[galaxy-dev] Something wrong with connecting Galaxy with mysql/postgresql server when uploading datasets
Hello, Galaxy developers: I'm a Galaxy user and to customize and deploy Galaxy server locally. I need to build a connection between Galaxy and database server now. MySQL and PostgreSQL are both configured to test the connection. #for mysql server and db name is galaxy database_connection=mysql:///galaxy?unix_socket=/var/run/mysqld/mysqld.sock&user=&passwd= #for postgresql and db name is galaxy database_connection=postgresql:///galaxy?host=/var/run/postgresql&user=postgres&password= Now starting Galaxy server has no errors and I can create a user account on local Galaxy server successfully. But when uploading datasets into Galaxy(mostly less than 1 MB size) it remains "uploading" status(Dataset is uploading) and cannot complete datasets uploading job. I tested both PostgreSQL and MySQL and it really did not work. Shockingly using PostgreSQL the dataset uploading job can be accomplished very very slowly 3 or 4 times. wangdan ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error in installing Galaxy.
Thanks for the reply.. Yeah i am using the Host=0.0.0.0 but i couldn't connect.. now after installing ngnix and reloading i am getting error like.. Traceback (most recent call last): File "./scripts/paster.py", line 33, in serve.run() File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1056, in run invoke(command, command_name, options, args[1:]) File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1062, in invoke exit_code = runner.run(args) File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 227, in run result = self.command() File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 677, in command serve() File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 661, in serve server(app) File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 292, in server_wrapper **context.local_conf) File "/illumina/apps/galaxy/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call val = callable(*args, **kw) File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1342, in server_runner serve(wsgi_app, **kwargs) File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1291, in serve request_queue_size=request_queue_size) File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1134, in __init__ request_queue_size=request_queue_size) File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1113, in __init__ request_queue_size=request_queue_size) File "/illumina/apps/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 328, in __init__ HTTPServer.__init__(self, server_address, RequestHandlerClass) File "/usr/lib64/python2.6/SocketServer.py", line 402, in __init__ self.server_bind() File "/usr/lib64/python2.6/BaseHTTPServer.py", line 108, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib64/python2.6/SocketServer.py", line 413, in server_bind self.socket.bind(self.server_address) File "", line 1, in bind socket.error: [Errno 98] Address already in use galaxy.jobs.handler INFO 2013-05-10 10:22:14,360 sending stop signal to worker thread galaxy.jobs.handler INFO 2013-05-10 10:22:14,360 job handler queue stopped galaxy.jobs.runners INFO 2013-05-10 10:22:14,360 LWRRunner: Sending stop signal to monitor thread galaxy.jobs.runners INFO 2013-05-10 10:22:14,360 LWRRunner: Sending stop signal to 3 worker threads galaxy.jobs.runners INFO 2013-05-10 10:22:14,360 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2013-05-10 10:22:14,362 sending stop signal to worker thread galaxy.jobs.handler INFO 2013-05-10 10:22:14,362 job handler stop queue stopped Exception in thread LWRRunner.monitor_thread (most likely raised during interpreter shutdown):Exception in thread JobHandlerQueue.monitor_thread (most likely raised during interpreter shutdown): Traceback (most recent call last): Traceback (most recent call last): On Thu, May 9, 2013 at 5:15 PM, Dannon Baker wrote: > On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan < > sridhar2bioi...@gmail.com> wrote: > >> and it is working.. but i could'nt connect to the webpage >> http://127.0.0.1:8080/ from another system in same network.. >> >> > By default, galaxy will only be serving on 127.0.0.1 (localhost), which is > a loopback and only accessible on the machine itself. Accessing 127.0.0.1 > using another machine on the network is actually making requests to the > machine you're trying that from, which I assume isn't running galaxy. > > In your universe_wsgi.ini, you can edit this via the 'host' setting. Just > use 0.0.0.0 to listen to all connections. > > -Dannon > ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Shed test framework breaking where run_functional_tests.sh works
Peter, As of my latest commit, the automated test results should now match that of run_functional_tests.sh. --Dave B. On 5/9/13 06:06:16.000, Peter Cock wrote: On Thu, May 9, 2013 at 10:59 AM, Peter Cock wrote: On Thu, May 9, 2013 at 10:49 AM, Peter Cock wrote: Hi Dave, As you hoped, these test now shows up on the tool page (as expected they are test failures - apparently my install script isn't quite right yet): ... This one is more interesting, and appears to be a problem with the test framework (both tests pass locally via run_functional_tests.sh): http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 Functional test results for changeset revision 16a1a5ae98e9 of seq_rename 0 tests passed, 2 tests failed, 0 tests missing test components. I'll raise that on a new thread, Here's the output from the (Test) Tool Shed where the tests fail: ... Both tests fail with the following assertion: AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the tag set. Both tests pass on my development machine run via: $ ./run_functional_tests.sh -id seq_rename The two tests are defined as follows - identical bar the style used for the column arguments - I was wondering if the Tool Shed testing was stricter about numeric column names, but that does not seem to be relevant: I can retest with the latest galaxy-dist once this issue is resolved: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.htm Correction, I'm trying to update to the latest galaxy-central (I was using f8d07c98812903dc98de2665874a2c31b65b84da from 2013-04-29 where these tests pass). 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Handling of tool_dependencies.xml errors in Tool Shed testing
