Re: [galaxy-dev] History not updating automatically
Joachim, is your history panel still not updating or did you find a
solution from the info in this thread?
If not, can you post the contents of the alert/popup message?
Thanks,
Carl
On Tue, Jan 29, 2013 at 5:26 AM, Joachim Jacob |VIB|
joachim.ja...@vib.bewrote:
Hi,
I have a similar - but not identical issue. The history panel is not being
updated: I have to restart Galaxy to see the updated panel.
It appears only to happen after an error relating to the history API of
Galaxy (it's a popup error, and I have closed it).
My apache config (thanks for any hints and tweaks to improve my setup).
[galaxy@galaxy conf.d]$ cat galaxy_web.conf
NameVirtualHost 157.193.230.103:80
VirtualHost 157.193.230.103:80
ServerName galaxy.bits.vib.be
Proxy balancer://galaxy
BalancerMember http://localhost:8080
BalancerMember http://localhost:8081
BalancerMember http://localhost:8082
BalancerMember http://localhost:8083
BalancerMember http://localhost:8084
BalancerMember http://localhost:8085
BalancerMember http://localhost:8086
BalancerMember http://localhost:8087
BalancerMember http://localhost:8088
BalancerMember http://localhost:8089
BalancerMember http://localhost:8090
BalancerMember http://localhost:8091
BalancerMember http://localhost:8092
/Proxy
RewriteEngine on
RewriteLog /tmp/apacheGalaxy.log
### LDAP authentication will be implemented later
# Location /
# AuthType Basic
# AuthBasicProvider ldap
# AuthLDAPURL
ldap://smeagol.vib.be:389/DC=**vib,DC=local?sAMAccountNamehttp://smeagol.vib.be:389/DC=vib,DC=local?sAMAccountName
# AuthLDAPBindDN vib\administrator
# AuthLDAPBindPassword tofillin
# AuthzLDAPAuthoritative off
# Require valid-user
# # Set the REMOTE_USER header to the contents of the LDAP query
response's uid attribute
# RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}
# /Location
RewriteRule ^/static/style/(.*)
/home/galaxy/galaxy-dist/**static/june_2007_style/blue/$1
[L]
RewriteRule ^/static/scripts/(.*)
/home/galaxy/galaxy-dist/**static/scripts/packed/$1
[L]
RewriteRule ^/static/(.*) /home/galaxy/galaxy-dist/**static/$1 [L]
RewriteRule ^/favicon.ico /home/galaxy/galaxy-dist/**static/favicon.ico
[L]
RewriteRule ^/robots.txt /home/galaxy/galaxy-dist/**static/robots.txt [L]
RewriteRule ^(.*) balancer://galaxy$1 [P]
/VirtualHost
Cheers,
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 01/28/2013 09:02 PM, Langhorst, Brad wrote:
Nate:
I used the config from the wiki directly…
Location /
…
RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}**e
...
/Location
but I also had a section like this below it...
# Location /api
# Satisfy Any
# Allow from all
# /Location
I thought that the /api location would inherit the auth and headers stuff
of it's container, but that's not true.
Commenting the api location fixes the problem form e.
Brad
On Jan 28, 2013, at 2:35 PM, Nate Coraor n...@bx.psu.edu
wrote:
Hi Brad and Sajoscha,
Is there any chance that your proxy configurations are not passing the
username in the REMOTE_USER header when the request is to an /api path?
Could you provide the relevant portions of your proxy server configs?
Thanks,
--nate
On Jan 28, 2013, at 7:12 AM, Langhorst, Brad wrote:
Hi Sajoscha:
I have exactly the same problem… it started about a month ago.
Also with external ldap auth.
I have not yet investigated in detail, since it's not crippling - just
annoying.
Brad
On Jan 28, 2013, at 6:38 AM, Sajoscha Sauer sa...@embl.de
wrote:
Hi list,
I have a weird problem after updating to the latest version.
After doing the update as usual, the history panel is not updating
automatically anymore. And when I press refresh, I get an javascript popup
saying:
Error getting history updates from the server.
