addResources: addResources

In Bioconductor/ExperimentHubData: Add resources to ExperimentHub

addResources

Description

Add resource metadata to a local ExperimentHub database

Usage

addResources(pathToPackage, fileName=character(), insert = FALSE, ...)

Arguments

pathToPackage	Full path to data package including package name.
fileName	Name of single metadata file located in "inst/extdata". If none is provided the function looks for a file named "metadata.csv".
insert	A logical to control if metadata are inserted in the ExperimentHub db. By default this option is FALSE which is a useful state in which to test a new recipe and confirm the metadata fields are correct. When insert = TRUE, the "EXPERIMENT_HUB_SERVER_POST_URL" global option must be set to the http location of the ExperimentHubServer in the global environment or .Rprofile. This option controls Additionally, AWS command line tools must be installed on the local machine to push files to S3 buckets. See https://aws.amazon.com/cli/ for installation instructions.
...	TDB. Currently not used.

Details

This function is used by the Bioconductor Core team to add new metadata to the production database.

When insert is TRUE, addResources attempts to add the metadata to the local database. (NOTE: A local database can be created with the ExperimentHub docker). Records in ExperimentHub must have unique file names. If the new metadata have duplicate file names a warning is thrown and the records are omitted from those added to the database.

This function does not add data to an AWS S3 bucket. ExperimentHub packages do not have 'recipes' that generate data on the fly. Instead, data files are provided by the maintainer in final form and added to the appropriate S3 location in a separate step.

Value

A list of ExperimentHubMetadata objects.

See Also

• ExperimentHubMetadata

• AnnotationHubMetadata

• makeExperimentHubMetadata

Examples

  ## Not run: 
    ## Generate metadata for inspection
    addResources("/home/vobencha/mypackage", insert=FALSE)
    ## Inset metadata into ExperimentHub database
    addResources("/home/vobencha/mypackage", insert=TRUE)
  
## End(Not run)

Bioconductor/ExperimentHubData documentation built on Oct. 31, 2024, 7 a.m.