On Thu, May 9, 2013 at 6:21 PM, Björn Grüning wrote: > Hi Greg and Peter, > > two examples from my side. > > One of my tools (osra) has 7 dependencies. A few of them, GraphicsMagick > for example, makes sense to include as separate repo. But I feel that > the other are too special. I made the same judgement call with clinod (command line NoD), which needs a single binary tool 'batchman' (either on the path or next to the clinod install) from a 3rd party package, the Stuttgart Neural Network Simulator (SNNS). http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/ I could have tried to work out how to download and install the whole of the SNNS package, but that in turn would trigger more dependencies. Instead I am just installing batchman by putting it in the clinod $INSTALL_DIR - this is far simpler and less likely to break. (If it turns out in six months time that some other Galaxy Tools also use bits of SNNS, then I'd reconsider this choice.) 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Handling of tool_dependencies.xml errors in Tool Shed testing
On Thu, May 9, 2013 at 6:05 PM, Greg Von Kuster wrote: > Currently I feel that a tool dependency definition should allow for only a > singe > download of some item, and if that item requires other items. they should be > defined as separate dependencies that are installed using the > prior_installation_required=True attribute. That seems too idealised: Not every tool is bundled up nicely for a clean install, often there are bits and pieces which must be fetched individually. In some cases this is a judgement call about when this should be a separate dependency. > Is there a case where this is not possible? If so, I'm willing to enable > downloading more than 1 item per dependency package definition, but I > think we have to be careful in how we go about this. Yes, effectiveT3 comes as four JAR files - the core tool and three models: http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3 This is an example of a fairly common pattern where there is a core tool, plus one or more essential data files to be downloaded individually. > In any case, wget should not be used yet as it requires wget to be on the > installation server, and we have not yet decided what 3rd party utilities we > can assume exist in that environment. > > If there is justification for allowing download_by_url multiple times in the > same package dependency definition, then I would rather enhance the > tool shed framework to support that. If you won't want us to use wget, then we will likely also need a download_by_url variant which DOES NOT decompress anything. I'm thinking of compressed data files which should stay compressed. Regards, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Invalid Galaxy URL: None - Installing Tools Shed
Greg, Thanks for the tip on Safari. I have switched to another browser and working now! Thanks, -Adam -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Wed, May 8, 2013 at 6:50 AM, Greg Von Kuster wrote: > In addition, it's helpful to know which browser you are using. Safari has > fairly strict policies on 3rd-party cookies if you have them blocked. Chrome > and firefox are less strict, so unblocking 3rd-party cookies if using Safari > or simply switching to chrome or firefox will probably solve this issue. > > Greg Von Kuster > > On May 8, 2013, at 9:45 AM, Dave Bouvier wrote: > >> Adam, >> >> Normally, the Galaxy URL should be automatically determined and set in a >> cookie during the repository installation process. >> >> To help track down this issue, could you provide the revision of Galaxy >> you're running, and the end of the paster.log file when this error occurs? >> >> >> --Dave B. >> >> On 5/7/13 20:13:38.000, Adam Brenner wrote: >>> Howdy, >>> >>> I am trying to install a tools shed item, Emboss, but when I do this >>> via the admin interface, I get the following text: >>> >>> Repository installation is not possible due to an invalid Galaxy URL: >>> None. You may need to enable cookies in your browser. >>> >>> I have searched the universe_wsgi.ini file and could not find anything >>> that looks like Galaxy URL. Any ideas on how to set the Galaxy URL? >>> >>> Thanks, >>> -Adam >>> >>> -- >>> Adam Brenner >>> Computer Science, Undergraduate Student >>> Donald Bren School of Information and Computer Sciences >>> >>> Research Computing Support >>> Office of Information Technology >>> http://www.oit.uci.edu/rcs/ >>> >>> University of California, Irvine >>> www.ics.uci.edu/~aebrenne/ >>> aebre...@uci.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/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >> ___ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Handling of tool_dependencies.xml errors in Tool Shed testing
Hi Greg and Peter, two examples from my side. One of my tools (osra) has 7 dependencies. A few of them, GraphicsMagick for example, makes sense to include as separate repo. But I feel that the other are too special. - openbabel (is an extra repo) - GraphicsMagick - potrace - gocr - tclap - ocrad - cuneiform-linux Osra, on its own, needs a patch to be applied to install with my parameters. I used wget to fetch these patch. Maybe patch-action can be created to download and patch a package. But other corner cases will arise ;) Cheers, Bjoern > Currently I feel that a tool dependency definition should allow for only a > singe download of some item, and if that item requires other items. they > should be defined as separate dependencies that are installed using the > prior_installation_required=True attribute. > > Is there a case where this is not possible? If so, I'm willing to enable > downloading more than 1 item per dependency package definition, but I think > we have to be careful in how we go about this. > > In any case, wget should not be used yet as it requires wget to be on the > installation server, and we have not yet decided what 3rd party utilities we > can assume exist in that environment. > > If there is justification for allowing download_by_url multiple times in the > same package dependency definition, then I would rather enhance the tool shed > framework to support that. > > Greg Von Kuster > > > On May 9, 2013, at 12:15 PM, Peter Cock wrote: > > > On Thu, May 9, 2013 at 4:57 PM, Björn Grüning > > wrote: > >> Hi Peter, > >> > >> Afaik "download_by_url" is only supported as first action. To work > >> around that limitation, until its fixed, I used wget to fetch any > >> additional file. > >> > >> Ciao, > >> Björn > > > > Interesting tip - I don't see that on the wiki but it sounds believable. > > This would resolve by concerns about how this altered the current > > working directory since (assuming I understand correctly) after > > decompressing a tar ball, it changes into that new directory. > > > > I'll try the wget alternative - thanks! > > > > 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/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ > > > ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing revisions on (Test) Tool Shed
