"AnnotationHubMetadata" and methods AnnotationHubMetadata is used to represent record(s) in the
server data base.
AnnotationHubMetadata(AnnotationHubRoot, SourceUrl, SourceType, SourceVersion, SourceLastModifiedDate, SourceMd5 = NA_character_, SourceSize, DataProvider, Title, Description, Species, TaxonomyId, Genome, Tags, Recipe, RDataClass, RDataDateAdded, RDataPath, Maintainer, ..., BiocVersion = biocVersion(), Coordinate_1_based = TRUE, Notes = NA_character_, DispatchClass, Location_Prefix = "http://s3.amazonaws.com/annotationhub/")
jsonPath(x)
toJson(x)
constructAnnotationHubMetadataFromSourceFilePath(ahroot, originalFile)
constructMetadataFromJsonPath(ahroot, jsonpath)
constructSeqInfo(species, genome)
metadata(x, ...)
hubError(x)
inputFiles(object, ...)
outputFile(object)
ahmToJson(ahm)
deleteResources(id)
getImportPreparerClasses()
makeAnnotationHubResource(objName, makeAnnotationHubMetadataFunction, ..., where)character(1) Absolute path to
directory structure containing resources to be added to
AnnotationHubcharacter() URL where resource(s) can be
foundcharacter() which indicates what kind of
resource was initially processed. The preference is to name the
type of resource if it's a single file type and to name where the
resources came from if it is a compound resource. So Typical
answers would be like: 'BED','FASTA' or 'Inparanoid' etc.character(1) Version of original filePOSIXct() The date when the
source was last modified. Leaving this blank should allow the
values to be retrieved for you (if your sourceURL is valid).character() md5 hash of original filenumeric(1) Number of bytes in original filecharacter(1) Where did this resource come
from?character(1) Title for this resourcecharacter(1) Description of the resourcecharacter(1) Species namecharacter(1) NCBI codecharacter(1) Name of genome buildcharacter() Free-form tagscharacter(1) Name of recipe functioncharacter(1) Class of derived object
(e.g. ‘GRanges’)POSIXct() Date added to
AnnotationHub. Used to determine snapshots.character(1) file path to serialized formcharacter(1) Maintainer name and email
address, ‘A Maintainer a.maintainer@email.addr’character(1) Under which resource was builtlogical(1) Do coordinates start
with 1 or 0?character(1) string used to indicate
which code should be called by the client when the resource is
downloaded. This is often the same as the RDataClass. But it is
allowed to be a different value so that the client can do something
different internally if required.character(1) This was added for
resources where the metadata only is stored and the resource itself
comes from a third party web site. The location prefix says the
base path where the resource is coming from, and the default value
will be from our own site.character() Notes about the resource.AnnotationHubMetadata.AnnotationHubMetadata.character(1) full path to a JSON representation
of AnnotationHubMetadata-class.character(1) representing the value of
AnnotationHubRoot to be added to the returned instance.character(1)character(1) The organism, e.g., "Homo sapiens".character(1) The genome build, e.g., "hg19".character(1) The name of the preparerClass
object that you intend to have be used for dispatch. You can call
it whatever you want as long as you don't use an existing
preparerClass namefunction This is not
a string, but just the name of the function that makes AHMs out of
your resource of choice.AnnotationHubMetadata returns an instance of the class.jsonPath returns a character(1)) representation of the
full path to the location of the json file associated with this
record.toJson returns the JSON representation of the record.fromJson retuns an instance of the class, as parsed from the
JSON file.
AnnotationHubMetadata(). getClass("AnnotationHubMetadata")
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