[Gmod-ajax] trackMetadata url: why not relative to data directory?

[Loraine G. <lor...@sb...>]

Hi,

I wonder why the URL for metadata sources is relative to the JBrowse 
directory and not to the directory where the configuration file 
(trackList.json) is located, as is the case for all other url parameters 
in trackList.json (urlTemplate) ? Is there a reason for that ? Maybe 
because one single metadata source was intended to be used for all data 
repositories ?

I have one different trackMetadata file for each of my ~100 data 
repositories (~100 strains) which I would like to put into the related 
data repository (next to trackList.json), and I do not find it wise for 
maintenance reason to have a piece of absolute path (between the JBrowse 
and the data repository) in my trackList.json.

I guess I can use symbolic links to avoid using the path into the 
trackList.json, but whatever, I will have to manage this path somewhere.


Extract from 
http://jbrowse.org/docs/track_metadata.html#track-metadata-options: 
"-url - a URL (relative to JBrowse root directory, or absolute URL)"

TrackList.json configuration exemple :

{
  "trackMetadata": {
      "sources": [
           { "type": "csv", "url": 
"data/private/species/this_particular_strain.csv" }
      ]
},
    "tracks" : [
       {
          "category" : "Reference sequence",
          "chunkSize" : 20000,
          "label" : "DNA",
          "seqType" : "dna",
          "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
          "type" : "SequenceTrack",
          "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-"
       },
       {
          "compress" : 0,
          "label" : "this_strain.gff",
          "storeClass" : "JBrowse/Store/SeqFeature/NCList",
          "style" : {
             "className" : "feature"
          },
          "trackType" : "CanvasFeatures",
          "type" : "CanvasFeatures",
          "urlTemplate" : "tracks/this_strain.gff/{refseq}/trackData.json"
       },
       {
          "autoscale" : "local",
          "bicolor_pivot" : "zero",
          "label" : "bwFilename.bw",
          "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
          "type" : "JBrowse/View/Track/Wiggle/XYPlot",
          "urlTemplate" : 
"flat_data/RNAseq/coverage/RNAseq_this_strain_conditionX.bw"
       }
]
}



I would like to be able to write:

"trackMetadata": {
      "sources": [
           { "type": "csv", "url":  "this_particular_strain.csv" }
      ]
},


Thanks,

Loraine Guéguen

-- 
Loraine Guéguen

UMR8227 LBI2M (Laboratory of Integrative Biology of Marine Models)
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)

Station Biologique de Roscoff - CNRS | Sorbonne Université
Place Georges Teissier - CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://www.sb-roscoff.fr/en/laboratory-integrative-biology-marine-models
http://abims.sb-roscoff.fr/