filtering a <param> of type 'data' so only one type is available
by Dan Tenenbaum
Hi,
I have a tool wrapper with a <param> of type="data".
Currently, this renders as a text box with a drop down list that has
52 items in it (the number of things I have in my history, I guess).
I'd like to filter this list so that only some items in the history
(in my case any item whose name ends with '.rda') are shown in this
dropdown.
It seems like maybe the 'format' parameter to the 'param' tag is what
I want, but:
1) I tried format="rda" and that didn't seem to change anything.
2) "rda" is not in the datatypes.conf file which the documentation
suggests is required?
(.rda is an extension used for serialized R objects.)
The tool I'm working on only accepts rda files as input and the reason
I'm asking for this is that it is all too easy to accidentally feed it
a file of some other type. If the dropdown could be filtered so that
only items which will work with the tool are shown, that would be
great.
Is there a way to do that?
Thanks,
Dan
5 years, 3 months
API : Max retries exceeded
by Gildas Le Corguille
Hi,
I wrote a script which need to retrieve a list of all users on our
production instance.
It seems that we have too many users (325) :P
bioblend.galaxy.client.ConnectionError:
HTTPConnectionPool(host='galaxy.sb-roscoff.fr', port=8080): Max retries
exceeded with url: /api/users?key=fd420zefff9a9df586210fd8c8452d98
(Caused by <class 'socket.error'>: [Errno 111] Connection refused): None
My script is running on an test instance which have less users.
Is there a way to set this threshold ?
Thanks
Gildas
PS : don't try my api_key, little hacker, it's a fake :P
5 years, 4 months
Simple standard for API use of a global user/key that all loaded tools can draw upon?
by Dooley, Damion
Do any of you see the need to establish a way for tools to use a global (current site) API url/key combination? From a security perspective I'm assuming this is basically ok since tools run under the galaxy user anyways (and can directly read and write files to their heart's content). I understand that a particular user's API key could help limit what they have access to. My tool however wants to do some prepatory form display and post-job work on behalf of the Galaxy system in addition to working with user-centric data; I presume others have similar use-case needs.
I think it would amount to having a standard GALAXY_TOOL_API_URL and GALAXY_TOOL_API_KEY managed in universe_wsgi.ini (left blank if not desired by sys admin). The key would be generated by a galaxy admin using a real admin user id. These would be available as python or shell environment variables when it came time to execute a tool's <command interpreter="python"> etc. work.
The wee other detail is that I'm using <code file="versioned_data_form.py" /> in my tool xml because there is API information I have to retrieve to set up the form with. So the url and key need to be accessible in that execution environment too?!!
Am I missing the boat; alternately has this already been talked about?!
Thanks for advice ...
Damion
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
5 years, 4 months
'KeyError' in workflow extraction when using newer tool version
by Peter Briggs
Dear all
One of my users has encountered a problem with extracting a workflow from a history in our local Galaxy installation (tag latest_2014.08.11, changeset 14342:db520d154716).
The history was created with a version of a local tool which has since been updated, and the extraction page warns that the newer version of the tool will be used for those datasets i.e.:
Dataset was created with tool version "0.0.4", but workflow extraction will use version "0.0.7".
However when the extraction is run it fails immediately: the user sees the "Internal Server Error" page, and in the log I see:
=====
Error - <type 'exceptions.KeyError'>: 'platform'
URL: https://galaxy.ls.manchester.ac.uk/workflow/build_from_current_history
File '/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
app_iter = self.application(environ, sr_checker)
File '/home/galaxy/production/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
return self.application(environ, start_response)
File '/home/galaxy/production/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
return self.application(environ, start_response)
File '/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File '/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request
body = method( trans, **kwargs )
File '/home/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py', line 1220 in build_from_current_history
workflow_name=workflow_name
File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line 30 in extract_workflow
steps = extract_steps( trans, history=history, job_ids=job_ids, dataset_ids=dataset_ids, dataset_collection_ids=dataset_collection_ids )
File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line 104 in extract_steps
tool_inputs, associations = step_inputs( trans, job )
File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line 271 in step_inputs
associations = __cleanup_param_values( tool.inputs, param_values )
File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line 330 in __cleanup_param_values
cleanup( "", inputs, values )
File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', line 327 in cleanup
group_values = values[input.name]
KeyError: 'platform'
=====
'platform' is a conditional parameter that was introduced into the tool between the two versions. It looks like when tying to use the newer verison of the new tool, that the new parameter is not getting picked up. Is this expected behaviour?
(Btw I've seen a similar issue i.e. the "KeyError: 'platform' exception when I have the two versions of this tool installed from a local toolshed, and try switching between to the newer one from the older one.)
Any help or suggestions are greatly appreciated.
Many thanks
Peter
--
Peter Briggs peter.briggs(a)manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
5 years, 4 months
Login with a system user
by Daniel Ruiz Molina
Hello,
I have configured Galaxy, but I would be very interested in configure it
with PAM or /etc/passwd (/etc/shadow) instead of creating a user in the
web interface.
How can I configure Galaxy for authenticating with system files?
Thanks.
5 years, 4 months
Internal Server error when attemptng to use Admin Tab
by David Bernick
Good morning -
I have acquired an Internal server error on our local galaxy install. It seems to be an unterminated string. How do I resolve this?
thanks in advance -
David Bernick
UCSC
Here is the relevant portion of the log (I hope).
Error - <type 'exceptions.ValueError'>: Unterminated string starting at: line 1 column 65528 (char 65528)
URL: http://campusrocks.cse.ucsc.edu:8080/admin/index
File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/middleware/error.py', line 149 in __call__
app_iter = self.application(environ, sr_checker)
File '/projects/galaxy/bin/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py', line 84 in __call__
return self.application(environ, start_response)
File '/projects/galaxy/bin/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py', line 633 in __call__
return self.application(environ, start_response)
File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/base.py', line 132 in __call__
return self.handle_request( environ, start_response )
File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/base.py', line 190 in handle_request
body = method( trans, **kwargs )
File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 383 in decorator
return func( self, trans, *args, **kwargs )
File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/web/base/controllers/admin.py', line 34 in index
installing_repository_ids = suc.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=True )
File '/projects/galaxy/bin/galaxy-dist/lib/tool_shed/util/shed_util_common.py', line 277 in get_ids_of_tool_shed_repositories_being_installed
app.install_model.ToolShedRepository.status == loading_datatypes_status ) ):
File '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py', line 2348 in instances
File '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 2120 in _instance
File '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py', line 1974 in populate_state
File '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/strategies.py', line 150 in fetch_col
File '/projects/galaxy/bin/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/types.py', line 658 in process
File '/projects/galaxy/bin/galaxy-dist/lib/galaxy/model/custom_types.py', line 52 in process_result_value
return json_decoder.decode( str( _sniffnfix_pg9_hex(value) ) )
File '/usr/lib64/python2.6/json/decoder.py', line 319 in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File '/usr/lib64/python2.6/json/decoder.py', line 336 in raw_decode
obj, end = self._scanner.iterscan(s, **kw).next()
File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
rval, next_pos = action(m, context)
File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject
value, end = iterscan(s, idx=end, context=context).next()
File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
rval, next_pos = action(m, context)
File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray
value, end = iterscan(s, idx=end, context=context).next()
File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
rval, next_pos = action(m, context)
File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject
value, end = iterscan(s, idx=end, context=context).next()
File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
rval, next_pos = action(m, context)
File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray
value, end = iterscan(s, idx=end, context=context).next()
File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
rval, next_pos = action(m, context)
File '/usr/lib64/python2.6/json/decoder.py', line 183 in JSONObject
value, end = iterscan(s, idx=end, context=context).next()
File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
rval, next_pos = action(m, context)
File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray
value, end = iterscan(s, idx=end, context=context).next()
File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
rval, next_pos = action(m, context)
File '/usr/lib64/python2.6/json/decoder.py', line 217 in JSONArray
value, end = iterscan(s, idx=end, context=context).next()
File '/usr/lib64/python2.6/json/scanner.py', line 55 in iterscan
rval, next_pos = action(m, context)
File '/usr/lib64/python2.6/json/decoder.py', line 155 in JSONString
return scanstring(match.string, match.end(), encoding, strict)
ValueError: Unterminated string starting at: line 1 column 65528 (char 65528)
5 years, 4 months
Disk space issue - again
by Patel, Viren
Hello. I have a Galaxy user whose disk usage remains at 91% even after
deleting and purging all histories and datasets (The initial disk usage
was 99%). I have searched the mailing list (e.g.
http://dev.list.galaxyproject.org/disk-space-usage-td4660164.html) and
wiki posts and followed all the steps, including purging hidden data. I
have the cleanup scripts running once a day via cron:
01 01 * * * cd ~/galaxy-dist && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -1
11 01 * * * cd ~/galaxy-dist && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -2
21 01 * * * cd ~/galaxy-dist && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -4
31 01 * * * cd ~/galaxy-dist && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -5
41 01 * * * cd ~/galaxy-dist && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -3
51 01 * * * cd ~/galaxy-dist && python
scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -r -d 60 -6
01 02 * * * find ~/tmp -mtime +60 -delete
I have manually run the above commands with -d 1 to delete anything older
than 1 day and I have restarted the Galaxy service. However the user¹s
disk usage remains at 91%. I am at a loss of what to try next. Any
suggestions or ideas of what the issue could be, or what I need to do
additionally? I am running the April 2014 distribution of Galaxy. Thanks.
Viren
________________________________
This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.
If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).
5 years, 4 months
datatype directory
by David Hoover
Why isn't there a datatype for a directory of files? This seems like such a simple thing. If an executable generates or expects a directory as its input or output, why must a fancy complicated composite datatype be created to handle this?
David Hoover
--------------------
David Hoover, PhD
Helix Systems Staff
SCB/DCSS/CIT/NIH
301-435-2986
http://helix.nih.gov
5 years, 4 months
