GBRowse CGI-Parameter "add" is not working on my installation

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GBRowse CGI-Parameter "add" is not working on my installation

Oliver Pelz
Hi again,

after I could fix my problems with the wrong session type on my centos machine (see mailing list email about topic "cannot set admin password") I run in the next trouble.

For me  GBrowes's "add" functionality is not working (http://gmod.org/wiki/GBrowse_Configuration/URL_schema)

1.If I access the following URL with or without user_accounts enabled, everything works fine:

http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on


2.If I "add" some custom track information using the add-parameter e.g.:
http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on;add=3L+E-RNAi+wls:1+11159720..11160708;add=3L+E-RNAi+wls:2+11160919..11161014;add=3L+E-RNAi+wls:3+11161237..11162741;style=E-RNAi+glyph=segments+fgcolor=black+bgcolor=plum;

I get an "Internal Server Error" in the browser. Looking at apache log file I see:

[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.
[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Premature end of script headers: gbrowse_img

There is another "Sessionid unavailable" - thread in the mailing list, but it was never resolved (http://generic-model-organism-system-database.450254.n5.nabble.com/Sessionid-unavailable-with-gbrowse-img-and-login-system-td5711879.html).
Also if i set gbrowse_img path to gbrowse I get the same error.
I suspect it has something to do with the user accounts but I cannot find anything.
I played around again with the following GBrowse.conf parameters:

session lock type
upload_db_adaptor
user_account_db
admin_account
admin_dbs

but nothing can cure my problem.

The flybase database is a mysql database I imported from gbrowse 1.7 and which I migrated the database conf file. As I can see all the data when not using the cgi parameter "add" I think this is not the issue.

My setup is:
* Using centos 6.5
* building perl v.5.18.1
* installed latest cpan, bioperl and gbrowse using cpan:
* as of 14/10/14: CPAN 2.05, BioPerl-1.6.923., GBrowse-2.55




Best,
Oliver


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Re: GBRowse CGI-Parameter "add" is not working on my installation

Oliver Pelz
Hi again,

Please ignore the domain b110-ernai in my previous post (at step 3), this is a typo and should be localhost (I substituted everything by hand to hide this information from you ;) )

I just looked at the apache error log again, If I substiture the url ../gbrowse_img/.. with ../gbrowse/.. I also get the "sessionid unavailable" error as mentioned in my previous post but slightly more:

[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] RUN(): GET: http://localhost/cgi-bin/gb2/gbrowse/flybase/ name=wls;type=GENE%20TXN;width=580;keystyle=between;grid=on;add=3L%20E-RNAi%20wls%3A1%2011159720..11160708;add=3L%20E-RNAi%20wls%3A2%2011160919..11161014;add=3L%20E-RNAi%20wls%3A3%2011161237..11162741;style=E-RNAi%20glyph%3Dsegments%20fgcolor%3Dblack%20bgcolor%3Dplum at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 240.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] session id = ae5bfecb9cb84cd45e364bab2f332f1a at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 244.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 273.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 276.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 287.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 290.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] Premature end of script headers: gbrowse

Hope this helps,
Thank you for your help in advance,
Oliver



2014-10-17 9:34 GMT+02:00 Oliver Pelz <[hidden email]>:
Hi again,

after I could fix my problems with the wrong session type on my centos machine (see mailing list email about topic "cannot set admin password") I run in the next trouble.

For me  GBrowes's "add" functionality is not working (http://gmod.org/wiki/GBrowse_Configuration/URL_schema)

1.If I access the following URL with or without user_accounts enabled, everything works fine:

http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on


2.If I "add" some custom track information using the add-parameter e.g.:
http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on;add=3L+E-RNAi+wls:1+11159720..11160708;add=3L+E-RNAi+wls:2+11160919..11161014;add=3L+E-RNAi+wls:3+11161237..11162741;style=E-RNAi+glyph=segments+fgcolor=black+bgcolor=plum;

I get an "Internal Server Error" in the browser. Looking at apache log file I see:

[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.
[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Premature end of script headers: gbrowse_img

There is another "Sessionid unavailable" - thread in the mailing list, but it was never resolved (http://generic-model-organism-system-database.450254.n5.nabble.com/Sessionid-unavailable-with-gbrowse-img-and-login-system-td5711879.html).
Also if i set gbrowse_img path to gbrowse I get the same error.
I suspect it has something to do with the user accounts but I cannot find anything.
I played around again with the following GBrowse.conf parameters:

session lock type
upload_db_adaptor
user_account_db
admin_account
admin_dbs

but nothing can cure my problem.

