 
        files=character(0),
        probation=TRUE
    )
    completeUpload(init) 

    # Approving the probation:
    approveProbation("test-R", "probation-approve", "v1")

    # Just cleaning up after we're done.
    removeProjectAsset("test-R", "probation-approve")
}

Cache directory

Description

Specify the cache directory in the local filesystem for gypsum-related data.

Usage

cacheDirectory(dir)
cacheDirectory(dir)

Arguments

dir

String containing the path to a cache directory.

Details

If the GYPSUM_CACHE_DIR environment variable is set before the first call to cacheDirectory, it is used as the initial location of the cache directory. Otherwise, the initial location is based on R_user_dir.

Value

If dir is missing, the current setting of the cache directory is returned.

If dir is provided, it is used to replace the current setting of the cache directory, and the previous setting is invisibly returned.

Author(s)

Aaron Lun

Examples

cacheDirectory()
old <- cacheDirectory(tempfile())
cacheDirectory()
cacheDirectory(old) # setting it back.

cacheDirectory()
old <- cacheDirectory(tempfile())
cacheDirectory()
cacheDirectory(old) # setting it back.

Clone a version's directory structure

Description

Clone the directory structure for a versioned asset into a separate location. This is typically used to prepare a new version for a lightweight upload.

Usage

cloneVersion(
  project,
  asset,
  version,
  destination,
  download = TRUE,
  cache = cacheDirectory(),
  url = restUrl(),
  config = NULL,
  ...
)
cloneVersion(
  project,
  asset,
  version,
  destination,
  download = TRUE,
  cache = cacheDirectory(),
  url = restUrl(),
  config = NULL,
  ...
)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`version`	String containing the version name.
`destination`	String containing a path to a destination directory at which to create the clone.
`download`	Logical scalar indicating whether the version's files should be downloaded first. This can be set to `FALSE` to create a clone without actually downloading any of the version's files.
`cache`	String containing the path to the cache directory.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.
`...`	Further arguments to pass to `saveVersion`. Only used if `download=TRUE`.

Details

Cloning of a versioned asset involves creating a directory at destination that has the same contents as the corresponding project-asset-version directory. All files in the specified version are represented as symlinks from destination to the corresponding file in the cache. The idea is that, when destination is used in prepareDirectoryUpload, the symlinks are converted into upload links, i.e., links= in startUpload. This allows users to create new versions very cheaply as duplicate files are not uploaded to/stored in the backend.

Users can more-or-less do whatever they want inside the cloned destination, but they should treat the symlink targets as read-only. That is, they should not modify the contents of the linked-to file, as these refer to assumed-immutable files in the cache. If a file in destination needs to be modified, the symlink should be deleted and replaced with an actual file; this avoids mutating the cache and it ensures that prepareDirectoryUpload recognizes that a new file actually needs to be uploaded.

Advanced users can set download=FALSE, in which case symlinks are created even if their targets are not present in cache. In such cases, destination should be treated as write-only due to the potential presence of dangling symlinks. This mode is useful for uploading a new version of an asset without downloading the files from the existing version, assuming that the modifications associated with the former can be achieved without reading any of the latter.

On Windows, the user may not have permissions to create symbolic links, so the function will transparently fall back to creating hard links or copies instead. This precludes any optimization by prepareDirectoryUpload as the hard links/copies cannot be converted into upload links. It also assumes that download=TRUE as dangling links/copies cannot be created.

Value

The directory structure of the specified version is cloned to destination, and a NULL is invisibly returned.

Author(s)

Aaron Lun

Examples

tmp <- tempfile()
out <- cloneVersion("test-R", "basic", "v1", destination=tmp)
list.files(tmp, recursive=TRUE)
Sys.readlink(file.path(tmp, "foo", "bar.txt"))

# Files should be replaced rather than modified via the symlink:
existing <- file.path(tmp, "foo", "bar.txt")
unlink(existing) # Deleting the symlink...
write(file=existing, "YAY") # ... and writing a replacement file.

# Symlinks are converted to upload links:
prepareDirectoryUpload(tmp)
tmp <- tempfile()
out <- cloneVersion("test-R", "basic", "v1", destination=tmp)
list.files(tmp, recursive=TRUE)
Sys.readlink(file.path(tmp, "foo", "bar.txt"))

# Files should be replaced rather than modified via the symlink:
existing <- file.path(tmp, "foo", "bar.txt")
unlink(existing) # Deleting the symlink...
write(file=existing, "YAY") # ... and writing a replacement file.

# Symlinks are converted to upload links:
prepareDirectoryUpload(tmp)

Complete an upload

Description

Complete an upload session after all files have been uploaded.

Usage

completeUpload(init, url = restUrl())
completeUpload(init, url = restUrl())

Arguments

`init`	List containing `complete_url` and `session_token`. This is typically the return value from `startUpload`.
`url`	String containing the URL of the gypsum REST API.

Value

NULL is invisibly returned on successful completion.

Author(s)

Aaron Lun

Examples

tmp <- tempfile()
dir.create(tmp)
write(file=file.path(tmp, "blah.txt"), LETTERS)
dir.create(file.path(tmp, "foo"))
write(file=file.path(tmp, "foo", "bar.txt"), 1:10)

if (interactive()) {
    init <- startUpload(
        project="test-R", 
        asset="upload-complete-check", 
        version="v1", 
        files=list.files(tmp, recursive=TRUE),
        probation=TRUE,
        directory=tmp
    )
    uploadFiles(init, directory=tmp)

    # Finishing the upload.
    completeUpload(init) 
}

tmp <- tempfile()
dir.create(tmp)
write(file=file.path(tmp, "blah.txt"), LETTERS)
dir.create(file.path(tmp, "foo"))
write(file=file.path(tmp, "foo", "bar.txt"), 1:10)

if (interactive()) {
    init <- startUpload(
        project="test-R", 
        asset="upload-complete-check", 
        version="v1", 
        files=list.files(tmp, recursive=TRUE),
        probation=TRUE,
        directory=tmp
    )
    uploadFiles(init, directory=tmp)

    # Finishing the upload.
    completeUpload(init) 
}

Create a new project

Description

Create a new project with the associated permissions.