Ah, forgot one: tool functional test results On May 9, 2013, at 1:11 PM, Greg Von Kuster wrote: > Only revisions that are associated with metadata are displayed in the select > list on the manage repository page because metadata is required to fill in > the contents of the page. > Metadata is generated for the following items currently - this list evolves > over time: > > custom datatypes > valid/ invalid tools, > valid / invalid repository dependencies > valid / invalid tool_dependencies > orphan tool dependencies > valid / invalid data manager tools > exported workflows > readme files > > Greg Von Kuster > > > On May 9, 2013, at 12:27 PM, Peter Cock wrote: > >> Hi all, >> >> There is probably a good reason for this, but why is Galaxy hiding >> revisions from me on the main 'manage repository' page? >> >> e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod >> >> Here the drop down box only lets me view: >> 4:07f2d99bc2de (current tip) >> 0:f886a0b8b117 >> >> Why is it hiding revisions 1, 2 and 3? >> 3:a66a914c39b5 >> 2:3213023deae1 >> 2:3213023deae1 >> >> If I try to be sneaky and use a revision specific URL like this, >> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5 >> then rather than going to the requested revision it jumps to >> (what is currently) the repository tip. >> >> I want to look at these intermediate revisions to see what >> effect the changes had on the unit tests. >> >> Thanks, >> >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > > > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing revisions on (Test) Tool Shed
Only revisions that are associated with metadata are displayed in the select list on the manage repository page because metadata is required to fill in the contents of the page. Metadata is generated for the following items currently - this list evolves over time: custom datatypes valid/ invalid tools, valid / invalid repository dependencies valid / invalid tool_dependencies orphan tool dependencies valid / invalid data manager tools exported workflows readme files Greg Von Kuster On May 9, 2013, at 12:27 PM, Peter Cock wrote: > Hi all, > > There is probably a good reason for this, but why is Galaxy hiding > revisions from me on the main 'manage repository' page? > > e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod > > Here the drop down box only lets me view: > 4:07f2d99bc2de (current tip) > 0:f886a0b8b117 > > Why is it hiding revisions 1, 2 and 3? > 3:a66a914c39b5 > 2:3213023deae1 > 2:3213023deae1 > > If I try to be sneaky and use a revision specific URL like this, > http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5 > then rather than going to the requested revision it jumps to > (what is currently) the repository tip. > > I want to look at these intermediate revisions to see what > effect the changes had on the unit tests. > > Thanks, > > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Handling of tool_dependencies.xml errors in Tool Shed testing
Currently I feel that a tool dependency definition should allow for only a singe download of some item, and if that item requires other items. they should be defined as separate dependencies that are installed using the prior_installation_required=True attribute. Is there a case where this is not possible? If so, I'm willing to enable downloading more than 1 item per dependency package definition, but I think we have to be careful in how we go about this. In any case, wget should not be used yet as it requires wget to be on the installation server, and we have not yet decided what 3rd party utilities we can assume exist in that environment. If there is justification for allowing download_by_url multiple times in the same package dependency definition, then I would rather enhance the tool shed framework to support that. Greg Von Kuster On May 9, 2013, at 12:15 PM, Peter Cock wrote: > On Thu, May 9, 2013 at 4:57 PM, Björn Grüning > wrote: >> Hi Peter, >> >> Afaik "download_by_url" is only supported as first action. To work >> around that limitation, until its fixed, I used wget to fetch any >> additional file. >> >> Ciao, >> Björn > > Interesting tip - I don't see that on the wiki but it sounds believable. > This would resolve by concerns about how this altered the current > working directory since (assuming I understand correctly) after > decompressing a tar ball, it changes into that new directory. > > I'll try the wget alternative - thanks! > > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: invalid start byte
Thank you so much Subject: Re: [galaxy-dev] UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: invalid start byte From: d...@bx.psu.edu Date: Thu, 9 May 2013 12:45:25 -0400 CC: galaxy-dev@lists.bx.psu.edu To: ramao_tiago_tibur...@hotmail.com Assuming you checked Galaxy out using mercurial, stop your Galaxy instance and go into the Galaxy root directory and execute: hg pull -u Then start your Galaxy instance back up. On May 9, 2013, at 12:36 PM, Ramon Tiburski wrote:OK. thank you so much, but how can I update my instance? Subject: Re: [galaxy-dev] UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: invalid start byte From: d...@bx.psu.edu Date: Thu, 9 May 2013 11:02:46 -0400 CC: galaxy-dev@lists.bx.psu.edu To: ramao_tiago_tibur...@hotmail.com Hi Ramon, I've committed a patch to the stable branch that should resolve this issue. Please update your Galaxy instance and let us know if this has fixed it for you. Thanks for using Galaxy, Dan On May 9, 2013, at 8:40 AM, Ramon Tiburski wrote:Hi, I uploaded some data and when I click in the eye to see the data I get the following error. I don't know what can I do to fix this problem, I trying install some packges from python but didn't solve my problem. I'm starting think about my operational system, I have ubuntu 12.04 32bit, maybe I need get a 64bit. Someone can help me?Server Error URL: http://localhost:8080/datasets/8c49be448cfe29bc/display/?preview=True Module paste.exceptions.errormiddleware:144 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:194 in handle_request >> return body( environ, start_response ) Module galaxy.web.framework:876 in render >> template.render_context( context ) Module mako.template:319 in render_context >> **kwargs) Module mako.runtime:692 in _render_context >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template >> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body >> __M_writer(unicode(next.body())) Module _dataset_large_file_mako:45 in render_body >> __M_writer(filters.html_escape(unicode( unicode( truncated_data, 'utf-8' ) >> ))) UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: invalid start byte ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: invalid start byte
