Oliver Pelz
2014-10-17 07:34:16 UTC
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.
3. If I disable user_accounts, it works again but not showing the custom
"add" tracks with the URL fom point 2, e.g.:
http://b110-ernai/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 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
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.
3. If I disable user_accounts, it works again but not showing the custom
"add" tracks with the URL fom point 2, e.g.:
http://b110-ernai/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 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