Tips on getting the GBrowse displayer to work?

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Tips on getting the GBrowse displayer to work?

Sam Hokin-3
I've followed the instructions on installing the GBrowse displayer, and it's failing with nothing that I can find in the logs, but
just the message "???sequenceFeature.GBrowse.message??? There was a problem rendering the displayer" on the page.  Here's my config
in webconfig-model.xml:

         <reportdisplayer javaClass="org.intermine.bio.web.displayer.GBrowseDisplayer"
                                          jspName="model/gbrowseDisplayer.jsp"
                                          replacesFields=""
                                          placement="summary"
                                          types="SequenceFeature"/>

Here's my lines in intermine.properties:

# external GBrowse URLs
gbrowse.prefix=http://legumeinfo.org/gb2/gbrowse/Ca1.0/
gbrowse_image.prefix=http://legumeinfo.org/gbrowse2/i/Ca1.0/
gbrowse.database.source=LegumeInfo.org

(I added gbrowse.database.source because that was being complained about in an earlier error message.)

If I look at a gene on a chromosome, I get a location, and if I paste that location into a query string for the genome browser, it
works great, e.g.

http://legumeinfo.org/gb2/gbrowse/Ca1.0/?Ca6:2725-4166

So I think things are named consistently between the InterMine and the genome browser. Any ideas for things to look for???

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Re: Tips on getting the GBrowse displayer to work?

Justin Clark-Casey
So, I'm not familiar with this but looking through the docs I am confused!

 From direct inspection of gbrowseDisplayer.jsp, it looks like the gbrowse.database.source is concatenated on to gbrowse.prefix by line 96 in the jQuery request

.attr('src',
"${WEB_PROPERTIES['gbrowse_image.prefix']}/${WEB_PROPERTIES['gbrowse.database.source']}?source=${WEB_PROPERTIES['gbrowse.database.source']};label=${label};type=${type};name=${name};width=600;b=1")

So you might want to try

gbrowse.prefix=http://legumeinfo.org/gb2/gbrowse
gbrowse.database.source=Ca1.0

Failing this, I suggest running the browser debugger and seeing what http request is made to gbrowse, posting the results here if it's still unclear.

If one does need to specify gbrowse.database.source then we can amend the docs once this is confirmed.

I believe that the ???sequenceFeature.GBrowse.message??? is appearing if no sequenceFeature.GBrowse.message has been set.  For some reason this is only being
set in Flymine atm, even though it's not used there any longer, e.g.

./flymine/webapp/resources/model.properties:sequenceFeature.GBrowse.message=Genome browser view (GBrowse)

It should probably have something set by default.  However, I don't believe the lack of a message would cause this issue.

--
Justin Clark-Casey, Synbiomine/InterMine Software Developer
http://synbiomine.org
http://twitter.com/justincc

On 28/10/15 23:25, Sam Hokin wrote:

> I've followed the instructions on installing the GBrowse displayer, and it's failing with nothing that I can find in the logs, but just the message
> "???sequenceFeature.GBrowse.message??? There was a problem rendering the displayer" on the page.  Here's my config in webconfig-model.xml:
>
>          <reportdisplayer javaClass="org.intermine.bio.web.displayer.GBrowseDisplayer"
>                                           jspName="model/gbrowseDisplayer.jsp"
>                                           replacesFields=""
>                                           placement="summary"
>                                           types="SequenceFeature"/>
>
> Here's my lines in intermine.properties:
>
> # external GBrowse URLs
> gbrowse.prefix=http://legumeinfo.org/gb2/gbrowse/Ca1.0/
> gbrowse_image.prefix=http://legumeinfo.org/gbrowse2/i/Ca1.0/
> gbrowse.database.source=LegumeInfo.org
>
> (I added gbrowse.database.source because that was being complained about in an earlier error message.)
>
> If I look at a gene on a chromosome, I get a location, and if I paste that location into a query string for the genome browser, it works great, e.g.
>
> http://legumeinfo.org/gb2/gbrowse/Ca1.0/?Ca6:2725-4166
>
> So I think things are named consistently between the InterMine and the genome browser. Any ideas for things to look for???
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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Re: Tips on getting the GBrowse displayer to work?