Assuming you checked Galaxy out using mercurial, stop your Galaxy instance and go into the Galaxy root directory and execute: hg pull -u Then start your Galaxy instance back up. On May 9, 2013, at 12:36 PM, Ramon Tiburski wrote: > OK. thank you so much, but how can I update my instance? > > Subject: Re: [galaxy-dev] UnicodeDecodeError: 'utf8' codec can't decode byte > 0xb9 in position 15: invalid start byte > From: d...@bx.psu.edu > Date: Thu, 9 May 2013 11:02:46 -0400 > CC: galaxy-dev@lists.bx.psu.edu > To: ramao_tiago_tibur...@hotmail.com > > Hi Ramon, > > I've committed a patch to the stable branch that should resolve this issue. > Please update your Galaxy instance and let us know if this has fixed it for > you. > > > Thanks for using Galaxy, > > Dan > > > On May 9, 2013, at 8:40 AM, Ramon Tiburski wrote: > > Hi, > > I uploaded some data and when I click in the eye to see the data I get the > following error. I don't know what can I do to fix this problem, I trying > install some packges from python but didn't solve my problem. I'm starting > think about my operational system, I have ubuntu 12.04 32bit, maybe I need > get a 64bit. > > Someone can help me? > Server Error > > URL: http://localhost:8080/datasets/8c49be448cfe29bc/display/?preview=True > Module paste.exceptions.errormiddleware:144 in __call__ > >> app_iter = self.application(environ, sr_checker) > Module paste.debug.prints:106 in __call__ > >> environ, self.app) > Module paste.wsgilib:543 in intercept_output > >> app_iter = application(environ, replacement_start_response) > Module paste.recursive:84 in __call__ > >> return self.application(environ, start_response) > Module paste.httpexceptions:633 in __call__ > >> return self.application(environ, start_response) > Module galaxy.web.framework.base:132 in __call__ > >> return self.handle_request( environ, start_response ) > Module galaxy.web.framework.base:194 in handle_request > >> return body( environ, start_response ) > Module galaxy.web.framework:876 in render > >> template.render_context( context ) > Module mako.template:319 in render_context > >> **kwargs) > Module mako.runtime:692 in _render_context > >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) > Module mako.runtime:718 in _exec_template > >> callable_(context, *args, **kwargs) > Module _base_mako:42 in render_body > >> __M_writer(unicode(next.body())) > Module _dataset_large_file_mako:45 in render_body > >> __M_writer(filters.html_escape(unicode( unicode( truncated_data, 'utf-8' > >> ) ))) > UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: > invalid start byte > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: invalid start byte
OK. thank you so much, but how can I update my instance? Subject: Re: [galaxy-dev] UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: invalid start byte From: d...@bx.psu.edu Date: Thu, 9 May 2013 11:02:46 -0400 CC: galaxy-dev@lists.bx.psu.edu To: ramao_tiago_tibur...@hotmail.com Hi Ramon, I've committed a patch to the stable branch that should resolve this issue. Please update your Galaxy instance and let us know if this has fixed it for you. Thanks for using Galaxy, Dan On May 9, 2013, at 8:40 AM, Ramon Tiburski wrote:Hi, I uploaded some data and when I click in the eye to see the data I get the following error. I don't know what can I do to fix this problem, I trying install some packges from python but didn't solve my problem. I'm starting think about my operational system, I have ubuntu 12.04 32bit, maybe I need get a 64bit. Someone can help me?Server Error URL: http://localhost:8080/datasets/8c49be448cfe29bc/display/?preview=True Module paste.exceptions.errormiddleware:144 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:194 in handle_request >> return body( environ, start_response ) Module galaxy.web.framework:876 in render >> template.render_context( context ) Module mako.template:319 in render_context >> **kwargs) Module mako.runtime:692 in _render_context >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template >> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body >> __M_writer(unicode(next.body())) Module _dataset_large_file_mako:45 in render_body >> __M_writer(filters.html_escape(unicode( unicode( truncated_data, 'utf-8' ) >> ))) UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: invalid start byte ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Missing revisions on (Test) Tool Shed
Hi all, There is probably a good reason for this, but why is Galaxy hiding revisions from me on the main 'manage repository' page? e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod Here the drop down box only lets me view: 4:07f2d99bc2de (current tip) 0:f886a0b8b117 Why is it hiding revisions 1, 2 and 3? 3:a66a914c39b5 2:3213023deae1 2:3213023deae1 If I try to be sneaky and use a revision specific URL like this, http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5 then rather than going to the requested revision it jumps to (what is currently) the repository tip. I want to look at these intermediate revisions to see what effect the changes had on the unit tests. Thanks, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Handling of tool_dependencies.xml errors in Tool Shed testing
On Thu, May 9, 2013 at 4:57 PM, Björn Grüning wrote: > Hi Peter, > > Afaik "download_by_url" is only supported as first action. To work > around that limitation, until its fixed, I used wget to fetch any > additional file. > > Ciao, > Björn Interesting tip - I don't see that on the wiki but it sounds believable. This would resolve by concerns about how this altered the current working directory since (assuming I understand correctly) after decompressing a tar ball, it changes into that new directory. I'll try the wget alternative - thanks! 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Handling of tool_dependencies.xml errors in Tool Shed testing
