Metadata requirements

[lgatto]

From the vignette

• The Recipe is a short function, typically named NameOfDataOrigformatToFinalformat, that converts the original data into on compatible with R/Bioconductor.
• Location_Prefix is either .amazonBaseUrl, when the file to be loaded/read by the user exists on the AH Amazon S3 instance, or .prideBaseUrl when it lives on the PRIDE ftp server.
• SourceURL is the full location of the original file. This is generally the third-party server, but not necessarily.
• RDataPath is the path and filename of the file to be read into R and provided to the user. This field does not contain the server address .prideBaseUrl or .amazonBaseUrl (see (Location_Prefix).
• The metadata list, used to create the AnnotationHubResources also uses a SourceBaseUrl, which is the full url minus file name (that is in File) of the original file. Used to construct SourceUrl.

@sonali-bioc before checking the issues for the individual files, could you check the following, to make sure I got it right.

[sonali-bioc]

@lgatto - yes the above is correct. Only change to Recipe is that it is not necessary to create the original data into compatible R/Bioconductor. For some fasta files, the recipe function uses Rsamtools::indexFa to create an index file for this fasta files. But most of the times, it is true.

[lgatto]

Thanks.

[sonali-bioc]

FYI - Title looks good now..

Did not want to pollute the other issues - so adding it here.

> library(AnnotationHub)
> ah = AnnotationHub()
updating AnnotationHub metadata: retrieving 1 resource
  |======================================================================| 100%
snapshotDate(): 2015-07-30
There were 50 or more warnings (use warnings() to see the first 50)
> length(ah)
[1] 34809
> tail(ah)
AnnotationHub with 6 records
# snapshotDate(): 2015-07-30
# $dataprovider: PRIDE, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Erwinia carotovora, Lactobacillus jensenii_JV-V16, Methanocaldoc...
# $rdataclass: OrgDb, AAStringSet, MSnSet, mzRident, mzRpwiz
# additional mcols(): taxonomyid, genome, description, tags, sourceurl,
#   sourcetype
# retrieve records with, e.g., 'object[["AH49004"]]'

            title
  AH49004 | org.Methanocaldococcus_infernus_ME.eg.sqlite
  AH49005 | org.Lactobacillus_jensenii_JV-V16.eg.sqlite
  AH49006 | PXD000001: Erwinia carotovora and spiked-in protein fasta file
  AH49007 | PXD000001: Peptide-level quantitation data
  AH49008 | PXD000001: raw mass spectrometry data
  AH49009 | PXD000001: MS-GF+ identiciation data

[lgatto]

Excellent!