disable sequence export in gff3 adapter not working

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disable sequence export in gff3 adapter not working

Chris Childers
Hi all,

The changes in the new release are great, and we're in the middle of testing this before doing a site-wide update.  I've run into an issue with the gff3 data adapter.  I set the export_genomic_sequence tag to false and restarted both the instance and tomcat, but it is still not recognizing that change.  I've been able to adjust the metadata in column 9 that get exported, so I know the changes are being recognized.  I've included my gff3_adapter XML below. 

Has anyone else run into this issue?

Thanks,
Chris



<?xml version="1.0" encoding="UTF-8"?>

<!-- configuration file for GFF3 data adapter -->

<gff3_config>

    <!-- path to where to put generated GFF3 file.  This path is a
    relative path that will be where you deployed your WebApollo
    instance (so that it's accessible from HTTP download requests) -->
    <tmp_dir>tmp</tmp_dir>

    <!-- value to use in the source column (column 2) of the generated
    GFF3 file. -->
    <source>WebApollo</source>

    <!-- which metadata to export as an attribute - optional.
    Default is to export everything except owner, date_creation, and date_last_modified -->

    <metadata_to_export>
        <metadata type="name" />
        <metadata type="symbol" />
        <metadata type="description" />
        <metadata type="status" />
        <metadata type="dbxrefs" />
        <metadata type="attributes" />
        <metadata type="comments" />
        <metadata type="owner" />
        <metadata type="date_creation" />
        <metadata type="date_last_modified" />
    </metadata_to_export>


<!-- added 04-04-2014  -->
    <!-- whether to export underlying genomic sequence - optional.
    Defaults to true -->
    <export_genomic_sequence>false</export_genomic_sequence>

</gff3_config>

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Re: disable sequence export in gff3 adapter not working

Colin
Ah, I can confirm this as well. Good catch. Apparently the source code is looking for
export_source_genomic_sequence

Instead of
export_genomic_sequence

If you change the config xml to reference this variable instead, it should work as expected.


-Colin
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Re: disable sequence export in gff3 adapter not working

Chris Childers
Hi Colin,

That is exactly what I needed. 

Thanks!
Chris


On Fri, Apr 4, 2014 at 1:35 PM, Colin <[hidden email]> wrote:
Ah, I can confirm this as well. Good catch. Apparently the source code is looking for

export_source_genomic_sequence

Instead of
export_genomic_sequence

If you change the config xml to reference this variable instead, it should work as expected.


-Colin

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Re: disable sequence export in gff3 adapter not working

Ed Lee
Thanks for noticing this.  I guess at some point I had changed the tag name in the source code and forgot to update the release configuration.  The release's been updated to have the correct tag name.

Cheers,
Ed


On Fri, Apr 4, 2014 at 10:44 AM, Chris Childers <[hidden email]> wrote:
Hi Colin,

That is exactly what I needed. 

Thanks!
Chris


On Fri, Apr 4, 2014 at 1:35 PM, Colin <[hidden email]> wrote:
Ah, I can confirm this as well. Good catch. Apparently the source code is looking for
export_source_genomic_sequence

Instead of
export_genomic_sequence

If you change the config xml to reference this variable instead, it should work as expected.


-Colin