Hi Peter, > Hi all, > > For defining the 'install script' for some of my tool wrappers, I have > mainly following http://wiki.galaxyproject.org/ToolShedToolFeatures > and looking at one or two examples. > > I've got some of my tools to work, but not all. For instance, this one > appears not to be downloading or moving JAR files correctly: > http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/5644c28cf965 > > > > > > > > > action="set_to">$INSTALL_DIR > > > type="download_by_url">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar > type="move_file">TTSS_GUI-1.0.1.jar$INSTALL_DIR/ > > $INSTALL_DIR/module > type="download_by_url">http://effectors.org/download/module/TTSS_ANIMAL-1.0.1.jar > type="move_file">TTSS_ANIMAL-1.0.1.jar$INSTALL_DIR/module/ > type="download_by_url">http://effectors.org/download/module/TTSS_PLANT-1.0.1.jar > type="move_file">TTSS_PLANT-1.0.1.jar$INSTALL_DIR/module/ > type="download_by_url">http://effectors.org/download/module/TTSS_STD-1.0.1.jar > type="move_file">TTSS_STD-1.0.1.jar$INSTALL_DIR/module/ > > > > Downloads effectiveT3 v1.0.1 and the three models from http://effectors.org/ > > > Afaik "download_by_url" is only supported as first action. To work around that limitation, until its fixed, I used wget to fetch any additional file. Ciao, Björn > Here my Python wrapper script has evidently read the $EFFECTIVET3 > environment variable (defined in the tool_dependencies.xml to point > to the tool's $INSTALL_DIR), but the JAR file isn't there: > > Effective T3 JAR file not found: > /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpYR9FXD/effectiveT3/1.0.1/peterjc/effectivet3/5644c28cf965/TTSS_GUI-1.0.1.jar > > > My previous revision set the $EFFECTIVET3 environment variable > at the end of the tool_dependencies.xml file, and from the test failure > it appeared not to be getting set. My hunch is something breaks > part way through the installation but the Tool Shed isn't reporting > this - or am I just not looking in the right place? It would make > sense to show any installation issues under the "Tool Dependencies" > entry on the main tool page. > > Related to this, I'd like to suggest another couple of assertion action > types, used for checking if directories or files exist, which would > abort the installation with a clear error if the check fails: > > $INSTALL_DIR/module/ > type="assert_file_exists">$INSTALL_DIR/module/TTSS_STD-1.0.1.jar > > An obvious application of these would be immediately after an > line to sanity test the download > (and decompression) worked as expected - and didn't for example > just download an HTML error page for instance. > > (In this case I am worried that perhaps the download_by_url > action has been overly enthusiastic and unzipped the JAR file, > perhaps based on the mime-type?). > > Thanks, > > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Handling of tool_dependencies.xml errors in Tool Shed testing
Hi all, For defining the 'install script' for some of my tool wrappers, I have mainly following http://wiki.galaxyproject.org/ToolShedToolFeatures and looking at one or two examples. I've got some of my tools to work, but not all. For instance, this one appears not to be downloading or moving JAR files correctly: http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/5644c28cf965 $INSTALL_DIR http://effectors.org/download/version/TTSS_GUI-1.0.1.jar TTSS_GUI-1.0.1.jar$INSTALL_DIR/ $INSTALL_DIR/module http://effectors.org/download/module/TTSS_ANIMAL-1.0.1.jar TTSS_ANIMAL-1.0.1.jar$INSTALL_DIR/module/ http://effectors.org/download/module/TTSS_PLANT-1.0.1.jar TTSS_PLANT-1.0.1.jar$INSTALL_DIR/module/ http://effectors.org/download/module/TTSS_STD-1.0.1.jar TTSS_STD-1.0.1.jar$INSTALL_DIR/module/ Downloads effectiveT3 v1.0.1 and the three models from http://effectors.org/ Here my Python wrapper script has evidently read the $EFFECTIVET3 environment variable (defined in the tool_dependencies.xml to point to the tool's $INSTALL_DIR), but the JAR file isn't there: Effective T3 JAR file not found: /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpYR9FXD/effectiveT3/1.0.1/peterjc/effectivet3/5644c28cf965/TTSS_GUI-1.0.1.jar My previous revision set the $EFFECTIVET3 environment variable at the end of the tool_dependencies.xml file, and from the test failure it appeared not to be getting set. My hunch is something breaks part way through the installation but the Tool Shed isn't reporting this - or am I just not looking in the right place? It would make sense to show any installation issues under the "Tool Dependencies" entry on the main tool page. Related to this, I'd like to suggest another couple of assertion action types, used for checking if directories or files exist, which would abort the installation with a clear error if the check fails: $INSTALL_DIR/module/ $INSTALL_DIR/module/TTSS_STD-1.0.1.jar An obvious application of these would be immediately after an line to sanity test the download (and decompression) worked as expected - and didn't for example just download an HTML error page for instance. (In this case I am worried that perhaps the download_by_url action has been overly enthusiastic and unzipped the JAR file, perhaps based on the mime-type?). Thanks, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: invalid start byte
Hi Ramon, I've committed a patch to the stable branch that should resolve this issue. Please update your Galaxy instance and let us know if this has fixed it for you. Thanks for using Galaxy, Dan On May 9, 2013, at 8:40 AM, Ramon Tiburski wrote: > Hi, > > I uploaded some data and when I click in the eye to see the data I get the > following error. I don't know what can I do to fix this problem, I trying > install some packges from python but didn't solve my problem. I'm starting > think about my operational system, I have ubuntu 12.04 32bit, maybe I need > get a 64bit. > > Someone can help me? > Server Error > > URL: http://localhost:8080/datasets/8c49be448cfe29bc/display/?preview=True > Module paste.exceptions.errormiddleware:144 in __call__ > >> app_iter = self.application(environ, sr_checker) > Module paste.debug.prints:106 in __call__ > >> environ, self.app) > Module paste.wsgilib:543 in intercept_output > >> app_iter = application(environ, replacement_start_response) > Module paste.recursive:84 in __call__ > >> return self.application(environ, start_response) > Module paste.httpexceptions:633 in __call__ > >> return self.application(environ, start_response) > Module galaxy.web.framework.base:132 in __call__ > >> return self.handle_request( environ, start_response ) > Module galaxy.web.framework.base:194 in handle_request > >> return body( environ, start_response ) > Module galaxy.web.framework:876 in render > >> template.render_context( context ) > Module mako.template:319 in render_context > >> **kwargs) > Module mako.runtime:692 in _render_context > >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) > Module mako.runtime:718 in _exec_template > >> callable_(context, *args, **kwargs) > Module _base_mako:42 in render_body > >> __M_writer(unicode(next.body())) > Module _dataset_large_file_mako:45 in render_body > >> __M_writer(filters.html_escape(unicode( unicode( truncated_data, 'utf-8' > >> ) ))) > UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: > invalid start byte > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problems running functional tests
