Hub-utils: Get information for selected ids

Description Usage Arguments Value details Author(s) See Also Examples

Description

Gets information from the Hub database for the given selection of ids. The information collected is ah_id, fetch_id, title, rdataclass, availablitiy status, biocversion when added, date when added, date when removed, and file size.

Usage

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  getInfoOnIds(hub, ids)

Arguments

hub

Hub object.

ids

List of ids to get from database. Can be left unset to use all active ids in the hub. If given, it is either a numeric or character vector. See details section.

Value

data.frame of information for selected ids. The information collected is ah_id, fetch_id, title, rdataclass, availablitiy status, biocversion when added, date when added, date when removed, and file size.

details

If a hub object is passed into the function with no ids given, it will use all active ids associated with that hub object (names(ah)). It is recommended to only run this option if you are using a smaller subset Hub object. The ids argument can be specified as either a character vector or a numeric vector. If using a character vector, the function assumes the 'ah_ids' were used, and each entry takes the form similar to c("AH2", "AH5012"). If a numeric vector is specified, the function assume the 'fetch_ids' were used. The 'fetch_id' is the identifier that is used for the file name. For older versions of the cache these were the file names directly.

This function was designed as a helper function when converting between old versions of Hubs to the newer versions that utilize BiocFileCache. If files were not able to be redownloaded, one could put the ids into this function to get more information on them. Note: Some resources may appear available but could not be redownloaded. Most likely these files are rdataclass 'OrgDb'. 'OrgDb' are only valid for a given release cycle and are masked to any future release cycle. It is recommended to update to the current 'OrgDb' but if the old file was not able to be downloaded and still desired, one could download manually download using the fetch_id. Example if the file not able to be downloaded was "~./AnnotationHub/69303" then the fetch call is: "https://annotationhub.bioconductor.org/fetch/69303". While the convertHub function will not automatically download it is still possible to keep track in the cache by doing a manually addition. Although not recommended. In reality these file will not be updated so the original file could also still be used.

This function could also be a utility function to help determine any given resources download size.

Author(s)

Lori Shepherd

See Also

AnnotationHub, convertHub

Examples

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## Not run: 
getInfoOnIds(hub, c("AH2","AH5012"))
getInfoOnIds(hub, 69303)


## End(Not run)

# If using in conjunction with convertHub,
#
# File not downloaded options:
#

## Not run: 
# 1. Use the original file. In reality the file is not going to be
  updated or should change. The original file does not need to be
  tracked and could now be referenced directly for usage. It will not be
  available in the Hub.

# 2. You could simply download the file for use
# The file will not change and not be updated so its static download not
# in the cache is fine

# You could type the following into a web browswer
"https://annotationhub.bioconductor.org/fetch/69303"

# or in R
httr::GET("https://annotationhub.bioconductor.org/fetch/69303",
	  write_disk(<pathToSave/69303>, overwrite=FALSE))

# 3. To add to a hub cache (not recommended)
hub <- AnnotationHub()
bfc <- AnnotationHub:::.get_cache(hub)

# the hub creates the rname is in the format of 'ah_id : fetch_id'
bfcadd(bfc, fpath="https://annotationhub.bioconductor.org/fetch/69303",
rname="AH62557 : 69303")

## End(Not run)

Bioconductor/AnnotationHub documentation built on Dec. 2, 2019, 10:48 p.m.