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lgatto / ProteomicsAnnotationHubData

Annotation hub data for proteomics data
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different SourceUrls for PXD000001MzID #11

Closed lgatto closed 9 years ago

lgatto commented 9 years ago 
ah <- AnnotationHub::AnnotationHub()
> loc <- ProteomicsAnnotationHubData:::PXD000001MzID[[1]]
> rem <- ah["AH49009"]
> rem$sourceurl
[1] "http://s3.amazonaws.com/annotationhub/pride/data/archive/2012/03/PXD000001/"
> loc@SourceUrl
[1] "http://s3.amazonaws.com/annotationhub/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid"

In all other cases, these match exactly. @sonali-bioc - is this normal?

sonali-bioc commented 9 years ago

Hi Laurent ,

This is the mzId file and we discussed this issue here in issue#8

Since the file now exists on amazon - I will update the sourceurl to contain its name.

But I think the recipe needs to handle this - to clarify, the recipe should make sure that the sourceurl already has a name attached to it and is not truncated (we know what the filename is going to be - so it can be appended to "http://s3.amazonaws.com/annotationhub/pride/data/archive/2012/03/PXD000001/")

lgatto commented 9 years ago

But I think the recipe needs to handle this

The latest version handles these cases specifically and constructs the SourceUrl properly. Thanks for updating the field on AH directly.

sonali-bioc commented 9 years ago

ok - This is now fixed !

> library(AnnotationHub) 
> ah = AnnotationHub()
updating AnnotationHub metadata: retrieving 1 resource
  |===================================================================================| 100%
snapshotDate(): 2015-08-17
There were 50 or more warnings (use warnings() to see the first 50)
> test = query(ah, "Proteomics")
> test$sourceurl
[1] "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/erwinia_carotovora.fasta"                                                       
[2] "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/F063721.dat-mztab.txt"                                                          
[3] "ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"            
[4] "http://s3.amazonaws.com/annotationhub/pride/data/archive/2012/03/PXD000001/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid"