makeMetadataFromCsv: Metadata File Helpers
Description
Read metadata file for an ExperimentHub resource into RUsage
makeExperimentHubMetadata(pathToPackage)
readMetadataFromCsv(pathToPackage)
Arguments
pathToPackage
full path to package
Value
readMetadataFromCsv() returns a data.frame and
makeExperimetHubMetadata() returns a list of
ExperimentHubMetadata objects.
Details
- makeExperimentHubMetadata:
{
Called by addResources. This function reads in the metadata.csv
file of a contributed package and creates a ExperimentHubMetadata
object to be inserted in the ExperimentHub database.
}
- readMetadataFromCsv:
{
Called by makeExperimentHubMetadata. This function reads in
the metadata.csv file located in inst/extdata of the
pathToPackage. It performs checks for required columns and
data types and can be used by package authors to validate their
metadata.csv.
The rows of metadata.csv represent individual ExperimentHub
resources (i.e., data objects) and the columns are the metadata
fields. All fields should be a single character string of length 1.
BiocVersion and Tags can have multiple comma-separated
values within the string.
Required fields in metadata.csv:
- Title:
character. Name of the resource. - Description:
character. Brief description of the resource,
similar to the 'Description' field in a package DESCRIPTION file. - BiocVersion:
character. All Bioconductor versions
the resource should be made available for; comma separated. - Genome:
character. Genome. - SourceType:
character. Format of original data, e.g., FASTA,
BAM, BigWig, etc. - SourceUrl:
character. Location of original data. - SourceVersion:
character. Version of original data. - Species:
character. Species. - TaxonomyId:
character(1). Taxonomy ID. - Coordinate_1_based:
logical. TRUE if data are 1-based. - DataProvider:
character. Name of original data provider. - Maintainer:
character. Maintainer name and email in the
following format: Maintainer Name . - RDataClass:
character. R / Bioconductor class the data
are stored in. - Tags:
character. Free-form search terms to be used withqueryon an ExperimentHub object. ThebiocViewsterms
from the package DESCRIPTION are added to the Tag field when
adding metadata to the database.
}