The flybase database is a mysql database I imported from gbrowse 1.7 and which I migrated the database conf file. As I can see all the data when not using the cgi parameter "add" I think this is not the issue.

My setup is:
* Using centos 6.5
* building perl v.5.18.1
* installed latest cpan, bioperl and gbrowse using cpan:
* as of 14/10/14: CPAN 2.05, BioPerl-1.6.923., GBrowse-2.55




Best,
Oliver



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Re: GBRowse CGI-Parameter "add" is not working on my installation

Oliver Pelz
Hi all,

Would it be helpful if I would provide a Virtual Machine with the exact problem using Centos 6.5?

Best,
Oliver

2014-10-17 10:09 GMT+02:00 Oliver Pelz <[hidden email]>:
Hi again,

Please ignore the domain b110-ernai in my previous post (at step 3), this is a typo and should be localhost (I substituted everything by hand to hide this information from you ;) )

I just looked at the apache error log again, If I substiture the url ../gbrowse_img/.. with ../gbrowse/.. I also get the "sessionid unavailable" error as mentioned in my previous post but slightly more:

[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] RUN(): GET: http://localhost/cgi-bin/gb2/gbrowse/flybase/ name=wls;type=GENE%20TXN;width=580;keystyle=between;grid=on;add=3L%20E-RNAi%20wls%3A1%2011159720..11160708;add=3L%20E-RNAi%20wls%3A2%2011160919..11161014;add=3L%20E-RNAi%20wls%3A3%2011161237..11162741;style=E-RNAi%20glyph%3Dsegments%20fgcolor%3Dblack%20bgcolor%3Dplum at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 240.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] session id = ae5bfecb9cb84cd45e364bab2f332f1a at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 244.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 273.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 276.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 287.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 290.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] Premature end of script headers: gbrowse

Hope this helps,
Thank you for your help in advance,
Oliver



2014-10-17 9:34 GMT+02:00 Oliver Pelz <[hidden email]>:
Hi again,

after I could fix my problems with the wrong session type on my centos machine (see mailing list email about topic "cannot set admin password") I run in the next trouble.

For me  GBrowes's "add" functionality is not working (http://gmod.org/wiki/GBrowse_Configuration/URL_schema)

1.If I access the following URL with or without user_accounts enabled, everything works fine:

http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on


2.If I "add" some custom track information using the add-parameter e.g.:
http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on;add=3L+E-RNAi+wls:1+11159720..11160708;add=3L+E-RNAi+wls:2+11160919..11161014;add=3L+E-RNAi+wls:3+11161237..11162741;style=E-RNAi+glyph=segments+fgcolor=black+bgcolor=plum;

I get an "Internal Server Error" in the browser. Looking at apache log file I see:

[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.
[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Premature end of script headers: gbrowse_img

There is another "Sessionid unavailable" - thread in the mailing list, but it was never resolved (http://generic-model-organism-system-database.450254.n5.nabble.com/Sessionid-unavailable-with-gbrowse-img-and-login-system-td5711879.html).
Also if i set gbrowse_img path to gbrowse I get the same error.
I suspect it has something to do with the user accounts but I cannot find anything.
I played around again with the following GBrowse.conf parameters:

session lock type
upload_db_adaptor
user_account_db
admin_account
admin_dbs

but nothing can cure my problem.

The flybase database is a mysql database I imported from gbrowse 1.7 and which I migrated the database conf file. As I can see all the data when not using the cgi parameter "add" I think this is not the issue.