Forbidden
Also, in the log I see the following:
galaxy.web.framework WARNING 2013-01-28 12:30:01,673 User logged in as
'(null)' externally, but has a cookie as 'sa...@embl.de' invalidating
session
We are using LDAP to connect to Galaxy, but I don't know if this has
something to do with the problem. As I said, it was working perfectly fine
before the update.
Does someone know the problem or has any ideas?
Thanks for your help,
Sajoscha
__**_
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
--
Brad Langhorst
langho...@neb.com
__**_
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
Re: [galaxy-dev] History not updating automatically
Hi,
I have a similar - but not identical issue. The history panel is not
being updated: I have to restart Galaxy to see the updated panel.
It appears only to happen after an error relating to the history API of
Galaxy (it's a popup error, and I have closed it).
My apache config (thanks for any hints and tweaks to improve my setup).
[galaxy@galaxy conf.d]$ cat galaxy_web.conf
NameVirtualHost 157.193.230.103:80
VirtualHost 157.193.230.103:80
ServerName galaxy.bits.vib.be
Proxy balancer://galaxy
BalancerMember http://localhost:8080
BalancerMember http://localhost:8081
BalancerMember http://localhost:8082
BalancerMember http://localhost:8083
BalancerMember http://localhost:8084
BalancerMember http://localhost:8085
BalancerMember http://localhost:8086
BalancerMember http://localhost:8087
BalancerMember http://localhost:8088
BalancerMember http://localhost:8089
BalancerMember http://localhost:8090
BalancerMember http://localhost:8091
BalancerMember http://localhost:8092
/Proxy
RewriteEngine on
RewriteLog /tmp/apacheGalaxy.log
### LDAP authentication will be implemented later
# Location /
# AuthType Basic
# AuthBasicProvider ldap
# AuthLDAPURL ldap://smeagol.vib.be:389/DC=vib,DC=local?sAMAccountName
# AuthLDAPBindDN vib\administrator
# AuthLDAPBindPassword tofillin
# AuthzLDAPAuthoritative off
# Require valid-user
# # Set the REMOTE_USER header to the contents of the LDAP query
response's uid attribute
# RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}
# /Location
RewriteRule ^/static/style/(.*)
/home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*)
/home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
RewriteRule ^/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) balancer://galaxy$1 [P]
/VirtualHost
Cheers,
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 01/28/2013 09:02 PM, Langhorst, Brad wrote:
Nate:
I used the config from the wiki directly…
Location /
…
RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e
...
/Location
but I also had a section like this below it...
# Location /api
# Satisfy Any
# Allow from all
# /Location
I thought that the /api location would inherit the auth and headers stuff of
it's container, but that's not true.
Commenting the api location fixes the problem form e.
Brad
On Jan 28, 2013, at 2:35 PM, Nate Coraor n...@bx.psu.edu
wrote:
Hi Brad and Sajoscha,
Is there any chance that your proxy configurations are not passing the username
in the REMOTE_USER header when the request is to an /api path? Could you
provide the relevant portions of your proxy server configs?
Thanks,
--nate
On Jan 28, 2013, at 7:12 AM, Langhorst, Brad wrote:
Hi Sajoscha:
I have exactly the same problem… it started about a month ago.
Also with external ldap auth.
I have not yet investigated in detail, since it's not crippling - just annoying.
Brad
On Jan 28, 2013, at 6:38 AM, Sajoscha Sauer sa...@embl.de
wrote:
Hi list,
I have a weird problem after updating to the latest version.
After doing the update as usual, the history panel is not updating
automatically anymore. And when I press refresh, I get an javascript popup
saying:
Error getting history updates from the server.
Forbidden
Also, in the log I see the following:
galaxy.web.framework WARNING 2013-01-28 12:30:01,673 User logged in as '(null)'
externally, but has a cookie as 'sa...@embl.de' invalidating session
We are using LDAP to connect to Galaxy, but I don't know if this has something
to do with the problem. As I said, it was working perfectly fine before the
update.
Does someone know the problem or has any ideas?