Usage

createProject(
  project,
  owners,
  uploaders = list(),
  baseline = NULL,
  growth = NULL,
  year = NULL,
  url = restUrl(),
  token = accessToken()
)
createProject(
  project,
  owners,
  uploaders = list(),
  baseline = NULL,
  growth = NULL,
  year = NULL,
  url = restUrl(),
  token = accessToken()
)

Arguments

`project`	String containing the project name.
`owners`	Character vector containing the GitHub users or organizations that are owners of this project.
`uploaders`	List specifying the authorized uploaders for this project. See the `uploaders` field in the `fetchPermissions` return value for the expected format.
`baseline`	Numeric scalar specifying the baseline quota in bytes. If `NULL`, the backend's default is used.
`growth`	Numeric scalar specifying the quota's annual growth rate in bytes. If `NULL`, the backend's default is used.
`year`	Integer scalar specifying the year of the project creation. If `NULL`, the backend's default is used - this should be the current year.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to a gypsum administrator account.

Value

NULL is invisibly returned if the project was successfully created.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    createProject(
        "test-R-create", 
        owners="LTLA", 
        uploaders=list(list(id="ArtifactDB-bot"))
    )
}
if (interactive()) {
    createProject(
        "test-R-create", 
        owners="LTLA", 
        uploaders=list(list(id="ArtifactDB-bot"))
    )
}

Fetch the latest version

Description

Fetch the latest version of a project's asset.

Usage

fetchLatest(project, asset, url = restUrl(), config = NULL)
fetchLatest(project, asset, url = restUrl(), config = NULL)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

String containing the latest version of the project.

Author(s)

Aaron Lun

Examples

fetchLatest("test-R", "basic")

fetchLatest("test-R", "basic")

Fetch version manifest

Description

Fetch the manifest for a version of an asset of a project.

Usage

fetchManifest(
  project,
  asset,
  version,
  cache = cacheDirectory(),
  overwrite = FALSE,
  url = restUrl(),
  config = NULL
)
fetchManifest(
  project,
  asset,
  version,
  cache = cacheDirectory(),
  overwrite = FALSE,
  url = restUrl(),
  config = NULL
)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`version`	String containing the version name.
`cache`	String containing the cache directory. If `NULL`, no caching is performed.
`overwrite`	Logical scalar indicating whether to overwrite an existing file in `cache`, if one is present.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

List containing the manifest for this version. Each element is named after the relative path of a file in this version. The value of each element is another list with the following fields:

size, an integer specifying the size of the file in bytes.
md5sum, a string containing the hex-encoded MD5 checksum of the file.
link (optional): a list specifying the link destination for a file. This contains the strings project, asset, version and path. If the link destination is itself a link, an ancestor list will be present that specifies the final location of the file after resolving all intermediate links.

Author(s)

Aaron Lun

Examples

fetchManifest("test-R", "basic", "v1")

fetchManifest("test-R", "basic", "v1")

Fetch a metadata database

Description

Fetch a SQLite database containing metadata from the gypsum backend (see https://github.com/ArtifactDB/bioconductor-metadata-index). Each database is generated by aggregating metadata across multiple assets and/or projects, and can be used to perform searches for interesting objects.

Usage

fetchMetadataDatabase(
  name = "bioconductor.sqlite3",
  cache = cacheDirectory(),
  overwrite = FALSE
)
fetchMetadataDatabase(
  name = "bioconductor.sqlite3",
  cache = cacheDirectory(),
  overwrite = FALSE
)

Arguments

`name`	String containing the name of the database. This can be the name of any SQLite file in https://github.com/ArtifactDB/bioconductor-metadata-index/releases/tag/latest.
`cache`	String containing the cache directory. If `NULL`, no caching is performed.
`overwrite`	Logical scalar indicating whether to overwrite an existing file in `cache`, if one is present.

Details

This function will automatically check for updates to the SQLite files and will download new versions accordingly. New checks are performed when one hour or more has elapsed since the last check. If the check fails, a warning is raised and the function returns the currently cached file.

Value

String containing a path to the downloaded database.

Author(s)

Aaron Lun

Examples

fetchMetadataDatabase()
fetchMetadataDatabase()

Fetch a metadata schema

Description

Fetch a JSON schema file for metadata to be inserted into a SQLite database (see https://github.com/ArtifactDB/bioconductor-metadata-index). Each SQLite database is created from metadata files uploaded to the gypsum backend, so clients uploading objects to be incorporated into the database should validate their metadata against the corresponding JSON schema.

Usage

fetchMetadataSchema(
  name = "bioconductor/v1.json",
  cache = cacheDirectory(),
  overwrite = FALSE
)
fetchMetadataSchema(
  name = "bioconductor/v1.json",
  cache = cacheDirectory(),
  overwrite = FALSE
)

Arguments

`name`	String containing the name of the schema. This can be the name of any JSON schema file published at https://github.com/ArtifactDB/bioconductor-metadata-index.
`cache`	String containing the cache directory. If `NULL`, no caching is performed.
`overwrite`	Logical scalar indicating whether to overwrite an existing file in `cache`, if one is present.

Value

String containing a path to the downloaded schema.

Author(s)

Aaron Lun

Examples

fetchMetadataSchema()
fetchMetadataSchema()

Fetch project permissions

Description

Fetch the permissions for a project.

Usage

fetchPermissions(project, url = restUrl(), config = NULL)
fetchPermissions(project, url = restUrl(), config = NULL)

Arguments

`project`	String containing the project name.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

List containing the permissions for this project. This has the following elements:

owners, a character vector containing the GitHub users or organizations that are owners of this project.
uploaders, a list of lists specifying the users or organizations who are authorzied to upload to this project. Each entry is a list with the following fields:
- id, a string containing the GitHub user or organization that is authorized to upload.
- (optional) asset, a string containing the name of the asset that the uploader is allowed to upload to. If not provided, there is no restriction on the uploaded asset name.
- (optional) version, a string containing the name of the version that the uploader is allowed to upload to. If not provided, there is no restriction on the uploaded version name.
- (optional) until, a POSIXct object containing the expiry date of this authorization. If not provided, the authorization does not expire.
- (optional) trusted, whether the uploader is trusted. If not provided, defaults to FALSE.

Author(s)

Aaron Lun

Examples

fetchPermissions("test-R")

fetchPermissions("test-R")

Fetch project quota details

Description

Fetch the quota details for a project.

Usage

fetchQuota(project, url = restUrl(), config = NULL)
fetchQuota(project, url = restUrl(), config = NULL)

Arguments

`project`	String containing the project name.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

List containing baseline, the baseline quota at time zero in bytes; growth_rate, the annual growth rate for the quota in bytes; and year, the creation year (i.e., time zero) for this project.

Author(s)

Aaron Lun

Examples

fetchQuota("test-R")

fetchQuota("test-R")

Fetch version summary

Description

Fetch the summary for a version of an asset of a project.