My setup is:
* Using centos 6.5
* building perl v.5.18.1
* installed latest cpan, bioperl and gbrowse using cpan:
* as of 14/10/14: CPAN 2.05, BioPerl-1.6.923., GBrowse-2.55




Best,
Oliver




------------------------------------------------------------------------------
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Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
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Re: GBRowse CGI-Parameter "add" is not working on my installation

Oliver Pelz
On analyzing this further I have new insight and a proposed solution to the sessionid problem with the "add" cgi URL parameter.

If I clear the browsers cache (and apparently the gbrowse cookie which stores the session id called "gbrowse_sess") and directly go to a ../gbrowse_img/.. "add" URL
(e.g.: /gb2/gbrowse_img/yeast/?name=chrI%3A80%2C000..120%2C000;add=chrI+oli+pelz+100100..100200)
I get this sessionid error mession from above e.g.:
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.

If I clear the browse cache, then go to a ../gbrowse/.. URL WITHOUT THE ADD URL (e.g. with firebug cookie inspector open) I see that there it creates the missing "gbrowse_sess" cookie.
If I than go to a ../gbrowse_img/.. URL with ADD parameter it works because the cookie has been set before.
So the problem is that there is code in the gbrowse which creates a session id cookie only when browsing to the standard gbrowse pages and not in gbrowse_img with "add" parameter.

Since our website makes requests to our gbrowse server through ../gbrowse_img/.. URLS only using the ADD parameter
my suggested solution would be to create the missing session id and cookie on the ../gbrowse_img/.. requests if it is not available (e.g. from clearing browser), etc.


Best,
Oliver

2014-10-20 11:28 GMT+02:00 Oliver Pelz <[hidden email]>:
Hi all,

Would it be helpful if I would provide a Virtual Machine with the exact problem using Centos 6.5?

Best,
Oliver

2014-10-17 10:09 GMT+02:00 Oliver Pelz <[hidden email]>:
Hi again,

Please ignore the domain b110-ernai in my previous post (at step 3), this is a typo and should be localhost (I substituted everything by hand to hide this information from you ;) )

I just looked at the apache error log again, If I substiture the url ../gbrowse_img/.. with ../gbrowse/.. I also get the "sessionid unavailable" error as mentioned in my previous post but slightly more:

[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] RUN(): GET: http://localhost/cgi-bin/gb2/gbrowse/flybase/ name=wls;type=GENE%20TXN;width=580;keystyle=between;grid=on;add=3L%20E-RNAi%20wls%3A1%2011159720..11160708;add=3L%20E-RNAi%20wls%3A2%2011160919..11161014;add=3L%20E-RNAi%20wls%3A3%2011161237..11162741;style=E-RNAi%20glyph%3Dsegments%20fgcolor%3Dblack%20bgcolor%3Dplum at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 240.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] session id = ae5bfecb9cb84cd45e364bab2f332f1a at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 244.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 273.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 276.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 287.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 290.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] Premature end of script headers: gbrowse

Hope this helps,
Thank you for your help in advance,
Oliver



2014-10-17 9:34 GMT+02:00 Oliver Pelz <[hidden email]>:
Hi again,

after I could fix my problems with the wrong session type on my centos machine (see mailing list email about topic "cannot set admin password") I run in the next trouble.

For me  GBrowes's "add" functionality is not working (http://gmod.org/wiki/GBrowse_Configuration/URL_schema)

1.If I access the following URL with or without user_accounts enabled, everything works fine:

http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on


2.If I "add" some custom track information using the add-parameter e.g.:
http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on;add=3L+E-RNAi+wls:1+11159720..11160708;add=3L+E-RNAi+wls:2+11160919..11161014;add=3L+E-RNAi+wls:3+11161237..11162741;style=E-RNAi+glyph=segments+fgcolor=black+bgcolor=plum;

I get an "Internal Server Error" in the browser. Looking at apache log file I see:

[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.
[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Premature end of script headers: gbrowse_img

There is another "Sessionid unavailable" - thread in the mailing list, but it was never resolved (http://generic-model-organism-system-database.450254.n5.nabble.com/Sessionid-unavailable-with-gbrowse-img-and-login-system-td5711879.html).
Also if i set gbrowse_img path to gbrowse I get the same error.
I suspect it has something to do with the user accounts but I cannot find anything.
I played around again with the following GBrowse.conf parameters:

session lock type
upload_db_adaptor
user_account_db
admin_account
admin_dbs

but nothing can cure my problem.