This only affects tests that are run manually, the automated testing framework correctly resolves tool dependencies. --Dave B. On 5/9/13 10:41:22.000, Peter Cock wrote: On 5/8/13 20:08:08.000, Ira Cooke wrote: Hi All, I'm starting to add functional tests to my tools but I've found that I can't get the test framework to work well with tool dependencies. The tool I'm considering is xtandem http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem When I install this tool on my local galaxy instance (on a clean install) the tool runs fine and if I look in the handler logs I see executing: PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh; PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh; rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /home/iracooke/galaxy-central/database/files/000/dataset_1.dat --var-mods='57.021464__at__C' --fix-mods=' 15.994915__at__M' /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination (destination id: local:///) Note that in this case the tool environments from my tool dependencies are loaded ... and the tool runs fine. When running functional tests however the tests are executed without first loading the environments from tool dependencies ... and naturally the tool fails. On my local machine I get the following when running the tests (Note that no loading of dependency shel environments occurs). (This seems to be the same issue on the testtoolshed.g2.bx.psu.edu ). Job dispatched galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat --var-mods=' 15.994915__at__M, ' --fix-mods=' 57.021464__at__C' /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat--var-mods=' 15.994915__at__M,' --fix-mods=' 57.021464__at__C' /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files ... galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR Is there something wrong with the way I've defined my tool dependencies for this tool? Or perhaps it's a bug in the testing framework. Cheers Ira On Thu, May 9, 2013 at 3:10 PM, Dave Bouvier wrote: Ira, There is a known issue with resolving tool dependencies when running functional tests. One workaround is to set the GALAXY_TOOL_DEPENDENCY_DIR environment variable to the path configured in your universe_wsgi.ini. This issue is documented in https://trello.com/c/eVT3QWJF --Dave B. Does this issue affect the Tool Shed tests as well, or just when run via run_functional_test.sh? (I'm working though a couple of test failures related to the dependency installation breaking somehow). Thanks, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problems running functional tests
> On 5/8/13 20:08:08.000, Ira Cooke wrote: >> >> Hi All, >> >> I'm starting to add functional tests to my tools but I've found that I >> can't get the test framework to work well with tool dependencies. >> >> The tool I'm considering is xtandem >> >> http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem >> >> When I install this tool on my local galaxy instance (on a clean install) >> the tool runs fine and if I look in the handler logs I see >> >> executing: >> PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab; >> export PACKAGE_BASE; . >> /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh; >> PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab; >> export PACKAGE_BASE; . >> /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh; >> rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d >> /home/iracooke/galaxy-central/database/files/000/dataset_1.dat >> --var-mods='57.021464__at__C' --fix-mods=' >> 15.994915__at__M' >> /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o >> /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r >> --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 >> --strict-monoisotopic-mass --keep-params-files >> galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination >> (destination id: local:///) >> >> >> Note that in this case the tool environments from my tool dependencies are >> loaded ... and the tool runs fine. >> >> When running functional tests however the tests are executed without first >> loading the environments from tool dependencies ... and naturally the tool >> fails. On my local machine I get the following when running the tests (Note >> that no loading of dependency shel environments occurs). (This seems to be >> the same issue on the testtoolshed.g2.bx.psu.edu ). >> >> Job dispatched >> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm >> 1.9.3@protk-1.2.0 do tandem_search.rb -d >> /tmp/tmp3I8GgN/database/files/000/dataset_1.dat --var-mods=' >> 15.994915__at__M, ' --fix-mods=' >> 57.021464__at__C' >> /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o >> /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin >> --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 >> --strict-monoisotopic-mass --keep-params-files >> galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination >> (destination id: local:///) >> galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution >> finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d >> /tmp/tmp3I8GgN/database/files/000/dataset_1.dat--var-mods=' >> 15.994915__at__M,' --fix-mods=' >> 57.021464__at__C' >> /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o >> /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin >> --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 >> --strict-monoisotopic-mass --keep-params-files >> ... >> galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR >> >> >> Is there something wrong with the way I've defined my tool dependencies >> for this tool? Or perhaps it's a bug in the testing framework. >> >> Cheers >> Ira On Thu, May 9, 2013 at 3:10 PM, Dave Bouvier wrote: > Ira, > > There is a known issue with resolving tool dependencies when running > functional tests. One workaround is to set the GALAXY_TOOL_DEPENDENCY_DIR > environment variable to the path configured in your universe_wsgi.ini. > > This issue is documented in https://trello.com/c/eVT3QWJF > >--Dave B. Does this issue affect the Tool Shed tests as well, or just when run via run_functional_test.sh? (I'm working though a couple of test failures related to the dependency installation breaking somehow). Thanks, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Multiple values in tags for parameters
