Custom Track Upload Process

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Custom Track Upload Process

Cruncher
Hi guys,

I emailed the mailing list recently about a problem I was having doing custom track uploads with very large files, here. I'm still grappling with this problem, I wasn't able to perform the upload using GBrowse's UserTracks object like I had wanted because of a series of strange error messages that led me to a dead end.

Since the files being uploaded are already located on the same machine as the GBrowse installation I'm going to recreate the file structure for the custom tracks myself. As I understand it the structure should be like this:

userdata/
    datasource_name/
        user_uploadsid/
            feature_name/
                index.SQLite    <------Can be created using bp_seqfeature_load
                STATUS
                feature_name.conf    <-----Configuration for the feature and it's datasource
                SOURCES/
                    feature_name    <-------unmodified source of the feature


My question is this: Is there a step in the uploading process where GBrowse is notified that a new custom track has been created? I have manually created this folder structure as a test and my newly created custom track isn't appearing in GBrowse.

Thanks,
Brad

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Re: Custom Track Upload Process

Cruncher
Hi guys,

I ended up figuring this out myself. The piece I was missing was the user accounts database. There's a table within the database called uploads that needs a new entry for each uploaded file. GBrowse checks that table when it's generating the list of custom tracks.

To summarize, for anyone else trying to do something like this; the procedure for manually adding a custom track is:

1. Create the following file structure inside your GBrowse userdata folder:

userdata/
    datasource_name/
        user_uploadsid/
            feature_name/
                index.SQLite    <------Can be created using bp_seqfeature_load
                STATUS        <-------------Just contains "processing complete", this file is used by GBrowse's internal uploading mechanism for synchronization, not sure if it's necessary for the tracks to work but I left it in
                feature_name.conf    <-----Configuration for the feature and it's datasource
                SOURCES/
                    feature_name    <-------unmodified source of the feature

2. Add an entry to the uploads table of your user accounts database pointing to the file structure you just created
    ex:
        userid    sharing_plicy    path               description    trackid                                                  data_source     modification_date          creation_date                 public_count    title                   imported
        "2"        "private"           "xyplot_test2"    ""            "feee299376ee81b00ebd314e34b44e99"    "Toceanica2"    "2014-03-25 14:33:07"    "2014-03-25 14:33:07"    ""                    "xyplot_test2"    "0"

          It seems that trackid is just a random 32 character alphanumeric sequence, you should be able to generate a random sequence to be used as the trackid.



Thanks,
Brad

               




On Tue, Mar 25, 2014 at 11:06 AM, Brad Covey <[hidden email]> wrote:
Hi guys,

I emailed the mailing list recently about a problem I was having doing custom track uploads with very large files, here. I'm still grappling with this problem, I wasn't able to perform the upload using GBrowse's UserTracks object like I had wanted because of a series of strange error messages that led me to a dead end.

Since the files being uploaded are already located on the same machine as the GBrowse installation I'm going to recreate the file structure for the custom tracks myself. As I understand it the structure should be like this:

userdata/
    datasource_name/
        user_uploadsid/
            feature_name/
                index.SQLite    <------Can be created using bp_seqfeature_load
                STATUS
                feature_name.conf    <-----Configuration for the feature and it's datasource
                SOURCES/
                    feature_name    <-------unmodified source of the feature


My question is this: Is there a step in the uploading process where GBrowse is notified that a new custom track has been created? I have manually created this folder structure as a test and my newly created custom track isn't appearing in GBrowse.

Thanks,
Brad


------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse