History not updating automatically
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 'sauer@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
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 <sauer@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 'sauer@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:
-- Brad Langhorst langhorst@neb.com
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 <sauer@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 'sauer@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:
-- Brad Langhorst langhorst@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:
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 <nate@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 <sauer@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 'sauer@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:
-- Brad Langhorst langhorst@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:
-- Brad Langhorst langhorst@neb.com
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 <nate@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 <sauer@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 'sauer@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 langhorst@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:
-- Brad Langhorst langhorst@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:
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.jacob@vib.be>wrote:
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<http://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 <nate@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 <sauer@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 'sauer@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:
-- Brad Langhorst langhorst@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:
--
Brad Langhorst langhorst@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:
______________________________**_____________________________ 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:
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 <sauer@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 'sauer@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:
-- Brad Langhorst langhorst@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:
participants (5)
-
Carl Eberhard -
Joachim Jacob |VIB| -
Langhorst, Brad -
Nate Coraor -
Sajoscha Sauer