Sam Hokin-3
Thanks, Justin. Good idea, but, unfortunately, no improvement. However I'm using their JBrowse displayer now, which worked "out of
the box", so I'm less inclined to struggle to get the external GBrowse displayer working.

On 11/03/2015 11:44 AM, Justin Clark-Casey wrote:

> So, I'm not familiar with this but looking through the docs I am confused!
>
> From direct inspection of gbrowseDisplayer.jsp, it looks like the gbrowse.database.source is concatenated on to gbrowse.prefix by
>  line 96 in the jQuery request
>
> .attr('src',
> "${WEB_PROPERTIES['gbrowse_image.prefix']}/${WEB_PROPERTIES['gbrowse.database.source']}?source=${WEB_PROPERTIES['gbrowse.database.source']};label=${label};type=${type};name=${name};width=600;b=1")
>
> So you might want to try
>
> gbrowse.prefix=http://legumeinfo.org/gb2/gbrowse gbrowse.database.source=Ca1.0
>
> Failing this, I suggest running the browser debugger and seeing what http request is made to gbrowse, posting the results here if
>  it's still unclear.
>
> If one does need to specify gbrowse.database.source then we can amend the docs once this is confirmed.

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Re: Tips on getting the GBrowse displayer to work?

Justin Clark-Casey
Nice.  Funnily enough, I'm currently having issues getting JBrowse
working where jbrowse is hosted on a different host than InterMine
itself.  Is your setup all on the same host?

On 2015-11-03 21:28, Sam Hokin wrote:

> Thanks, Justin. Good idea, but, unfortunately, no improvement. However
> I'm using their JBrowse displayer now, which worked "out of the box",
> so I'm less inclined to struggle to get the external GBrowse displayer
> working.
>
> On 11/03/2015 11:44 AM, Justin Clark-Casey wrote:
>> So, I'm not familiar with this but looking through the docs I am
>> confused!
>>
>> From direct inspection of gbrowseDisplayer.jsp, it looks like the
>> gbrowse.database.source is concatenated on to gbrowse.prefix by
>>  line 96 in the jQuery request
>>
>> .attr('src',
>> "${WEB_PROPERTIES['gbrowse_image.prefix']}/${WEB_PROPERTIES['gbrowse.database.source']}?source=${WEB_PROPERTIES['gbrowse.database.source']};label=${label};type=${type};name=${name};width=600;b=1")
>>
>> So you might want to try
>>
>> gbrowse.prefix=http://legumeinfo.org/gb2/gbrowse 
>> gbrowse.database.source=Ca1.0
>>
>> Failing this, I suggest running the browser debugger and seeing what
>> http request is made to gbrowse, posting the results here if
>>  it's still unclear.
>>
>> If one does need to specify gbrowse.database.source then we can amend
>> the docs once this is confirmed.
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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Re: Tips on getting the GBrowse displayer to work?

Sam Hokin-3
Nope, the JBrowse I'm using is on legumeinfo.org, the InterMine is on a local dev server.

webapp/resources/webapp/WEB-INF/webconfig-model.xml:

     <reportdisplayer javaClass="org.intermine.bio.web.displayer.JBrowseDisplayer"
                      jspName="model/jbrowseDisplayer.jsp"
                      replacesFields=""
                      placement="Genomics"
                      types="SequenceFeature"/>

webapp/resources/web.properties:

genomicRegionSearch.jbrowse.display = true
genomicRegionSearch.jbrowse.url = http://legumeinfo.org/jbrowse/?data=Ca1.0
genomicRegionSearch.jbrowse.3827 = Cicer_arietinum
#genomicRegionSearch.jbrowse.chrPattern = Ca{0}
#genomicRegionSearch.jbrowse.tracks = Gene Track:CaGeneCa|DNA Track:DNA

jbrowse = true


On 11/04/2015 03:28 AM, J. Clark-Casey wrote:
> Nice.  Funnily enough, I'm currently having issues getting JBrowse working where jbrowse is hosted on a different host than
> InterMine itself.  Is your setup all on the same host?