Usage

fetchSummary(
  project,
  asset,
  version,
  cache = cacheDirectory(),
  overwrite = FALSE,
  url = restUrl(),
  config = NULL
)
fetchSummary(
  project,
  asset,
  version,
  cache = cacheDirectory(),
  overwrite = FALSE,
  url = restUrl(),
  config = NULL
)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`version`	String containing the version name.
`cache`	String containing the cache directory. If `NULL`, no caching is performed.
`overwrite`	Logical scalar indicating whether to overwrite an existing file in `cache`, if one is present.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

List containing the summary for this version, with the following fields:

upload_user_id, string containing the identity of the uploader.
upload_start, a POSIXct object containing the upload start time.
upload_finish, a POSIXct object containing the upload finish time.
on_probation (optional), a logical scalar indicating whether the upload is probational. If missing, this can be assumed to be FALSE.

Author(s)

Aaron Lun

Examples

fetchSummary("test-R", "basic", "v1")

fetchSummary("test-R", "basic", "v1")

Fetch project usage details

Description

Fetch the quota usage for a project.

Usage

fetchUsage(project, url = restUrl(), config = NULL)
fetchUsage(project, url = restUrl(), config = NULL)

Arguments

`project`	String containing the project name.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

Numeric scalar specifying the quota usage for the project, in bytes.

Author(s)

Aaron Lun

Examples

fetchUsage("test-R")

fetchUsage("test-R")

Format object-related metadata

Description

Create object-related metadata to validate against the default schema from fetchMetadataSchema. This is intended for downstream package developers who are auto-generating metadata documents to be validated by validateMetadata.

Usage

formatObjectMetadata(x)
formatObjectMetadata(x)

Arguments

`x`	An R object, typically an instance of a Bioconductor class.

Value

List containing the object-related metadata, typically stored in the applications.takane field of the metadata.

Author(s)

Aaron Lun

Examples

df <- S4Vectors::DataFrame(alpha=LETTERS, numeric=runif(26))
formatObjectMetadata(df)

df <- S4Vectors::DataFrame(alpha=LETTERS, numeric=runif(26))
formatObjectMetadata(df)

List assets

Description

List all assets in a project.

Usage

listAssets(project, url = restUrl(), config = NULL)
listAssets(project, url = restUrl(), config = NULL)

Arguments

`project`	String containing the project name.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

Character vector of asset names.

Author(s)

Aaron Lun

Examples

listAssets("test-R")

listAssets("test-R")

List files for a version

Description

List files belonging to a version of a project asset.

Usage

listFiles(
  project,
  asset,
  version,
  prefix = NULL,
  include.. = TRUE,
  url = restUrl(),
  config = NULL
)
listFiles(
  project,
  asset,
  version,
  prefix = NULL,
  include.. = TRUE,
  url = restUrl(),
  config = NULL
)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`version`	String containing the version name.
`prefix`	String containing the remaining prefix for the object key. If provided, a file is only listed if its object key starts with `{project}/{asset}/{version}/{prefix}`. If `NULL`, all files associated with this version of the asset are listed.
`include..`	Logical scalar indicating whether to list files with `/..` in their object keys.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

Character vector of relative paths of files associated with the versioned asset.

Author(s)

Aaron Lun

Examples

listFiles("test-R", "basic", "v1")

listFiles("test-R", "basic", "v1")

List all projects

Description

List all projects in the gypsum backent.

Usage

listProjects(url = restUrl(), config = NULL)
listProjects(url = restUrl(), config = NULL)

Arguments

`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

Character vector of project names.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    listProjects()
}

if (interactive()) {
    listProjects()
}

List asset versions

Description

List all versions of a project asset.

Usage

listVersions(project, asset, url = restUrl(), config = NULL)
listVersions(project, asset, url = restUrl(), config = NULL)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

Character vector of versions.

Author(s)

Aaron Lun

Examples

listVersions("test-R", "basic")

listVersions("test-R", "basic")

Prepare to upload a directory

Description

Prepare to upload a directory's contents via startUpload. This goes through the directory to list its contents and convert symlinks to upload links.

Usage

prepareDirectoryUpload(
  directory,
  links = c("auto", "always", "never"),
  cache = cacheDirectory()
)
prepareDirectoryUpload(
  directory,
  links = c("auto", "always", "never"),
  cache = cacheDirectory()
)

Arguments

directory

String containing the path to a directory, the contents of which are to be uploaded via startUpload.

links

String indicating how to handle symlinks in directory.

"auto" will attempt to convert symlinks into upload links. If the conversion fails, a regular upload is performed.
"always" will attempt to convert symlinks into upload links. If the conversion fails, an error is raised.
"never" will never attempt to convert symlinks into upload links. All symlinked files are treated as regular uploads.

cache

String containing a path to the cache directory, used to convert symlinks into upload links.

Details

Files in directory (that are not symlinks) are used as regular uploads, i.e., files= in startUpload.

If directory contains a symlink to a file in cache, we assume that it points to a file that was previously downloaded by, e.g., saveFile or saveVersion. Thus, instead of performing a regular upload, we attempt to create an upload link, i.e., links= in startUpload. This is achieved by examining the destination path of the symlink and inferring the link destination in the backend. Note that this still works if the symlinks are dangling.

If a symlink cannot be converted into an upload link, it will be used as a regular upload, i.e., the contents of the symlink destination will be uploaded by startUpload. In this case, an error will be raised if the symlink is dangling as there is no file that can actually be uploaded. If links="always", an error is raised instead upon symlink conversion failure.

This function is intended to be used with cloneVersion, which creates symlinks to files in cache.

Value

List containing files, a character vector to be used as files= in startUpload; and links, a data frame to be used as links= in startUpload.

Examples

tmp <- tempfile()
out <- cloneVersion("test-R", "basic", "v1", destination=tmp)
write(file=file.path(tmp, "heanna"), "sumire")
prepareDirectoryUpload(tmp)

tmp <- tempfile()
out <- cloneVersion("test-R", "basic", "v1", destination=tmp)
write(file=file.path(tmp, "heanna"), "sumire")
prepareDirectoryUpload(tmp)

Public S3 configuration

Description

Fetch S3 credentials and other configuration details for read-only access to the underlying gypsum bucket.

Usage

publicS3Config(refresh = FALSE, url = restUrl(), cache = cacheDirectory())
publicS3Config(refresh = FALSE, url = restUrl(), cache = cacheDirectory())

Arguments

`refresh`	Logical scalar indicating whether to refresh the credentials in the in-memory cache.
`url`	String containing a URL to the gypsum REST API.
`cache`	String containing a path to the cache directory, to store the configuration across R sessions.