On Thu, May 9, 2013 at 12:23 PM, Peter Cock wrote: > Hello all, > > I'm exploring a example where I would like to group some > of the select values into a single clause. Currently it seems > each value requires its own which leads to duplication and > worse. > > For example, I'd like to do something like this: > > > label="Source of sequence identifier list"> > Single file - want > sequences listed in ONE > tabular file > Union - want sequences > listed in ANY of given tabular files > Intersection - > want sequences listed in ALL of given tabular files > > > > format="tabular" > label="Tabular file containing sequence identifiers"/> > > > > > type="data" format="tabular" > label="Tabular file containing sequence identifiers"/> > > > Note that there is precedent for defaulting to a comma separator but allowing it to be over-ridden in the . Or perhaps sub-elements would work too... As an aside, looking at the documentation on the wiki, there seem to be two different tags, one within an tag set (which is documented) and one within a tag (which is not documented but is used in an example). http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Shed test framework breaking where run_functional_tests.sh works
Peter, I have duplicated this discrepancy in my local environment, and will be looking into the cause. I hope to have it resolved in short order. --Dave B. On 5/9/13 06:06:16.000, Peter Cock wrote: On Thu, May 9, 2013 at 10:59 AM, Peter Cock wrote: On Thu, May 9, 2013 at 10:49 AM, Peter Cock wrote: Hi Dave, As you hoped, these test now shows up on the tool page (as expected they are test failures - apparently my install script isn't quite right yet): ... This one is more interesting, and appears to be a problem with the test framework (both tests pass locally via run_functional_tests.sh): http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 Functional test results for changeset revision 16a1a5ae98e9 of seq_rename 0 tests passed, 2 tests failed, 0 tests missing test components. I'll raise that on a new thread, Here's the output from the (Test) Tool Shed where the tests fail: ... Both tests fail with the following assertion: AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the tag set. Both tests pass on my development machine run via: $ ./run_functional_tests.sh -id seq_rename The two tests are defined as follows - identical bar the style used for the column arguments - I was wondering if the Tool Shed testing was stricter about numeric column names, but that does not seem to be relevant: I can retest with the latest galaxy-dist once this issue is resolved: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.htm Correction, I'm trying to update to the latest galaxy-central (I was using f8d07c98812903dc98de2665874a2c31b65b84da from 2013-04-29 where these tests pass). 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Problems running functional tests
Ira, There is a known issue with resolving tool dependencies when running functional tests. One workaround is to set the GALAXY_TOOL_DEPENDENCY_DIR environment variable to the path configured in your universe_wsgi.ini. This issue is documented in https://trello.com/c/eVT3QWJF --Dave B. On 5/8/13 20:08:08.000, Ira Cooke wrote: Hi All, I'm starting to add functional tests to my tools but I've found that I can't get the test framework to work well with tool dependencies. The tool I'm considering is xtandem http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem When I install this tool on my local galaxy instance (on a clean install) the tool runs fine and if I look in the handler logs I see executing: PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh; PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh; rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /home/iracooke/galaxy-central/database/files/000/dataset_1.dat --var-mods='57.021464__at__C' --fix-mods=' 15.994915__at__M' /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination (destination id: local:///) Note that in this case the tool environments from my tool dependencies are loaded ... and the tool runs fine. When running functional tests however the tests are executed without first loading the environments from tool dependencies ... and naturally the tool fails. On my local machine I get the following when running the tests (Note that no loading of dependency shel environments occurs). (This seems to be the same issue on the testtoolshed.g2.bx.psu.edu ). Job dispatched galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat --var-mods=' 15.994915__at__M, ' --fix-mods='57.021464__at__C' /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat--var-mods=' 15.994915__at__M,' --fix-mods=' 57.021464__at__C' /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files ... galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR Is there something wrong with the way I've defined my tool dependencies for this tool? Or perhaps it's a bug in the testing framework. Cheers Ira ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Problems running functional tests
Hi All, I'm starting to add functional tests to my tools but I've found that I can't get the test framework to work well with tool dependencies. The tool I'm considering is xtandem http://testtoolshed.g2.bx.psu.edu/view/iracooke/xtandem When I install this tool on my local galaxy instance (on a clean install) the tool runs fine and if I look in the handler logs I see executing: PACKAGE_BASE=/home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/galaxy_protk/1.2.0/iracooke/xtandem/0940ff5d28ab/env.sh; PACKAGE_BASE=/home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab; export PACKAGE_BASE; . /home/iracooke/tool_dependencies/trans_proteomic_pipeline/4.6.1/iracooke/xtandem/0940ff5d28ab/env.sh; rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /home/iracooke/galaxy-central/database/files/000/dataset_1.dat --var-mods='57.021464__at__C' --fix-mods=' 15.994915__at__M' /home/iracooke/galaxy-central/database/files/000/dataset_2.dat -o /home/iracooke/galaxy-central/database/files/000/dataset_4.