Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple=true input datasets
Hi Kip, For the time being we are using this method to achieve the same result, although its not as nice as just having a multi-select menu in the form: command ... $input1 #for $r in $add_inputs $r.$input2 #end for ... /command In inputs: param name=input1 type=data/ repeat name=add_inputs param name=input2 type=data / /repeat best, Leandro On Thu, Jun 30, 2011 at 4:52 PM, Kip Bodi kip.b...@tufts.edu wrote: Sorry, I tried to edit that, to make it simpler, but missed the param block. The 'name' does match the one in the 'command' on my end (list_of_items_in_history). On Thu, Jun 30, 2011 at 10:45 AM, Kip Bodi kip.b...@tufts.edu wrote: Hi all, I'm having the same problem. I have a script that tries to take several history data sets as a single input: command interpreter=perlaggregate.pl --out $outfile $list_of_items_in_history/command inputs param format=txt name=fitness_tables type=data multiple=true label=Fitness score table, per site/ /inputs outputs data format=tabular name=outfile / /outputs If I select only one history item it works, but if I press 'ctrl' to select multiple items, it fails: File '/storage/apps/galaxy_dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/usr/lib/python2.6/site-packages/paste/debug/prints.py', line 106 in __call__ environ, self.app) File '/usr/lib/python2.6/site-packages/paste/wsgilib.py', line 543 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/lib/python2.6/site-packages/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/lib/python2.6/site-packages/paste/httpexceptions.py', line 633 in __call__ return self.application(environ, start_response) File '/storage/apps/galaxy_dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/storage/apps/galaxy_dist/lib/galaxy/web/controllers/tool_runner.py', line 68 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 979 in handle_input _, out_data = self.execute( trans, incoming=params, history=history ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 1271 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/actions/__init__.py', line 360 in execute for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): File '/storage/apps/galaxy_dist/lib/galaxy/tools/__init__.py', line 1274 in params_to_strings return params_to_strings( self.inputs, params, app ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/__init__.py', line 79 in params_to_strings value = params[ key ].value_to_basic( value, app ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 110 in value_to_basic return self.to_string( value, app ) File '/storage/apps/galaxy_dist/lib/galaxy/tools/parameters/basic.py', line 1457 in to_string return value.id AttributeError: 'list' object has no attribute 'id' Is using multiple history items as a single input not currently supported, or is there something else I'm doing wrong? Cheers, Kip On Thu, Jun 9, 2011 at 7:05 AM, Leandro Hermida soft...@leandrohermida.com wrote: Hi again, Sorry to ping again about this, just very interested in knowing if this is a missing feature in Galaxy or if I had configured something wrong. Is it possible in Galaxy to have a tool with a multiple=true input dataset parameter? It doesn't seem so? best, Leandro On Tue, May 24, 2011 at 1:31 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi Nate, Thanks for the ping, have fun at the conference! On Tue, May 24, 2011 at 11:22 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Leandro, The Galaxy Team has recently been preparing for and traveling in advance of the Galaxy Community Conference, which begins today. Unfortunately I don't have an answer for you, but when we're all back at work next week, someone should be able to respond. Thanks, --nate Leandro Hermida wrote: Hi again, Very sorry to ask again, just gotten no repsonse, but is this a Galaxy bug or does anyone have a functioning tool that takes multiple datasets as an input parameter??? i.e. param type=data multiple=true ... / regards, Leandro On Thu, May 19, 2011 at 7:15 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi again, I tried changing the format to txt and tabular which I have other datasets in my history and still the same error and stack trace in Galaxy. Is it
[galaxy-dev] Galaxy forgetting history and giving me new blank history
Having a very strange problem in the Galaxy web GUI that suddenly just started happening yesterday, getting very strange behavior in the history right panel. - Most of the time when I click on something in the GUI like to go to a tool page or to go to the Admin interface and come back suddenly Galaxy just replaces my current history and gives me a brand new history, its like it forgets what history I'm working with - In tool forms sometimes input data drop downs don't have anything in them even though there are datasets in my history that are of the right datatype. Could be related to problem above where it thinks maybe I'm in a new blank history Anyone have this ever happen? regards, Leandro ___ 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] public datasets/histories with external auth
Hi Shantanu,
Thank you for your update, I've done my config a little differently and it
appears to work just the same. The relevant part looks like this:
Location /
## ActiveDirectory authentication and authorization
AuthType Basic
AuthBasicProvider ldap
AuthName RD Galaxy Testing/QA Server
AuthLDAPURL ldap://my.server.com:389/OU=Users
Workstations,DC=domain,DC=com?sAMAccountName?sub?(|(objectClass=person)(objectClass=group))
# ...more AuthLDAP directives here...
RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e
/Location
Location /datasets
Order Allow,Deny
Allow from All
Satisfy Any
RequestHeader set REMOTE_USER anonymous
/Location
## Static content and reverse proxy
RewriteEngine On
RewriteRule ^/static/style/(.*)
/path/to/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*)
/path/to/galaxy/galaxy_dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /path/to/galaxy/galaxy_dist/static/$1 [L]
RewriteRule ^/favicon.ico /path/to/galaxy/galaxy_dist/static/favicon.ico
[L]
RewriteRule ^/robots.txt /path/to/galaxy/galaxy_dist/static/robots.txt
[L]
RewriteRule ^(.*) http://galaxy.server.hostname:8080 [P]
On Fri, Jul 1, 2011 at 12:13 AM, Shantanu Pavgi pa...@uab.edu wrote:
On Jun 30, 2011, at 6:34 AM, Leandro Hermida wrote:
Hi Nate and Shantanu,
Thanks so much for the clear guidance, this works and sorry I didn't
read the Apache docs properly
best,
Leandro
On Thu, Jun 30, 2011 at 6:14 AM, Shantanu Pavgi pa...@uab.edu wrote:
On Jun 29, 2011, at 12:21 PM, Nate Coraor wrote:
Leandro Hermida wrote:
Hi Shantanu,
In your Apache configuration exactly how did you set up an anonymous
REMOTE_USER just for specific locations like the /datasets/ path? I'm
just
looking at the Apache docs and the RequestHeader directive has a context
of
the entire VirtualHost and cannot be put into a Location container so
I'm
not sure how to do it.
Hi Leandro,
See the optional 'env=' argument and docs on the same for ways to make
RequestHeader conditional:
http://httpd.apache.org/docs/current/mod/mod_headers.html#requestheader
So, depending on the path accessed, you should be able to have
mod_rewrite set an environment variable specifying which REMOTE_USER
(real username or fake anonymouse user) should be set.
You could also just set it as the anonymous user to start with and then
use 'RequestHeader set' to overwrite it with the real username in the
case that a real username is available.
This is all just from glancing at the docs, though, I have not tried any
of it out, and this sort of Apache trickery is always difficult to get
right.
--nate
Leandro,
The RequestHeader has a context of 'directory' as well, which includes
Directory, Location, Files, and Proxy containers [1]. So you
should
be able to use it in Location directive.
Following is a configuration snippet related to what Nate described in
his
earlier response. We are setting REMOTE_USER variable to anonymous when
it's
not set/empty.
Location ~ /(datasets|history)/
AuthType shibboleth
ShibRequireSession off
Require shibboleth
RewriteCond %{LA-U:REMOTE_USER} =
RequestHeader set REMOTE_USER anonymous
/Location
Hope this helps.
1. http://httpd.apache.org/docs/current/mod/directive-dict.html#Context
--
Shantanu.
Leandro,
I realized that above mentioned configuration is wrong. It will set
RequestHeader to 'anonymous' regardless of authentication status. I think
following config should work (still testing). In our case it resides outside
of Location directive now. You may need to adjust it according to your
setup:
{{{
# Take the environment variable and set it as a header in the
proxy request.
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
# Set RU to anonymous if No REMOTE_USER
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} =
RewriteRule . - [E=RU:anonymous]
# Set RequestHeader
RequestHeader set REMOTE_USER %{RU}e
}}}
--
Shantanu.
___
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] public datasets/histories with external auth
Hi again,
I just realized that my setup is not going to work at all and does that
exact thing you just mentioned, even if you are logged in it will set the
REMOTE_USER to anonymous when you click on any /datasets URL. This causes
some strange Galaxy history behavior!
oops,
Leandro
On Fri, Jul 1, 2011 at 10:36 AM, Leandro Hermida soft...@leandrohermida.com
wrote:
Hi Shantanu,
Thank you for your update, I've done my config a little differently and it
appears to work just the same. The relevant part looks like this:
Location /
## ActiveDirectory authentication and authorization
AuthType Basic
AuthBasicProvider ldap
AuthName RD Galaxy Testing/QA Server
AuthLDAPURL ldap://my.server.com:389/OU=Users
Workstations,DC=domain,DC=com?sAMAccountName?sub?(|(objectClass=person)(objectClass=group))
# ...more AuthLDAP directives here...
RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e
/Location
Location /datasets
Order Allow,Deny
Allow from All
Satisfy Any
RequestHeader set REMOTE_USER anonymous
/Location
## Static content and reverse proxy
RewriteEngine On
RewriteRule ^/static/style/(.*)
/path/to/galaxy/galaxy_dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/scripts/(.*)
/path/to/galaxy/galaxy_dist/static/scripts/packed/$1 [L]
RewriteRule ^/static/(.*) /path/to/galaxy/galaxy_dist/static/$1 [L]
RewriteRule ^/favicon.ico /path/to/galaxy/galaxy_dist/static/favicon.ico
[L]
RewriteRule ^/robots.txt /path/to/galaxy/galaxy_dist/static/robots.txt
[L]
RewriteRule ^(.*) http://galaxy.server.hostname:8080 [P]
On Fri, Jul 1, 2011 at 12:13 AM, Shantanu Pavgi pa...@uab.edu wrote:
On Jun 30, 2011, at 6:34 AM, Leandro Hermida wrote:
Hi Nate and Shantanu,
Thanks so much for the clear guidance, this works and sorry I didn't
read the Apache docs properly
best,
Leandro
On Thu, Jun 30, 2011 at 6:14 AM, Shantanu Pavgi pa...@uab.edu wrote:
On Jun 29, 2011, at 12:21 PM, Nate Coraor wrote:
Leandro Hermida wrote:
Hi Shantanu,
In your Apache configuration exactly how did you set up an anonymous
REMOTE_USER just for specific locations like the /datasets/ path? I'm
just
looking at the Apache docs and the RequestHeader directive has a
context of
the entire VirtualHost and cannot be put into a Location container so
I'm
not sure how to do it.
Hi Leandro,
See the optional 'env=' argument and docs on the same for ways to make
RequestHeader conditional:
http://httpd.apache.org/docs/current/mod/mod_headers.html#requestheader
So, depending on the path accessed, you should be able to have
mod_rewrite set an environment variable specifying which REMOTE_USER
(real username or fake anonymouse user) should be set.
You could also just set it as the anonymous user to start with and then
use 'RequestHeader set' to overwrite it with the real username in the
case that a real username is available.
This is all just from glancing at the docs, though, I have not tried
any
of it out, and this sort of Apache trickery is always difficult to get
right.
--nate
Leandro,
The RequestHeader has a context of 'directory' as well, which includes
Directory, Location, Files, and Proxy containers [1]. So you
should
be able to use it in Location directive.
Following is a configuration snippet related to what Nate described in
his
earlier response. We are setting REMOTE_USER variable to anonymous when
it's
not set/empty.
Location ~ /(datasets|history)/
AuthType shibboleth
ShibRequireSession off
Require shibboleth
RewriteCond %{LA-U:REMOTE_USER} =
RequestHeader set REMOTE_USER anonymous
/Location
Hope this helps.
1.
http://httpd.apache.org/docs/current/mod/directive-dict.html#Context
--
Shantanu.
Leandro,
I realized that above mentioned configuration is wrong. It will set
RequestHeader to 'anonymous' regardless of authentication status. I think
following config should work (still testing). In our case it resides outside
of Location directive now. You may need to adjust it according to your
setup:
{{{
# Take the environment variable and set it as a header in the
proxy request.
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
# Set RU to anonymous if No REMOTE_USER
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} =
RewriteRule . - [E=RU:anonymous]
# Set RequestHeader
RequestHeader set REMOTE_USER %{RU}e
}}}
--
Shantanu.
___
Please keep all replies on the list by using reply all
in your mail client. To manage your
Re: [galaxy-dev] Galaxy forgetting history and giving me new blank history
Hi - you can ignore this message, I figured out what the problem was and it was caused by a change in my front end authentication setup On Fri, Jul 1, 2011 at 10:21 AM, Leandro Hermida soft...@leandrohermida.com wrote: Having a very strange problem in the Galaxy web GUI that suddenly just started happening yesterday, getting very strange behavior in the history right panel. - Most of the time when I click on something in the GUI like to go to a tool page or to go to the Admin interface and come back suddenly Galaxy just replaces my current history and gives me a brand new history, its like it forgets what history I'm working with - In tool forms sometimes input data drop downs don't have anything in them even though there are datasets in my history that are of the right datatype. Could be related to problem above where it thinks maybe I'm in a new blank history Anyone have this ever happen? regards, Leandro ___ 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] importing annotation with dataset
Hi David, If this request was property understood (include database assignment, etc. during import), it was addressed in the latest Galaxy distribution and is also live on Galaxy main. Comments about the implementation are welcomed. Best regards, Jen Galaxy team On 3/8/11 1:44 AM, Davide Cittaro wrote: Hi, is it just me or when I try to import a dataset from a library to a history, annotation is not retained (whereas info is)? d /* Davide Cittaro, PhD Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.citt...@ifom-ieo-campus.it mailto:davide.citt...@ifom-ieo-campus.it */ ___ 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/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ___ 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/