The flybase database is a mysql database I imported from gbrowse 1.7 and which I migrated the database conf file. As I can see all the data when not using the cgi parameter "add" I think this is not the issue.

My setup is:
* Using centos 6.5
* building perl v.5.18.1
* installed latest cpan, bioperl and gbrowse using cpan:
* as of 14/10/14: CPAN 2.05, BioPerl-1.6.923., GBrowse-2.55




Best,
Oliver





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Get alerted through email, SMS, voice calls or mobile push notifications.
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Re: GBRowse CGI-Parameter "add" is not working on my installation

Oliver Pelz
try on your own (tested in Firefox 33):
clear browser cache OR  "gbrowse_sess" cookie, than:
http://hostname/gb2/gbrowse_img/yeast/?name=chrI%3A80%2C000..120%2C000;add=chrI+oli+pelz+100100..100200
not working!
than:
http://hostname/gb2/gbrowse/yeast/  (works!)
than again url from point one:
http://hostname/gb2/gbrowse_img/yeast/?name=chrI%3A80%2C000..120%2C000;add=chrI+oli+pelz+100100..100200
now it works!

Can someone confirm?

Best,
Oliver

2014-10-22 15:02 GMT+02:00 Oliver Pelz <[hidden email]>:
On analyzing this further I have new insight and a proposed solution to the sessionid problem with the "add" cgi URL parameter.

If I clear the browsers cache (and apparently the gbrowse cookie which stores the session id called "gbrowse_sess") and directly go to a ../gbrowse_img/.. "add" URL
(e.g.: /gb2/gbrowse_img/yeast/?name=chrI%3A80%2C000..120%2C000;add=chrI+oli+pelz+100100..100200)
I get this sessionid error mession from above e.g.:
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.

If I clear the browse cache, then go to a ../gbrowse/.. URL WITHOUT THE ADD URL (e.g. with firebug cookie inspector open) I see that there it creates the missing "gbrowse_sess" cookie.
If I than go to a ../gbrowse_img/.. URL with ADD parameter it works because the cookie has been set before.
So the problem is that there is code in the gbrowse which creates a session id cookie only when browsing to the standard gbrowse pages and not in gbrowse_img with "add" parameter.

Since our website makes requests to our gbrowse server through ../gbrowse_img/.. URLS only using the ADD parameter
my suggested solution would be to create the missing session id and cookie on the ../gbrowse_img/.. requests if it is not available (e.g. from clearing browser), etc.


Best,
Oliver

2014-10-20 11:28 GMT+02:00 Oliver Pelz <[hidden email]>:
Hi all,

Would it be helpful if I would provide a Virtual Machine with the exact problem using Centos 6.5?

Best,
Oliver

2014-10-17 10:09 GMT+02:00 Oliver Pelz <[hidden email]>:
Hi again,

Please ignore the domain b110-ernai in my previous post (at step 3), this is a typo and should be localhost (I substituted everything by hand to hide this information from you ;) )

I just looked at the apache error log again, If I substiture the url ../gbrowse_img/.. with ../gbrowse/.. I also get the "sessionid unavailable" error as mentioned in my previous post but slightly more:

[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] RUN(): GET: http://localhost/cgi-bin/gb2/gbrowse/flybase/ name=wls;type=GENE%20TXN;width=580;keystyle=between;grid=on;add=3L%20E-RNAi%20wls%3A1%2011159720..11160708;add=3L%20E-RNAi%20wls%3A2%2011160919..11161014;add=3L%20E-RNAi%20wls%3A3%2011161237..11162741;style=E-RNAi%20glyph%3Dsegments%20fgcolor%3Dblack%20bgcolor%3Dplum at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 240.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] session id = ae5bfecb9cb84cd45e364bab2f332f1a at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 244.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] add_user_tracks() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 273.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] testing for asynchronous event() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 276.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] init() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 287.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] [2996] update_state() at /usr/local/lib64/perl5/Bio/Graphics/Browser2/Render.pm line 290.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.
[Fri Oct 17 10:05:54 2014] [error] [client 192.108.26.43] Premature end of script headers: gbrowse

Hope this helps,
Thank you for your help in advance,
Oliver



2014-10-17 9:34 GMT+02:00 Oliver Pelz <[hidden email]>:
Hi again,

after I could fix my problems with the wrong session type on my centos machine (see mailing list email about topic "cannot set admin password") I run in the next trouble.