Details

The configuration is obtained through a query to url on the first use of this function. The result is automatically cached in memory and on disk to reduce the number of network requests to the API. New credentials are automatically fetched if the on-disk cache is older than a week; this refresh can be performed manually by calling this function with refresh=TRUE.

Value

List containing:

key, a string containing the read-only S3 access key ID.
secret, a string containing the associated S3 access secret.
bucket, a string containing the name of the bucket.
endpoint, a string containing the URL for the S3 API.

Author(s)

Aaron Lun

Examples

publicS3Config()

publicS3Config()

Refresh the latest version

Description

Recompute the latest version of a project's asset. This is useful on rare occasions where multiple simultaneous uploads cause the latest version to be slightly out of sync.

Usage

refreshLatest(project, asset, url = restUrl(), token = accessToken())
refreshLatest(project, asset, url = restUrl(), token = accessToken())

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to a gypsum administrator account.

Value

String containing the latest version of the project, or NULL if there are no non-probational versions.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    refreshLatest("test-R", "basic")
}

if (interactive()) {
    refreshLatest("test-R", "basic")
}

Refresh the quota usage

Description

Recompute the quota usage of a project. This is useful on rare occasions where multiple simultaneous uploads cause the usage calculations to be out of sync.

Usage

refreshUsage(project, url = restUrl(), token = accessToken())
refreshUsage(project, url = restUrl(), token = accessToken())

Arguments

`project`	String containing the project name.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to a gypsum administrator account.

Value

Numeric scalar specifying the total quota usage of this project, in bytes.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    refreshUsage("test-R")
}

if (interactive()) {
    refreshUsage("test-R")
}

Reject a probational upload

Description

Pretty much as it says: reject a probational upload of a version of a project's asset. This removes all files associated with that version.

Usage

rejectProbation(
  project,
  asset,
  version,
  url = restUrl(),
  token = accessToken()
)
rejectProbation(
  project,
  asset,
  version,
  url = restUrl(),
  token = accessToken()
)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`version`	String containing the version name.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to an owner of `project`.

Value

NULL is invisibly returned upon successful rejection.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    # Mocking up a versioned asset.
    init <- startUpload(
        project="test-R", 
        asset="probation-reject", 
        version="v1", 
        files=character(0),
        probation=TRUE
    )
    completeUpload(init) 

    # Rejecting the probation:
    rejectProbation("test-R", "probation-reject", "v1")
}

if (interactive()) {
    # Mocking up a versioned asset.
    init <- startUpload(
        project="test-R", 
        asset="probation-reject", 
        version="v1", 
        files=character(0),
        probation=TRUE
    )
    completeUpload(init) 

    # Rejecting the probation:
    rejectProbation("test-R", "probation-reject", "v1")
}

Remove an asset

Description

Remove an asset of a project from the gypsum backend.

Usage

removeAsset(project, asset, url = restUrl(), token = accessToken())
removeAsset(project, asset, url = restUrl(), token = accessToken())

Arguments

`project`	String containing the project to remove.
`asset`	String containing the asset to remove.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to a gypsum administrator account.

Value

NULL is invisibly returned if the asset was successfully removed.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    # Mocking up a versioned asset.
    init <- startUpload(
        project="test-R", 
        asset="removal", 
        version="v1", 
        files=character(0),
        probation=TRUE
    )
    completeUpload(init) 

    removeAsset("test-R", asset="removal")
}
if (interactive()) {
    # Mocking up a versioned asset.
    init <- startUpload(
        project="test-R", 
        asset="removal", 
        version="v1", 
        files=character(0),
        probation=TRUE
    )
    completeUpload(init) 

    removeAsset("test-R", asset="removal")
}

Remove a project

Description

Remove a project from the gypsum backend.

Usage

removeProject(project, url = restUrl(), token = accessToken())
removeProject(project, url = restUrl(), token = accessToken())

Arguments

`project`	String containing the project to remove.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to a gypsum administrator account.

Value

NULL is invisibly returned if the project was successfully removed.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    createProject("test-R-remove", owners="LTLA")
    removeProject("test-R-remove")
}
if (interactive()) {
    createProject("test-R-remove", owners="LTLA")
    removeProject("test-R-remove")
}

Remove a version of an asset

Description

Remove a version of an asset from the gypsum backend.

Usage

removeVersion(project, asset, version, url = restUrl(), token = accessToken())
removeVersion(project, asset, version, url = restUrl(), token = accessToken())

Arguments

`project`	String containing the project to remove.
`asset`	String containing the asset to remove.
`version`	String containing the version of the asset to remove.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to a gypsum administrator account.

Value

NULL is invisibly returned if the project or its contents was successfully removed.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    # Mocking up a versioned asset.
    init <- startUpload(
        project="test-R", 
        asset="removal", 
        version="v1", 
        files=character(0),
        probation=TRUE
    )
    completeUpload(init) 

    removeVersion("test-R", asset="removal", version="v1")
}
if (interactive()) {
    # Mocking up a versioned asset.
    init <- startUpload(
        project="test-R", 
        asset="removal", 
        version="v1", 
        files=character(0),
        probation=TRUE
    )
    completeUpload(init) 

    removeVersion("test-R", asset="removal", version="v1")
}

Resolve links in the cache directory

Description

Create hard links (or copies, if filesystem links are not supported) for linked-from files to their link destinations.

Usage

resolveLinks(
  project,
  asset,
  version,
  cache = cacheDirectory(),
  overwrite = FALSE,
  url = restUrl(),
  config = NULL
)
resolveLinks(
  project,
  asset,
  version,
  cache = cacheDirectory(),
  overwrite = FALSE,
  url = restUrl(),
  config = NULL
)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`version`	String containing the version name.
`cache`	String containing the path to the cache directory.
`overwrite`	Logical scalar indicating whether to replace existing files at the linked-from paths.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

NULL is returned on successful completion.

Author(s)

Aaron Lun

Examples

cache <- tempfile()
saveVersion("test-R", "basic", "v3", relink=FALSE, cache=cache)
list.files(cache, recursive=TRUE, all.files=TRUE)

resolveLinks("test-R", "basic", "v3", cache=cache)
list.files(cache, recursive=TRUE, all.files=TRUE)

cache <- tempfile()
saveVersion("test-R", "basic", "v3", relink=FALSE, cache=cache)
list.files(cache, recursive=TRUE, all.files=TRUE)

resolveLinks("test-R", "basic", "v3", cache=cache)
list.files(cache, recursive=TRUE, all.files=TRUE)

URL for the REST API

Description

Get or set the URL for the gypsum REST API.

