[Gmod-ajax] Name search problem

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[Gmod-ajax] Name search problem

Keiran Raine
Hi,

Can anyone confirm how the name search works?

I have data for different species loaded in each of the ‘Genome’ selectors.  Currently I’m finding that the name search is showing the data for the Human genome rather than the Mouse genome I currently have selected.

In my ‘trackList.json’ I have defined the following, but I’m guessing it needs to know where to pick up the ‘names’ folder, e.g. ‘../MOUSE/GRCm38/names/meta.json’?

{
    "refSeqs": "../MOUSE/GRCm38/seq/refSeqs.json", 
    "tracks": [], 
    "trackSelector": {
        "renameFacets": {
            "TYPE": "TYPE", 
            "SAMPLE": "SAMPLE", 
            "category": "Category"
        }, 
        "selectableFacets": [
            "category", 
            "SAMPLE", 
            "TYPE"
        ], 
        "displayColumns": [
            "category", 
            "SAMPLE", 
            "TYPE"
        ], 
        "type": "Faceted"
    }, 
    "dataset_id": "1296", 
    "formatVersion": 1
}

I suspect this has been a long standing oversight that none of our users have noticed for 5 years...

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
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Re: Name search problem

Keiran Raine
Hi all,

I’ve figured this out by extrapolating from the defaults in the global config (which isn’t in json):

Needed to add the following at the top level of each datasource json file (pointing to the relevant names directory):

{
  "names":{"url":"../MOUSE/GRCm38/names","type":"Hash”},
  “refSeqs”:: "../MOUSE/GRCm38/seq/refSeqs.json”, 
  ….
}

Regards,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 12 May 2016, at 16:36, Keiran Raine <[hidden email]> wrote:

Hi,

Can anyone confirm how the name search works?

I have data for different species loaded in each of the ‘Genome’ selectors.  Currently I’m finding that the name search is showing the data for the Human genome rather than the Mouse genome I currently have selected.

In my ‘trackList.json’ I have defined the following, but I’m guessing it needs to know where to pick up the ‘names’ folder, e.g. ‘../MOUSE/GRCm38/names/meta.json’?

{
    "refSeqs": "../MOUSE/GRCm38/seq/refSeqs.json", 
    "tracks": [], 
    "trackSelector": {
        "renameFacets": {
            "TYPE": "TYPE", 
            "SAMPLE": "SAMPLE", 
            "category": "Category"
        }, 
        "selectableFacets": [
            "category", 
            "SAMPLE", 
            "TYPE"
        ], 
        "displayColumns": [
            "category", 
            "SAMPLE", 
            "TYPE"
        ], 
        "type": "Faceted"
    }, 
    "dataset_id": "1296", 
    "formatVersion": 1
}

I suspect this has been a long standing oversight that none of our users have noticed for 5 years...

Thanks,

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax