Re: [galaxy-dev] Question about installing NCBI BLAST+ onto Galaxy
On Thu, Jun 30, 2011 at 1:26 AM, George Yianni Michopoulos wrote: Hey Peter, Thanks so much for your help, your comments helped me realize what was wrong. The issue was that I wasn't including the name of the database within the path, just the folder it was in! Best, George Michopoulos Easily done, I'm glad its working now. Peter ___ 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/
[galaxy-dev] Using the tool after log in
Hi All, I have local instance of galaxy . I want to make changes in such a way that after log in, user should able to submit any job or run any tool. Log in should be compulsory to run any tool including upload tool. Whenever someone clicks on tool without log in ,it should display message like You must be logged in http://192.168.62.51:8089/user/login?webapp=galaxy to use Galaxy . Reagrds shashi shekhar ___ 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 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.
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Re: [galaxy-dev] Refreshing/Reloading Files
Hi Paul Please keep all replies on the list by using reply all A simple solution, which we use quite a lot, is the following: we use the dynamic_options attribute, eg: inputs param name=foo type=select label=what help=Use tickboxes to select display=radio dynamic_options=ds_fooOptions()/ /inputs outputs data format=fasta name=output label=more foo / /outputs code file=extra_code_for_foo_list.py / help /help /tool and then we have a little python script (extra_code_for_foo_list.py) with the ds_fooOptions function, which can read your file (ie your list of databases), eg def ds_fooOptions(): List available foos as tuples of (displayName,value) foos = whatever python code is required to generate the tuples return foos I hope this helps, Hans On 06/29/2011 08:09 PM, Admins de Galaxy wrote: Hi Hans, yes that's it. We are offering the list of databases as options to select in the GUI, before executing the script which compares the selected database with the sequence. Paul 2011/6/29 Hans-Rudolf Hotzh...@fmi.ch Hi Paul You probably need to be a bit more specific...at what stage is this '.txt file' read (or rather should be read)? - are you offering the (growing) list of databases as options to select in the GUI? Hans On 06/29/2011 10:20 AM, Admins de Galaxy wrote: Hello everyone, we have a problem with one of our selfwritten tools. We have a tool, that compares sequence with a database. The List of the available databases is loaded from a .txt file. One of our other tools, manages that a new database is added to the .txt file. But Galaxy doesn't recognize the change. It would be nice if someone could give us an advice. Best regards Paul K. Deuster @ Technische Hochschule Mittelhessen __**_ 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] How to set java heap size in Galaxy?
Hello Liu, I'm keeping our mail thread in the mailing list, as advised by its guidelines on the footer of each mail. Now, galaxy runs on top of paster, a minimal python webserver, but it has nothing to do with Java, looks like your out of memory error comes from your app then. Have you tried the suggested settings from Marco ? Namely: java -Xmx512m I bet there's an environment variable or config setting for Tomcat too if you're unsure about where your jar's are called. Hope that helps ! Roman On 2011-06-29 12:02, liu bo wrote: Thank you, Roman. Our app invoke a workflow server. I guess Galaxy has a self container like Tomcat, that is why we can access it via 127.0.0.1 from browser. I know in Tomcat, there is a file catalina.sh for setting JAVA_OPTS. Is there a similiar file in Galaxy to set JAVA_OPTS? Thank you very much. Regards, Bo On Tue, Jun 28, 2011 at 4:18 AM, Roman Valls brainst...@nopcode.org wrote: Hi Liu, Does your app execute Picard/GATK at some point ? In that case those would be the ones triggering your Java OOM error, in that case Bo's suggestion is the way to go. That's my best guess since Galaxy itself doesn't use java either (only python AFAIK). Regards, Roman On 2011-06-27 18:44, liu bo wrote: Hi Marco, Thanks for your kind reply. My app is a python file, and there's not an explicit command to run java. I just wonder whether there is a file to configure Galaxy, in order to set the Java heap size. Thank you. Best wishes, Bo On Mon, Jun 27, 2011 at 7:51 PM, Marco Moretto marco.more...@gmail.com wrote: Hi Liu, if you set up your application in the XML to run with Java, like java -jar yourapplication.jar, it is sufficient to add the -Xmx parameter. Something like java -Xmx512m -jar yourapplication.jar Greets --- Marco On 27 June 2011 12:15, liu bo liub...@gmail.com wrote: Dear all, I have added an application to Galaxy's Tools. Now there occurs an error java.lang.OutOfMemoryError: Java heap space. Do you know how to set java heap size in Galaxy? Thank you very much. Best regards, Bo ___ 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/ ___ 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] public datasets/histories with external auth
Shantanu Pavgi wrote: On Jun 28, 2011, at 2:15 PM, Nate Coraor wrote: Shantanu Pavgi wrote: I did a test by excluding following URLs from Apache-Shibboleth external authentication and it seems to be working: - /datasets/ - /u/username/h/history-name - /static/ (css and javascript) Do I need to exclude any other URLs so that published histories and datasets can be accessed from remote sites without authentication? Also, will it offer read-only access to the galaxy interface? Does it expose any job submission, file-uploads or any other modification/execution operations using web interface? Hi Shantanu, These should be sufficient and would not give access to anything job or tool related. However, since /datasets/ is exposed, this means that any dataset with no roles associated with the access permission (i.e. a public dataset) would be readable by anyone. Dataset IDs are encoded so as not to be easily guessable, but relying on this is essentially security by obscurity. Thanks for the reply Nate. We are able to view datasets over to UCSC site if we directly append /dataset URL as a query parameter to the main UCSC URL. But we discovered one more use case where datasets contained in a particular history have a different URL format for UCSC link. For example, you should be able to access following URL without authentication: https://galaxy.uabgrid.uab.edu/history/list_shared?sort=-update_timeoperation=Viewid=24d84bcf64116fe7 Now if you click on dataset-1 and then click on 'display at UCSC main' then the resulting URL is as follows: https://galaxy.uabgrid.uab.edu/datasets/3423/display_at/ucsc_main?redirect_url=http%3A%2F%2Fgenome.ucsc.edu%2Fcgi-bin%2FhgTracks%3Fdb%3Dmm9%26position%3Dchr1%3A20048750-20608024%26hgt.customText%3D%25sdisplay_url=http%3A%2F%2Fgalaxy.uabgrid.uab.edu%2Froot%2Fdisplay_as%3Fid%3D3423%26display_app%3Ducsc%26authz_method%3Ddisplay_at This link fails without authentication as we have exposed only /datasets URL pattern. I can manually insert /dataset URL for UCSC 'display_url', however it's not intuitive for end users. I am bit concerned about opening up /root/display_as URL pattern without knowing it's implications. I guess it doesn't expose any jobs or tools related access, but not sure about it. Any comments or suggestions? display_as is covered under Display at UCSC: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy You can expose it just to UCSC or globally. Since you're already exposing /datasets/ globally, doing the same with /root/display_as is probably not much different. --nate Also, can we prevent particular galaxy-user from carrying out certain actions, e.g. running jobs, file uploads etc.? Since galaxy will create 'anonymous' user account based on the REMOTE_USER variable set for unauthenticated requests, I am wondering if such locked-down mode will be possible for a particular galaxy-user. This cannot be done from within Galaxy, but it shouldn't be necessary since these actions are not exposed to the anonymous user. I think the user is not anonymous here as we have already written REMOTE_USER to 'anonymous' now. The galaxy receives this user as user-login/email as 'anonymous@mail.domainmailto:'anonymous@mail.domain'. Now we are opening up certain URL patterns to be accessed as 'anonymous@mail.domainmailto:'anonymous@mail.domain' user. These URL patterns include following formats as mentioned - /datasets, /history, /u/username/hhistory-name, and /static. In addition we may need to expose /root/display_as URL pattern as well. Rest of the site remains protected using real authentication. So as long as above URL patterns don't expose any job submission, file uploads or other galaxy tools operations then we should be OK with it. Thoughts? -- Thanks, 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/
[galaxy-dev] fasta integration in galaxy
Dear All, I have just finished integrating my blast data to my galaxy local instance, and now I would like to add my fasta files. Does anybody know how can I do that ? How should it look in the UI ? Thanks, best regards Ben ___ 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/
[galaxy-dev] output data filter
Hi I'm having an internal data source that is connected to Galaxy (version: second last distribution) through the data connection protocol. I have some parameters returned from my data source website which are parsed with a parameter request translation. Everything works fine except for establishing variable static output data (https://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput). I want to label my output data set according to a parameter value that is returned from my data source website. How can I use this parameter as a filter because the following statement does not work: request_param_translation request_param galaxy_name=dummy remote_name=output missing=test / outputs data name=output label=labelX filter$dummy == valueX /filter /data data name=output label=labelY filter$dummy != valueX /filter /data /outputs I have also tried without the dollar character (dummy = valueX) as stated in the link above but this gives a TypeError in the log. Using $dummy.value==valueX does not work either. If I print the Galaxy variables by Cheetah code ( #silent sys.stderr.write( searchList = '%s'\n % (str($searchList))) ), the parameter dummy is created. So, how can I use this type of parameter as a filter? thx for any suggestion regards Bram ___ 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] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple=true input datasets
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.comwrote: 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 possible at all to have a select multiple of datasets as an input parameter?? best, Leandro On Thu, May 19, 2011 at 6:59 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi Galaxy developers, Something seems maybe to be wrong with the format=html type... I forgot to add before that my tool input param the format=html attribute: param type=data multiple=true format=html name=input1 / In another tool I have it outputs format=html and this works and displays in Galaxy just fine. I would like to use multiple of these output datasets in my history as the input for this other tool but something seems to be wrong if you try to do this? a bit lost,
Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple=true input datasets
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 possible at all to have a select multiple of datasets as an input parameter?? best, Leandro On Thu, May 19, 2011 at 6:59 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi Galaxy developers, Something seems maybe to be wrong with the format=html type... I forgot to add before that my tool input param the format=html attribute: param type=data multiple=true format=html name=input1 /
Re: [galaxy-dev] database migration issue 64 -65 - postgresql
Sorry, for some reason, I attached the compiled version of the script to my
initial message - here's the code...
Migration script to add 'name' attribute to the JSON dict which describes
a form definition field and the form values in the database. In the 'form_values'
table, the 'content' column is now a JSON dict instead of a list.
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
from sqlalchemy.exc import *
from galaxy.util.json import from_json_string, to_json_string
from galaxy.model.custom_types import _sniffnfix_pg9_hex
import datetime
now = datetime.datetime.utcnow
import sys, logging
log = logging.getLogger( __name__ )
log.setLevel(logging.DEBUG)
handler = logging.StreamHandler( sys.stdout )
format = %(name)s %(levelname)s %(asctime)s %(message)s
formatter = logging.Formatter( format )
handler.setFormatter( formatter )
log.addHandler( handler )
metadata = MetaData( migrate_engine )
db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
def upgrade():
print __doc__
metadata.reflect()
try:
FormDefinition_table = Table( form_definition, metadata, autoload=True )
except Exception, e:
log.debug( Loading 'form_definition' table failed: %s % str( e ) )
try:
FormValues_table = Table( form_values, metadata, autoload=True )
except Exception, e:
log.debug( Loading 'form_values' table failed: %s % str( e ) )
def get_value(lst, index):
try:
return str(lst[index]).replace(', '')
except IndexError,e:
return ''
# Go through the entire table and add a 'name' attribute for each field
# in the list of fields for each form definition
cmd = SELECT f.id, f.fields FROM form_definition AS f
result = db_session.execute( cmd )
for row in result:
form_definition_id = row[0]
fields = str( row[1] )
if not fields.strip():
continue
fields_list = from_json_string( _sniffnfix_pg9_hex( fields ) )
if len( fields_list ):
for index, field in enumerate( fields_list ):
field[ 'name' ] = 'field_%i' % index
field[ 'helptext' ] = field[ 'helptext' ].replace(', '').replace('', )
field[ 'label' ] = field[ 'label' ].replace(', '')
fields_json = to_json_string( fields_list )
if migrate_engine.name == 'mysql':
cmd = UPDATE form_definition AS f SET f.fields='%s' WHERE f.id=%i %( fields_json, form_definition_id )
else:
cmd = UPDATE form_definition SET fields='%s' WHERE id=%i %( fields_json, form_definition_id )
db_session.execute( cmd )
# replace the values list in the content field of the form_values table with a name:value dict
cmd = SELECT form_values.id, form_values.content, form_definition.fields \
FROM form_values, form_definition \
WHERE form_values.form_definition_id=form_definition.id \
ORDER BY form_values.id ASC
result = db_session.execute( cmd )
for row in result:
form_values_id = int( row[0] )
if not str( row[1] ).strip():
continue
row1 = str(row[1]).replace('\n', '').replace('\r', '')
values_list = from_json_string( str( row1 ).strip() )
if not str( row[2] ).strip():
continue
fields_list = from_json_string( str( row[2] ).strip() )
if fields_list and type(values_list) == type(list()):
values_dict = {}
for field_index, field in enumerate( fields_list ):
field_name = field[ 'name' ]
values_dict[ field_name ] = get_value(values_list, field_index )
cmd = UPDATE form_values SET content='%s' WHERE id=%i %( to_json_string( values_dict ), form_values_id )
db_session.execute( cmd )
def downgrade():
metadata.reflect()
try:
FormDefinition_table = Table( form_definition, metadata, autoload=True )
except Exception, e:
log.debug( Loading 'form_definition' table failed: %s % str( e ) )
try:
FormValues_table = Table( form_values, metadata, autoload=True )
except Exception, e:
log.debug( Loading 'form_values' table failed: %s % str( e ) )
# remove the name attribute in the content column JSON dict in the form_values table
# and restore it to a list of values
cmd = SELECT form_values.id, form_values.content, form_definition.fields \
FROM form_values, form_definition \
WHERE form_values.form_definition_id=form_definition.id \
ORDER BY form_values.id ASC
result = db_session.execute( cmd )
for row in result:
form_values_id = int( row[0] )
if not str( row[1] ).strip():
continue
values_dict = from_json_string( str( row[1] ) )
if not str( row[2] ).strip():
Re: [galaxy-dev] New galaxy tool shed