Usage

restUrl(url)
restUrl(url)

Arguments

url

String containing the URL of the REST API.

Value

If url is missing, the current setting of the URL is returned.

If url is provided, it is used to replace the current setting of the URL, and the previous setting of the URL is invisibly returned.

Author(s)

Aaron Lun

Examples

restUrl()
old <- restUrl("https://some-other.rest-api.io") # replace it.
restUrl()
restUrl(old) # setting it back.
restUrl()
old <- restUrl("https://some-other.rest-api.io") # replace it.
restUrl()
restUrl(old) # setting it back.

Save a file from a version of a project asset

Description

Download a file from the gypsum bucket, for a version of an asset of a project.

Usage

saveFile(
  project,
  asset,
  version,
  path,
  cache = cacheDirectory(),
  overwrite = FALSE,
  url = restUrl(),
  config = NULL
)
saveFile(
  project,
  asset,
  version,
  path,
  cache = cacheDirectory(),
  overwrite = FALSE,
  url = restUrl(),
  config = NULL
)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`version`	String containing the version name.
`path`	String containing the suffix of the object key for the file of interest, i.e., the relative “path” inside the version's “subdirectory”. The full object key is defined as `{project}/{asset}/{version}/{path}`.
`cache`	String containing the path to the cache directory.
`overwrite`	Logical scalar indicating whether to overwrite an existing file in `cache`. If `FALSE` and the file exists in `cache`, the download is skipped.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Details

The full object key is defined as {project}/{asset}/{version}/{path}. If no file exists in the project-asset-version combination at path, this function will check the ..links file to check whether path refers to a linked-from file. If so, the contents of the link destination is downloaded to the cache and a link/copy is created at the returned file path.

Value

The file is downloaded to the local file system. The destination file path is returned.

Author(s)

Aaron Lun

Examples

out <- saveFile("test-R", "basic", "v1", "blah.txt")
readLines(out)

out <- saveFile("test-R", "basic", "v1", "blah.txt")
readLines(out)

Save all files for a version of a project asset

Description

Download all files associated with a version of an asset of a project from the gypsum bucket.

Usage

saveVersion(
  project,
  asset,
  version,
  cache = cacheDirectory(),
  overwrite = FALSE,
  relink = TRUE,
  concurrent = 1,
  url = restUrl(),
  config = NULL
)
saveVersion(
  project,
  asset,
  version,
  cache = cacheDirectory(),
  overwrite = FALSE,
  relink = TRUE,
  concurrent = 1,
  url = restUrl(),
  config = NULL
)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name.
`version`	String containing the version name.
`cache`	String containing the path to the cache directory.
`overwrite`	Logical scalar indicating whether to overwrite existing files in the cache. If `FALSE` and the files already exist in `cache`, the download is skipped.
`relink`	Logical scalar indicating whether links should be resolved, see `resolveLinks`.
`concurrent`	Integer specifying the number of concurrent downloads.
`url`	String containing the URL of the gypsum REST API.
`config`	Deprecated and ignored.

Value

The version's files are downloaded to the local file system, and the path to the local subdirectory is returned.

Author(s)

Aaron Lun

Examples

out <- saveVersion("test-R", "basic", "v1")
list.files(out, recursive=TRUE, all.files=TRUE)

out <- saveVersion("test-R", "basic", "v1")
list.files(out, recursive=TRUE, all.files=TRUE)

Search the metadata database

Description

Search a SQLite database containing metadata from the gypsum backend. This is based on a precomputed tokenization of all string properties in each metadata document; see https://github.com/ArtifactDB/bioconductor-metadata-index for details.

Usage

searchMetadata(path, query, latest = TRUE, include.metadata = TRUE)

gsc(
  text = NULL,
  project = NULL,
  asset = NULL,
  version = NULL,
  path = NULL,
  user = NULL,
  time = NULL,
  field = NULL,
  partial = FALSE,
  after = TRUE
)

searchMetadataFilter(
  query,
  pid.name = "paths.pid",
  project.name = "versions.project",
  asset.name = "versions.asset",
  version.name = "versions.version",
  path.name = "paths.path",
  user.name = "versions.user",
  time.name = "versions.time"
)
searchMetadata(path, query, latest = TRUE, include.metadata = TRUE)

gsc(
  text = NULL,
  project = NULL,
  asset = NULL,
  version = NULL,
  path = NULL,
  user = NULL,
  time = NULL,
  field = NULL,
  partial = FALSE,
  after = TRUE
)

searchMetadataFilter(
  query,
  pid.name = "paths.pid",
  project.name = "versions.project",
  asset.name = "versions.asset",
  version.name = "versions.version",
  path.name = "paths.path",
  user.name = "versions.user",
  time.name = "versions.time"
)

Arguments

`path`	For `searchMetadata`, a string containing a path to a SQLite file, usually obtained via `fetchMetadataDatabase`. For `gsc`, the suffix of the object key of the metadata document, i.e., the relative “path” to the metadata file inside the version's “directory”. This may be missing as long as other arguments are supplied to `gsc`.
`query`	A gypsum.search.clause object, typically produced by `gsc` or `translateTextQuery`.
`latest`	Logical scalar indicating whether to only search for matches within the latest version of each asset.
`include.metadata`	Logical scalar indicating whether metadata should be returned.
`text`	String containing the text to query on. This will be automatically tokenized, see Details. This may be missing as long as other arguments are supplied to `gsc`.
`project`	String containing the name of the project. This may be missing as long as other arguments are supplied to `gsc`.
`asset`	String containing the name of the asset. This may be missing as long as other arguments are supplied to `gsc`.
`version`	String containing the name of the version. This may be missing as long as other arguments are supplied to `gsc`.
`user`	String containing the user ID of the uploader. This may be missing as long as other arguments are supplied to `gsc`.
`time`	Number specifying the Unix timestamp (in seconds) at which the upload was finished. This may be missing as long as other arguments are supplied to `gsc`.
`field`	String specifying the name of the metadata field in which to search for `text`. If `NULL`, the search is performed on all available metadata fields.
`partial`	For `gsc`, a logical scalar indicating whether `text`, `project`, `asset`, `version`, `path` or `user` contains SQLite wildcards (`%`, `_`) for a partial search. For `text`, setting `partial=TRUE` also ensures that the wildcards are preserved during tokenization.
`after`	Logical scalar indicating whether to search for documents that were uploaded after `time`. If `FALSE`, the search will instead consider documents that were uploaded at or before `time`.
`pid.name`	String containing the name/alias of the column of the `paths` table that contains the path ID.
`project.name`	String containing the name/alias of the column of the `versions` table that contains the project name.
`asset.name`	String containing the name/alias of the column of the `versions` table that contains the asset name.
`version.name`	String containing the name/alias of the column of the `versions` table that contains the version name.
`path.name`	String containing the name/alias of the column of the `paths` table that contains the path name.
`user.name`	String containing the name/alias of the column of the `versions` table that contains the user ID of the uploader.
`time.name`	String containing the name/alias of the column of the `versions` table that contains the upload time.