For me  GBrowes's "add" functionality is not working (http://gmod.org/wiki/GBrowse_Configuration/URL_schema)

1.If I access the following URL with or without user_accounts enabled, everything works fine:

http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on


2.If I "add" some custom track information using the add-parameter e.g.:
http://localhost/cgi-bin/gb2/gbrowse_img/flybase/?name=wls;type=GENE+TXN;width=580;keystyle=between;grid=on;add=3L+E-RNAi+wls:1+11159720..11160708;add=3L+E-RNAi+wls:2+11160919..11161014;add=3L+E-RNAi+wls:3+11161237..11162741;style=E-RNAi+glyph=segments+fgcolor=black+bgcolor=plum;

I get an "Internal Server Error" in the browser. Looking at apache log file I see:

[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Sessionid unavailable at /usr/local/lib64/perl5/Bio/Graphics/Browser2/UserDB.pm line 502.
[Fri Oct 17 09:10:40 2014] [error] [client 192.108.26.43] Premature end of script headers: gbrowse_img

There is another "Sessionid unavailable" - thread in the mailing list, but it was never resolved (http://generic-model-organism-system-database.450254.n5.nabble.com/Sessionid-unavailable-with-gbrowse-img-and-login-system-td5711879.html).
Also if i set gbrowse_img path to gbrowse I get the same error.
I suspect it has something to do with the user accounts but I cannot find anything.
I played around again with the following GBrowse.conf parameters:

session lock type
upload_db_adaptor
user_account_db
admin_account
admin_dbs

but nothing can cure my problem.

The flybase database is a mysql database I imported from gbrowse 1.7 and which I migrated the database conf file. As I can see all the data when not using the cgi parameter "add" I think this is not the issue.

My setup is:
* Using centos 6.5
* building perl v.5.18.1
* installed latest cpan, bioperl and gbrowse using cpan:
* as of 14/10/14: CPAN 2.05, BioPerl-1.6.923., GBrowse-2.55




Best,
Oliver






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Re: GBRowse CGI-Parameter "add" is not working on my installation

John Portwood
I would like to bump this thread because I'm having the same issue and
Oliver's solution isn't working for me.

Curiously, the "Sessionid unavailable" issue does not occur when using add's
alias ("a=...;"). However, it still fails to draw the added glyph specified
in the parameters. Here's the URL I'm using:
http://localhost/fast/gbrowse_img/yeast/?name=chrI%3A80%2C000..120%2C000;a=chrI+Locus_Lookup+wx1+100100..110200

The same issue occurs when using the /gb2/ URL. The image is generated just
fine, with the correct region and specified tracks loaded. The only issue is
the added features are not getting drawn into the image.




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Re: GBRowse CGI-Parameter "add" is not working on my installation

Oliver Pelz
Thanks John for bumping this.
My solution is not really a workable solution and we postponed the new release of our web app until it is fixed because labeling gbrowse items is a core feature of our whole graphical view.
I would really appreciate someone fixing this problem!

Best,
Oliver

2014-12-18 20:54 GMT+01:00 John Portwood <[hidden email]>:
I would like to bump this thread because I'm having the same issue and
Oliver's solution isn't working for me.

Curiously, the "Sessionid unavailable" issue does not occur when using add's
alias ("a=...;"). However, it still fails to draw the added glyph specified
in the parameters. Here's the URL I'm using:
http://localhost/fast/gbrowse_img/yeast/?name=chrI%3A80%2C000..120%2C000;a=chrI+Locus_Lookup+wx1+100100..110200

The same issue occurs when using the /gb2/ URL. The image is generated just
fine, with the correct region and specified tracks loaded. The only issue is
the added features are not getting drawn into the image.




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Sent from the gmod-gbrowse mailing list archive at Nabble.com.

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