Hello Marcel, On Jun 28, 2011, at 5:23 PM, Marcel Schumann wrote: Hi Greg, Just two small points: -- the new 'detailed description' cannot yet display linebreaks correctly. Looks a little bit confusing this way (for an example, just have a look a the description text I pasted into the field for CADDSuite) ;-) This issue has been fixed - thanks for pointing it out. -- just to clarify: I actually meant that it would be very helpful if a version-number in the 'old' style (plain version number, not repository hash key) could be shown as well. This would make it easier for users to understand which release-version of the software is in the toolsuite. But otherwise, as a workaround, I could of course just add a version number to the toolsuite's short-description field ... Yes, attributes like tool_id, version, etc, fall into the category of repository metadata, a new feature which I am currently implementing. It should be available fairly soon. Cheers, Marcel On 06/28/2011 10:05 PM, Greg Von Kuster wrote: Hello Marcel, Thanks for your message - see my inline comments below. On Jun 28, 2011, at 5:55 AM, Marcel Schumann wrote: Hi Greg, hi Dave, I just uploaded a current version of CADDSuite for MacOS10.6 (in addition to the version for Linux) to the Galaxy tool shed. Thereby I noticed some problems and possible enhancements. I just wanted to let you know about them; I hope this is somewhat helpful ... Errors/problems: -- If _not_ logged in, clicking on any tool or category will produce Server error ! This bug has been corrected - thanks for letting us know about it. -- The new hg based tool shed does not display/support any tool(suite) version any more. I know that this was probably done on purpose, but I guess this will very confusing for users. If publicly available/published software has its own version number, it would be very nice if this could also be shown in the tool shed. Yes, versions are now the repository tip, which is displayed. -- The new tool shed also does not show detailed description texts any more (in contrast to the previous tool shed). However, I guess these description text could be very important for potential users who search for tools for their tasks. Guessing what a tool/toolsuite does by just reading the one-line description currently supported by the new tool shed is of course not very easy ;-) I've added a Detailed description text field for repositories in the tool shed - thanks for requesting this. Ideas for enhancements: -- It would be nice to have same kind of download counter I've added a field that displays the number of times a repository was downloaded using the pop-up menu options. Again, thanks for your request. -- some way to enable users to submit feedback or comments would also be great There is already a Rate repository option on the Repository options pop-up menu. This option allows you to add a 1 - 5 star rating, along with your own Review comments. -- last but not least, I think you should really advertise your tool shed on your homepages. On both getgalaxy.org and usegalaxy.org I never saw any link/description of the tool shed, but it really is a nice way to share tools :-) We'll look into this, thanks! Cheers, Marcel -- Marcel Schumann University of Tuebingen Wilhelm Schickard Institute for Computer Science Division for Applied Bioinformatics Room C304, Sand 14, D-72076 Tuebingen phone: +49 (0)7071-29 70437 fax: +49 (0)7071-29 5152 email: schum...@informatik.uni-tuebingen.de Greg Von Kuster Galaxy Development Team g...@bx.psu.edu -- Marcel Schumann University of Tuebingen Wilhelm Schickard Institute for Computer Science Division for Applied Bioinformatics Room C304, Sand 14, D-72076 Tuebingen phone: +49 (0)7071-29 70437 fax: +49 (0)7071-29 5152 email: schum...@informatik.uni-tuebingen.de Greg Von Kuster Galaxy Development Team g...@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] public datasets/histories with external auth
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.
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Re: [galaxy-dev] rgWebLogo3 with Probabilities instead of Entropy
Thanks - code to accompany good suggestions is always appreciated :) I'll write a test and get a patched version on test as soon as I get some time - travelling all day today - will let you know when it's done On Fri, Jul 1, 2011 at 7:20 AM, Assaf Gordon gor...@cshl.edu wrote: Hello Ross and Galaxy team, May I suggest this small patch, that enables WebLogo to plot either Entropy bits (the current default) or just nucleotides probabilities ? It uses the standard -U parameter of weblogo3. -gordon ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