Details

Each query string is tokenized by converting it to lower case and splitting it on characters that are not Unicode letters/numbers or a dash. We currently do not remove diacritics so these will need to be converted to ASCII by the user. If a text query involves only non-letter/number/dash characters, the filter will not be well-defined and will be ignored when constructing SQL statements. The metadata document/field is only considered to match the query string if all of the tokens can be found in that document/field (in any order).

Value

For searchMetadata, a data frame specifying the contaning the search results.

The project, asset and version columns specify the version of the project asset with matching metadata.
The path column contains the suffix of the object key of the metadata document, i.e., the relative “path” within the version's “directory” to the metadata document. The full object key of the document inside the bucket is defined as {project}/{asset}/{version}/{path}.
The user column contains the identity of the uploading user.
The time column contains the time of the upload.
If include.metadata=TRUE, a metadata column is present with the nested metadata for each match.
If latest=TRUE, a latest column is present indicating whether the matching version is the latest for its asset. Otherwise, only the latest version is returned.

For searchMetadataFilter, a list containing where, a string can be directly used as a WHERE filter condition in a SQL SELECT statement; and parameters, the parameter bindings to be used in where. The return value may also be NULL if the query has no well-defined filter.

For gsc, a gypsum.search.clause object that can be used in |, & and ! to create more complex queries involving multiple clauses.

Author(s)

Aaron Lun

Examples

path <- fetchMetadataDatabase()
searchMetadata(path, gsc("mouse brain"), include.metadata=FALSE)

# Now for a slightly more complex query:
query <- (gsc("brain") | gsc("pancreas")) & gsc("10090", field="taxonomy_id")
searchMetadata(path, query, include.metadata=FALSE)

# Throwing in some wildcards.
has.neuro <- gsc("Neuro%", partial=TRUE)
searchMetadata(path, has.neuro, include.metadata=FALSE)

# We can also query other properties.
datasets <- gsc(project="scRNAseq") & gsc(asset="l%", partial=TRUE)
searchMetadata(path, datasets, include.metadata=FALSE)

path <- fetchMetadataDatabase()
searchMetadata(path, gsc("mouse brain"), include.metadata=FALSE)

# Now for a slightly more complex query:
query <- (gsc("brain") | gsc("pancreas")) & gsc("10090", field="taxonomy_id")
searchMetadata(path, query, include.metadata=FALSE)

# Throwing in some wildcards.
has.neuro <- gsc("Neuro%", partial=TRUE)
searchMetadata(path, has.neuro, include.metadata=FALSE)

# We can also query other properties.
datasets <- gsc(project="scRNAseq") & gsc(asset="l%", partial=TRUE)
searchMetadata(path, datasets, include.metadata=FALSE)

Set project permissions

Description

Set the owner and uploader permissions for a project.

Usage

setPermissions(
  project,
  owners = NULL,
  uploaders = NULL,
  append = TRUE,
  url = restUrl(),
  token = accessToken()
)
setPermissions(
  project,
  owners = NULL,
  uploaders = NULL,
  append = TRUE,
  url = restUrl(),
  token = accessToken()
)

Arguments

`project`	String containing the project name.
`owners`	Character vector containing the GitHub users or organizations that are owners of this project. If `NULL`, no change is made to the existing owners of the project.
`uploaders`	List specifying the authorized uploaders for this project. See the `uploaders` field in the `fetchPermissions` return value for the expected format. If `NULL`, no change is made to the existing uploaders of the project.
`append`	Logical scalar indicating whether `owners` and `uploaders` should be appended to the existing owners and uploaders, respectively, of the project. If `FALSE`, the `owners` and `uploaders` are used to replace the existing values.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to an owner of the `project`.

Value

NULL is invisibly returned upon successful setting of the permissions.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    # Creating a project for demonstration purposes.
    createProject("test-R-perms", owners="LTLA")

    # Setting extra permissions on this project.
    setPermissions("test-R-perms",
        owners="jkanche", 
        uploaders=list(list(id="lawremi", until=Sys.time() + 1000))
    )
}

if (interactive()) {
    # Creating a project for demonstration purposes.
    createProject("test-R-perms", owners="LTLA")

    # Setting extra permissions on this project.
    setPermissions("test-R-perms",
        owners="jkanche", 
        uploaders=list(list(id="lawremi", until=Sys.time() + 1000))
    )
}

Set project quota

Description

Set the storage quota for a project.

Usage

setQuota(
  project,
  baseline = NULL,
  growth = NULL,
  year = NULL,
  url = restUrl(),
  token = accessToken()
)
setQuota(
  project,
  baseline = NULL,
  growth = NULL,
  year = NULL,
  url = restUrl(),
  token = accessToken()
)

Arguments

`project`	String containing the project name.
`baseline`	Numeric scalar specifying the baseline quota (i.e., at time zero) in bytes. If `NULL`, no change is made to the existing baseline of the project.
`growth`	Numeric scalar specifying the annual growth rate of the quota, in bytes. If `NULL`, no change is made to the existing growth rate of the project.
`year`	Integer scalar specifying the year of creation (i.e., time zero) for the project. If `NULL`, no change is made to the existing creation year of the project.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to a gypsum administrator account.

Value

NULL is invisibly returned upon successful setting of the quota.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    # Creating a project for demonstration purposes.
    createProject("test-R-quota", owners="LTLA")

    # Setting a baseline of 10 GB with 5 GB in growth per year.
    setQuota("test-R-quota", baseline=10^10, growth=5^9, year=2019)
}

if (interactive()) {
    # Creating a project for demonstration purposes.
    createProject("test-R-quota", owners="LTLA")

    # Setting a baseline of 10 GB with 5 GB in growth per year.
    setQuota("test-R-quota", baseline=10^10, growth=5^9, year=2019)
}

Start an upload

Description

Start an upload of a new version of an asset, or a new asset of a project.