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Re: Tips on getting the GBrowse displayer to work?

Justin Clark-Casey
Have you tried this with both Chrome and Firefox (and perhaps IE and Safari too)?  Looking back at my notes, the cross-domain requests were working fine on
Chrome but failed on Firefox (genome browser did not display).

--
Justin Clark-Casey, Synbiomine/InterMine Developer
http://synbiomine.org
http://twitter.com/justincc

On 04/11/15 14:18, Sam Hokin wrote:

> Nope, the JBrowse I'm using is on legumeinfo.org, the InterMine is on a local dev server.
>
> webapp/resources/webapp/WEB-INF/webconfig-model.xml:
>
>      <reportdisplayer javaClass="org.intermine.bio.web.displayer.JBrowseDisplayer"
>                       jspName="model/jbrowseDisplayer.jsp"
>                       replacesFields=""
>                       placement="Genomics"
>                       types="SequenceFeature"/>
>
> webapp/resources/web.properties:
>
> genomicRegionSearch.jbrowse.display = true
> genomicRegionSearch.jbrowse.url = http://legumeinfo.org/jbrowse/?data=Ca1.0
> genomicRegionSearch.jbrowse.3827 = Cicer_arietinum
> #genomicRegionSearch.jbrowse.chrPattern = Ca{0}
> #genomicRegionSearch.jbrowse.tracks = Gene Track:CaGeneCa|DNA Track:DNA
>
> jbrowse = true
>
>
> On 11/04/2015 03:28 AM, J. Clark-Casey wrote:
>> Nice.  Funnily enough, I'm currently having issues getting JBrowse working where jbrowse is hosted on a different host than
>> InterMine itself.  Is your setup all on the same host?

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Re: Tips on getting the GBrowse displayer to work?

Sam Hokin-3
JBrowseDisplayer works for me in Ubuntu Firefox and Chrome, but I wouldn't be surprised if there were problems in other OS/browser
combinations.

On 11/05/2015 05:42 AM, Justin Clark-Casey wrote:

> Have you tried this with both Chrome and Firefox (and perhaps IE and Safari too)?  Looking back at my notes, the cross-domain
> requests were working fine on Chrome but failed on Firefox (genome browser did not display).
>
> --
> Justin Clark-Casey, Synbiomine/InterMine Developer
> http://synbiomine.org
> http://twitter.com/justincc
>
> On 04/11/15 14:18, Sam Hokin wrote:
>> Nope, the JBrowse I'm using is on legumeinfo.org, the InterMine is on a local dev server.
>>
>> webapp/resources/webapp/WEB-INF/webconfig-model.xml:
>>
>>      <reportdisplayer javaClass="org.intermine.bio.web.displayer.JBrowseDisplayer"
>>                       jspName="model/jbrowseDisplayer.jsp"
>>                       replacesFields=""
>>                       placement="Genomics"
>>                       types="SequenceFeature"/>
>>
>> webapp/resources/web.properties:
>>
>> genomicRegionSearch.jbrowse.display = true
>> genomicRegionSearch.jbrowse.url = http://legumeinfo.org/jbrowse/?data=Ca1.0
>> genomicRegionSearch.jbrowse.3827 = Cicer_arietinum
>> #genomicRegionSearch.jbrowse.chrPattern = Ca{0}
>> #genomicRegionSearch.jbrowse.tracks = Gene Track:CaGeneCa|DNA Track:DNA
>>
>> jbrowse = true
>>
>>
>> On 11/04/2015 03:28 AM, J. Clark-Casey wrote:
>>> Nice.  Funnily enough, I'm currently having issues getting JBrowse working where jbrowse is hosted on a different host than
>>> InterMine itself.  Is your setup all on the same host?

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