Thanks for your help,
Sajoscha
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
--
Brad Langhorst
langho...@neb.com
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
--
Brad Langhorst
langho...@neb.com
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___
Please keep all replies on the list by using reply all
in your mail
Re: [galaxy-dev] History not updating automatically
Hi Nate,
We have an extra proxy entry for the path galaxy/api, where we also require
ldap authentication. When I now remove this, the problem with the javascript
popup is solved and the web is working perfectly fine.
But now my API is not secured anymore, and this is clearly not what we want. Is
there a way around that? Or do I just don't get the point?
My proxy config is:
RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*)
/g/funcgen/galaxy/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/(.*) /g/funcgen/galaxy/static/$1 [L]
RewriteRule ^/galaxy/images/(.*) /g/funcgen/galaxy/static/images/$1 [L]
RewriteRule ^/galaxy/upload/(.*) /g/funcgen/galaxy/static/automated_upload/$1
[L]
RewriteRule ^/galaxy/favicon.ico /g/funcgen/galaxy/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /g/funcgen/galaxy/static/robots.txt [L]
RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
Location /galaxy
AuthName Galaxy
AuthType Basic
AuthBasicProvider ldap
AuthLDAPURL ldap:/ldap
AuthzLDAPAuthoritative off
Require valid-user
/Location
Location /galaxy/api
AuthName Galaxy (API)
AuthType Basic
AuthBasicProvider ldap
AuthLDAPURL ldap://ldap
AuthzLDAPAuthoritative off
Satisfy any
Allow from all
/Location
Directory /g/funcgen/galaxy/static/automated_upload
AllowOverride Options FileInfo
/Directory
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
THanks a lot for your help!
Cheers,
Sajoscha
On Jan 28, 2013, at 8:35 PM, Nate Coraor wrote:
Hi Brad and Sajoscha,
Is there any chance that your proxy configurations are not passing the
username in the REMOTE_USER header when the request is to an /api path?
Could you provide the relevant portions of your proxy server configs?
Thanks,
--nate
On Jan 28, 2013, at 7:12 AM, Langhorst, Brad wrote:
Hi Sajoscha:
I have exactly the same problem… it started about a month ago.
Also with external ldap auth.
I have not yet investigated in detail, since it's not crippling - just
annoying.
Brad
On Jan 28, 2013, at 6:38 AM, Sajoscha Sauer sa...@embl.de
wrote:
Hi list,
I have a weird problem after updating to the latest version.
After doing the update as usual, the history panel is not updating
automatically anymore. And when I press refresh, I get an javascript popup
saying:
Error getting history updates from the server.
Forbidden
Also, in the log I see the following:
galaxy.web.framework WARNING 2013-01-28 12:30:01,673 User logged in as
'(null)' externally, but has a cookie as 'sa...@embl.de' invalidating
session
We are using LDAP to connect to Galaxy, but I don't know if this has
something to do with the problem. As I said, it was working perfectly fine
before the update.
Does someone know the problem or has any ideas?
Thanks for your help,
Sajoscha
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
--
Brad Langhorst
langho...@neb.com
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
Re: [galaxy-dev] History not updating automatically
Hi Brad and Sajoscha, Is there any chance that your proxy configurations are not passing the username in the REMOTE_USER header when the request is to an /api path? Could you provide the relevant portions of your proxy server configs? Thanks, --nate On Jan 28, 2013, at 7:12 AM, Langhorst, Brad wrote: Hi Sajoscha: I have exactly the same problem… it started about a month ago. Also with external ldap auth. I have not yet investigated in detail, since it's not crippling - just annoying. Brad On Jan 28, 2013, at 6:38 AM, Sajoscha Sauer sa...@embl.de wrote: Hi list, I have a weird problem after updating to the latest version. After doing the update as usual, the history panel is not updating automatically anymore. And when I press refresh, I get an javascript popup saying: Error getting history updates from the server. Forbidden Also, in the log I see the following: galaxy.web.framework WARNING 2013-01-28 12:30:01,673 User logged in as '(null)' externally, but has a cookie as 'sa...@embl.de' invalidating session We are using LDAP to connect to Galaxy, but I don't know if this has something to do with the problem. As I said, it was working perfectly fine before the update. Does someone know the problem or has any ideas? Thanks for your help, Sajoscha ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Brad Langhorst langho...@neb.com ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