Usage

startUpload(
  project,
  asset,
  version,
  files,
  links = NULL,
  deduplicate = TRUE,
  probation = FALSE,
  url = restUrl(),
  token = accessToken(),
  directory = NULL
)
startUpload(
  project,
  asset,
  version,
  files,
  links = NULL,
  deduplicate = TRUE,
  probation = FALSE,
  url = restUrl(),
  token = accessToken(),
  directory = NULL
)

Arguments

`project`	String containing the project name.
`asset`	String containing the asset name. This should not contain `/` or start with `..`.
`version`	String containing the version name. This should not contain `/` or start with `..`.
`files`	Character vector containing the paths of the files to be uploaded. These should be relative to the version's `directory`. Alternatively, a data frame where each row corresponds to a file and contains information about those files. This data frame should contain the following fields: `path`, a string containing the relative path of the file inside the version's subdirectory. `size`, a non-negative integer specifying the size of the file in bytes. `md5sum`, a string containing the hex-encoded MD5 checksum of the file. (optional) `dedup`, a logical indicating whether deduplication should be attempted for each file.
`links`	A data frame where each row corresponds to a linked-from file and contains the link destination for that file. This data frame should contain the following fields: `from.path`, a string containing the relative path of the file inside the version's subdirectory. `to.project`, a string containing the project of the list destination. `to.asset`, a string containing the asset of the list destination. `to.version`, a string containing the version of the list destination. `to.path`, a string containing the path of the list destination.
`deduplicate`	Logical scalar indicating whether the backend should attempt deduplication of `files` in the immediately previous version. Only has an effect if `files` is not a data frame or if the `dedup` field is missing.
`probation`	Logical scalar indicating whether to perform a probational upload. Such uploads must be approved by the project owner before they are considered official.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to a user that is authorized to upload to the specified `project`.
`directory`	String containing the path to a directory containing the `files` to be uploaded. This directory is assumed to correspond to a version of an asset. It only has an effect if `files` is a character vector, as it is used to determine the MD5 checksums and sizes. If `NULL`, `directory` is set to the current working directory.

Value

List containing:

file_urls, a list of lists containing information about each file to be uploaded. This is used by uploadFiles.
complete_url, a string containing the completion URL, to be used by completeUpload.
abort_url, a string specifying the abort URL, to be used by abortUpload.
session_token, a string for authenticating to the newly initialized upload session.

Author(s)

Aaron Lun

Examples

tmp <- tempfile()
dir.create(tmp)
write(file=file.path(tmp, "blah.txt"), LETTERS)
dir.create(file.path(tmp, "foo"))
write(file=file.path(tmp, "foo", "bar.txt"), 1:10)

if (interactive()) {
    blob <- startUpload(
        project="test-R", 
        asset="upload-start-check", 
        version="v1", 
        files=list.files(tmp, recursive=TRUE),
        directory=tmp
    )
    print(blob)

    abortUpload(blob) # just cleaning up after we're done.
}

tmp <- tempfile()
dir.create(tmp)
write(file=file.path(tmp, "blah.txt"), LETTERS)
dir.create(file.path(tmp, "foo"))
write(file=file.path(tmp, "foo", "bar.txt"), 1:10)

if (interactive()) {
    blob <- startUpload(
        project="test-R", 
        asset="upload-start-check", 
        version="v1", 
        files=list.files(tmp, recursive=TRUE),
        directory=tmp
    )
    print(blob)

    abortUpload(blob) # just cleaning up after we're done.
}

Translate a plain-text query to a gypsum.search.clause

Description

Translate a plain-text query in user-friendly format to a gypsum.search.clause, equivalent to that created by gsc with the corresponding boolean operations.

Usage

translateTextQuery(query)
translateTextQuery(query)

Arguments

query

String containing a query in user-friendly format to a gypsum.search.clause.

Details

For text searches, we support a more human-readable syntax for boolean operations in the query. The search string below will look for all metadata documents that match foo or bar but not whee:

(foo OR bar) AND NOT whee

The AND, OR and NOT (note the all-caps!) are automatically translated to the corresponding search clauses. This can be combined with parentheses to control precedence; otherwise, AND takes precedence over OR, and NOT takes precedence over both. Note that any sequence of adjacent text terms are implicitly AND'd together, so the two expressions below are equivalent:

foo bar whee
foo AND bar AND whee

Users can prefix any sequence of text terms with the name of a metadata field, to only search for matches within that field of the metadata file. For example:

(title: prostate cancer) AND (genome: GRCh38 OR genome: GRCm38)

Note that this does not extend to the AND, OR and NOT keywords, e.g., title:foo OR bar will not limit the search for bar to the title field.

If a % wildcard is present in a search term, its corresponding text search clause is configured to perform a partial search.

Value

A gypsum.search.clause representing query.

Author(s)

Aaron Lun

Examples

str(translateTextQuery("foo AND bar"))
str(translateTextQuery("foo AND bar%"))
str(translateTextQuery("(foo AND NOT bar) OR whee"))
str(translateTextQuery("blah:foo whee AND stuff: bar blob"))

str(translateTextQuery("foo AND bar"))
str(translateTextQuery("foo AND bar%"))
str(translateTextQuery("(foo AND NOT bar) OR whee"))
str(translateTextQuery("blah:foo whee AND stuff: bar blob"))

Unlock a project

Description

Unlock a project on the gypsum backend. This is typically caused by a partial upload that was not properly aborted.

Usage

unlockProject(project, url = restUrl(), token = accessToken())
unlockProject(project, url = restUrl(), token = accessToken())

Arguments

`project`	String containing the project to remove.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to a gypsum administrator account.

Value

NULL is invisibly returned if the project was successfully removed.

Author(s)

Aaron Lun

Examples

if (interactive()) {
    unlockProject("test-R")
}
if (interactive()) {
    unlockProject("test-R")
}

Upload a directory to the gypsum backend

Description

Convenience method to upload a directory to the gypsum backend as a versioned asset of a project. This requires uploader permissions to the relevant project.

