ExperimentHubMetadata-class: Class ExperimentHubMetadata objects and methods
In ExperimentHubData: Add resources to ExperimentHub

Description Usage Arguments Details Value See Also Examples

The ExperimentHubMetadata object is used to represent records in the server data base.

ExperimentHubMetadata(ExperimentHubRoot=NA_character_,
	BiocVersion=BiocManager::version(),
	SourceUrl=NA_character_,
	SourceType=NA_character_,
	SourceVersion=NA_character_,
	SourceLastModifiedDate=as.POSIXct(NA_character_),
	SourceMd5=NA_character_,
	SourceSize=NA_real_,
	DataProvider=NA_character_,
	Title=NA_character_,
	Description=NA_character_,
	Maintainer=NA_character_,
	Species=NA_character_,
	TaxonomyId=NA_integer_,
	Genome=NA_character_,
	Tags=NA_character_,
	RDataClass=NA_character_,
	RDataDateAdded=as.POSIXct(NA_character_),
	RDataPath=NA_character_,
	Coordinate_1_based=TRUE,
	Notes=NA_character_,
	DispatchClass=NA_character_,
	PreparerClass=NA_character_,
	Location_Prefix='http://s3.amazonaws.com/experimenthub/')

`ExperimentHubRoot`	`character(1)` Prefix of the local path to resources to be added to ExperimentHub. Internal use only.
`SourceUrl`	`character()` URL of original resource(s).
`SourceType`	`character()` Form of original data, e.g., BED, FASTA, etc. `getValidSourceTypes()` list currently acceptable values. If nothing seems appropiate for your data reach out to maintainer@bioconductor.org.
`SourceVersion`	`character(1)` Version of original file.
`SourceLastModifiedDate`	`POSIXct()` Date when resource was last modified.
`SourceMd5`	`character(1)` md5 hash of original file.
`SourceSize`	`numeric(1)` Number of bytes in original file.
`DataProvider`	`character(1)` Provider of original data, e.g., NCBI, UniProt etc.
`Title`	`character(1)` Title for the resource with version or genome build as appropriate. Titles must be unique and not match any existing title in ExperimentHub.
`Description`	`character(1)` Description of the resource. May include details such as data type, format, study origin, sequencing technology, treated vs control, number of samples etc.
`Species`	`character(1)` Species name.For help on valid species see `getSpeciesList, validSpecies, or suggestSpecies.`
`TaxonomyId`	`character(1)` NCBI code. Taxonomy ID. There are checks for valid taxonomyId given the Species which produce warnings. See GenomeInfoDb::loadTaxonomyDb() for full validation table.
`Genome`	`character(1)` Name of genome build.
`Tags`	‘Tags’ are search terms used to define a subset of resources in a `Hub` object, e.g, in a call to `query`. For ExperimentHub resources, ‘Tags’ are automatically generated from the ‘biocViews’ in the DESCRIPTION file of the accompanying software package. ‘Tags’ values supplied by the user are not be entered in the database and are not part of the formal metadata. This 'controlled vocabulary' approach was taken to limit the search terms to a well defined set and may change in the future.
`RDataClass`	`character(1)` Class of derived object (e.g. ‘GRanges’).
`RDataDateAdded`	`POSIXct()` Date resource was added to ExperimentHub. The default is today's date and is auto-generated when metadata are constructed. Resources will appear in snapshots with a date greater than or equal to the `RDataDateAdded`.
`RDataPath`	`character()` File path to where object is stored in AWS S3 bucket or on the web.The `Location_Prefix` will be prepended to `RDataPath` for the full path to the resource. If the resource is stored in Bioconductor's AWS S3 buckets, it should start with the name of the package associated with the metadata and should not start with a leading slash. It should include the resource file name. For strongly associated files, like a bam file and its index file, the two files should be separates with a colon `:`. This will link a single hub id with the multiple files.
`Maintainer`	`character(1)` Maintainer name and email address, ‘A Maintainer a.maintainer@email.addr’
`BiocVersion`	`character(1)`. The first Bioconductor version the resource was made available for. Unless removed from the hub, the resource will be available for all versions greater than or equal to this field.
`Coordinate_1_based`	`logical(1)` Do coordinates start with 1 or 0?
`DispatchClass`	`character(1)`. Determines how data are loaded into R. The value for this field should be ‘Rda’ if the data were serialized with `save()` and ‘Rds’ if serialized with `saveRDS`. The filename should have the appropriate ‘rda’ or ‘rds’ extension. A number of dispatch classes are pre-defined in AnnotationHub/R/AnnotationHubResource-class.R with the suffix ‘Resource’. For example, if you have sqlite files, the AnnotationHubResource-class.R defines SQLiteFileResource so the DispatchClass would be SQLiteFile. Contact maintainer@bioconductor.org if you are not sure which class to use.The function `AnnotationHub::DispatchClassList()` will output a matrix of currently implemented DispatchClass and brief description of utility. If a predefine class does not seem appropriate contact maintainer@bioconductor.org.
`Location_Prefix`	`character(1)` URL location of AWS S3 bucket or web site where resource is located.
`Notes`	`character()` Notes about the resource.
`PreparerClass`	`character(1)` Used internally.

In practice, instances of this class are generated by a call to addResources or makeExperimentHubMetadata instead of a direct call to the constructor.

addResources is a function used by the Bioconductor Core team when adding new metadata records to the production database. makeExperimentHubMetadata and the low-level helper

A ExperimentHubMetadata object.