Usage

uploadDirectory(
  directory,
  project,
  asset,
  version,
  cache = cacheDirectory(),
  deduplicate = TRUE,
  probation = FALSE,
  url = restUrl(),
  token = accessToken(),
  concurrent = 1,
  abort.failed = TRUE
)
uploadDirectory(
  directory,
  project,
  asset,
  version,
  cache = cacheDirectory(),
  deduplicate = TRUE,
  probation = FALSE,
  url = restUrl(),
  token = accessToken(),
  concurrent = 1,
  abort.failed = TRUE
)

Arguments

`directory`	String containing the path to a directory to be uploaded.
`project`	String containing the project name.
`asset`	String containing the asset name. This should not contain `/` or start with `..`.
`version`	String containing the version name. This should not contain `/` or start with `..`.
`cache`	String containing the path to the cache for saving files, e.g., in `saveVersion`. Used to convert symbolic links to upload links, see `prepareDirectoryUpload`.
`deduplicate`	Logical scalar indicating whether the backend should attempt deduplication of `files` in the immediately previous version. Only has an effect if `files` is not a data frame or if the `dedup` field is missing.
`probation`	Logical scalar indicating whether to perform a probational upload. Such uploads must be approved by the project owner before they are considered official.
`url`	String containing the URL of the gypsum REST API.
`token`	String containing a GitHub access token to authenticate to the gypsum REST API. The token must refer to a user that is authorized to upload to the specified `project`.
`concurrent`	Integer scalar specifying the number of concurrent uploads in `uploadFiles`.
`abort.failed`	Logical scalar indicating whether to abort the upload on any failure. Setting this to `FALSE` can be helpful for diagnosing upload problems.

Details

This function is a wrapper around prepareDirectoryUpload and startUpload and friends. The aim is to streamline the upload of a directory's contents when no customization of the file listing is required.

Value

On successful upload, NULL is invisibly returned.

Author(s)

Aaron Lun

Examples

tmp <- tempfile()
dir.create(tmp)
write(file=file.path(tmp, "blah.txt"), LETTERS)
dir.create(file.path(tmp, "foo"))
write(file=file.path(tmp, "foo", "bar.txt"), 1:10)

if (interactive()) {
    # Uploading a probational version for test purposes.
    uploadDirectory(staging, "test-R", "upload-dir-check", version, probation=TRUE)

    # Cleaning up after ourselves.
    gypsum::rejectProbation("test-R", "upload-dir-check", version)
}

tmp <- tempfile()
dir.create(tmp)
write(file=file.path(tmp, "blah.txt"), LETTERS)
dir.create(file.path(tmp, "foo"))
write(file=file.path(tmp, "foo", "bar.txt"), 1:10)

if (interactive()) {
    # Uploading a probational version for test purposes.
    uploadDirectory(staging, "test-R", "upload-dir-check", version, probation=TRUE)

    # Cleaning up after ourselves.
    gypsum::rejectProbation("test-R", "upload-dir-check", version)
}

Upload files for a versioned asset

Description

Upload files in an initialized upload session for a version of an asset.

Usage

uploadFiles(init, directory = NULL, url = restUrl(), concurrent = 1)
uploadFiles(init, directory = NULL, url = restUrl(), concurrent = 1)

Arguments

`init`	List containing `file_urls` and `session_token`. This is typically the return value from `startUpload`.
`directory`	String containing the path to a directory containing the `files` to be uploaded. This directory is assumed to correspond to a version of an asset. It only has an effect if `files` is a character vector, as it is used to determine the MD5 checksums and sizes. If `NULL`, `directory` is set to the current working directory.
`url`	String containing the URL of the gypsum REST API.
`concurrent`	Integer specifying the number of concurrent uploads.

Value

NULL is invisibly returned on successful upload of all files.

Author(s)

Aaron Lun

Examples

tmp <- tempfile()
dir.create(tmp)
write(file=file.path(tmp, "blah.txt"), LETTERS)
dir.create(file.path(tmp, "foo"))
write(file=file.path(tmp, "foo", "bar.txt"), 1:10)

if (interactive()) {
    init <- startUpload(
        project="test-R", 
        asset="upload-files-check", 
        version="v1", 
        files=list.files(tmp, recursive=TRUE),
        directory=tmp
    )

    # Executing the upload for all files.
    uploadFiles(init, directory=tmp)

    # Cleaning up after we're done.
    abortUpload(init) 
}

tmp <- tempfile()
dir.create(tmp)
write(file=file.path(tmp, "blah.txt"), LETTERS)
dir.create(file.path(tmp, "foo"))
write(file=file.path(tmp, "foo", "bar.txt"), 1:10)

if (interactive()) {
    init <- startUpload(
        project="test-R", 
        asset="upload-files-check", 
        version="v1", 
        files=list.files(tmp, recursive=TRUE),
        directory=tmp
    )

    # Executing the upload for all files.
    uploadFiles(init, directory=tmp)

    # Cleaning up after we're done.
    abortUpload(init) 
}

Validate metadata against a JSON schema

Description

Validate metadata against a JSON schema for a SQLite database. This ensures that it can be successfully inserted in the database in downstream indexing steps.

Usage

validateMetadata(metadata, schema = fetchMetadataSchema(), stringify = NULL)
validateMetadata(metadata, schema = fetchMetadataSchema(), stringify = NULL)

Arguments

`metadata`	Metadata to be checked. This is usually an R object like a named list, but may also be a JSON-formatted string.
`schema`	String containing a path to a schema.
`stringify`	Logical scalar indicating whether to convert `metadata` to a JSON-formatted string. Defaults to `TRUE` if `metadata` is not already a string.

Value

NULL is invisibly returned upon successful validation.

Author(s)

Aaron Lun

Examples

metadata <- list(
    title="Fatherhood",
    description="Luke ich bin dein Vater.",
    sources=list(
       list(provider="GEO", id="GSE12345")
    ),
    taxonomy_id=list("9606"),
    genome=list("GRCm38"),
    maintainer_name="Darth Vader",
    maintainer_email="[email protected]",
    bioconductor_version="3.10"
)

validateMetadata(metadata)

metadata <- list(
    title="Fatherhood",
    description="Luke ich bin dein Vater.",
    sources=list(
       list(provider="GEO", id="GSE12345")
    ),
    taxonomy_id=list("9606"),
    genome=list("GRCm38"),
    maintainer_name="Darth Vader",
    maintainer_email="[email protected]",
    bioconductor_version="3.10"
)

validateMetadata(metadata)

Package 'gypsum'

Help Index

Abort an upload

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Get and set GitHub access tokens

Description

Usage

Arguments

Value

Author(s)

Examples

Approve a probational upload

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Cache directory

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Clone a version's directory structure

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Complete an upload

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Create a new project

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Fetch the latest version

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Fetch version manifest

Description

Usage

Arguments

Value

Author(s)

Examples

Fetch a metadata database

Description

Usage

Arguments

Details

Value

Author(s)