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files galaxy.jobs DEBUG 2013-04-27 06:53:35,586 (4) Persisting job destination (destination id: local:///) Note that in this case the tool environments from my tool dependencies are loaded ... and the tool runs fine. When running functional tests however the tests are executed without first loading the environments from tool dependencies ... and naturally the tool fails. On my local machine I get the following when running the tests (Note that no loading of dependency shel environments occurs). (This seems to be the same issue on the testtoolshed.g2.bx.psu.edu ). Job dispatched galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,564 (3) executing: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat --var-mods=' 15.994915__at__M, ' --fix-mods='57.021464__at__C' /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files galaxy.jobs DEBUG 2013-04-27 06:55:19,730 (3) Persisting job destination (destination id: local:///) galaxy.jobs.runners.local DEBUG 2013-04-27 06:55:19,889 execution finished: rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d /tmp/tmp3I8GgN/database/files/000/dataset_1.dat--var-mods=' 15.994915__at__M,' --fix-mods=' 57.021464__at__C' /tmp/tmp3I8GgN/database/files/000/dataset_2.dat -o /tmp/tmp3I8GgN/database/files/000/dataset_3.dat -r --enzyme=Trypsin --precursor-ion-tol-units=ppm -v 0 -f 0.65 -p 100.0 --strict-monoisotopic-mass --keep-params-files ... galaxy.jobs DEBUG 2013-04-27 06:55:24,277 setting dataset state to ERROR Is there something wrong with the way I've defined my tool dependencies for this tool? Or perhaps it's a bug in the testing framework. Cheers Ira ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] migration error
On Thu, May 9, 2013 at 12:56 PM, Dannon Baker wrote: > This isn't an issue with postgresql or mysql; they don't use a temporary > table for table alterations. Oh good :) > Can you open up the sqlite database if you > still have it and see what the contents of the migrate_tmp table were? > They'll be a copy of a prior migrated table, I'm just curious what from -- > it should have been cleaned up previously in the event of successful > migrations. It looks like whatever was there has been lost (which doesn't really worry me on this machine - it is a test setup only): $ sqlite3 database/universe.sqlite SQLite version 3.6.20 Enter ".help" for instructions Enter SQL statements terminated with a ";" sqlite> select * from migrate_tmp; Error: no such table: migrate_tmp > My hunch is that previously various scripts threw a lot of errors for mysql > and so this table wasn't automatically cleaned up after after the execution > of one of those migration scripts, but the old version of sqlalchemy-migrate > didn't care if it existed or not and would overwrite it, while the new > version is more reticent to delete the table (which is probably more > reasonable, should you need to recover data after an unsuccessful > migration). That makes sense. > In any event, to fix it, you'll want to make sure that the contents of that > migrate_tmp table aren't something you want and drop it, downgrade to 114, > then upgrade to 115 again. If I can recreate this I'll work on a more > reasonable solution. One idea might be to name the migration_tmp tables using the schema revision to avoid clashes, e.g. migration_115_tmp in this case? 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Error with fastqc
Dannon, I've set up galaxy at the local linux. After data configuration, I run fastqc to check how it runs. Here I got error message as below -- error An error occurred running this job: Traceback (most recent call last): File "../galaxy-dist/tools/rgenetics/rgFastQC.py", line 158, in assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: ##r Here is the detail of the error -- Tool: FastQC:Read QC Name: FastQC_FASTQ Groomer on data 6.html Created: May 02, 2013 Filesize: 0 bytes Dbkey: mm9 Format: html Tool Version: Tool Standard Output: stdout Tool Standard Error: stderr Tool Exit Code: 1 Input Parameter Value Short read data from your current history 8: FASTQ Groomer on data 6 Title for the output file - to remind you what the job was for FastQC Contaminant list No dataset What might be the problem? Thank you! Kathryn___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Multiple values in tags for parameters
Yup, off list by mistake. -John On Thu, May 9, 2013 at 8:40 AM, Peter Cock wrote: > Off list by mistake? > > On Thu, May 9, 2013 at 1:25 PM, John Chilton wrote: >> This is one of the use cases I was trying to address with tool macros. This >> has the added benefit of reducing the level of XML nesting in such tools as >> well. >> >> https://bitbucket.org/galaxyp/galaxyp-toolshed-maxquant/src/fc2de41f51a9168e71d90756450e14f392d3be3a/maxquant.xml?at=default#cl-129 >> >> -John > > Yep - macros could be a solution here - and I could start using them in > the NCBI BLAST+ wrappers to reduce the duplication too. > > 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] How to transfer or upload datasets to Galaxy server automatically?
You can probably use the API for what you want to do, though your users will need to have an API key to make everything work smoothly. Documentation for the API is here: https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html An alternative approach would be to build a Galaxy data source tool that enables users to get a remote dataset from your site. Here are some information about this approach: http://wiki.galaxyproject.org/Admin/Internals/Data%20Sources Also, check out examples in the /tools/data_source directory. Good luck, J. On May 7, 2013, at 10:54 PM, 王聃Don wrote: > Hello, Galaxy developers and maintainers! > I'm a user in Chinese mainland and I'd like to deploy our Galaxy server > locally. There's some requirements I cannot realize and I still have no > idea after searching over all Galaxy Wiki pages and Galaxy Developer docs. > The problem is, I need to jump from another external webpage to Galaxy > index page through a JS action and a specific included dataset has to be > transferred to Galaxy at the same time. In other words, users click a > button on an external webpage and will transfer to Galaxy index page > with an automatic action of user-login and dataset-uploading in Galaxy > server. I've no idea how to realize someway and really need some help on it. > Thanks > Wang Dan > > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: invalid start byte
Hi, I uploaded some data and when I click in the eye to see the data I get the following error. I don't know what can I do to fix this problem, I trying install some packges from python but didn't solve my problem. I'm starting think about my operational system, I have ubuntu 12.04 32bit, maybe I need get a 64bit. Someone can help me?Server Error URL: http://localhost:8080/datasets/8c49be448cfe29bc/display/?preview=True Module paste.exceptions.errormiddleware:144 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:194 in handle_request >> return body( environ, start_response ) Module galaxy.web.framework:876 in render >> template.render_context( context ) Module mako.template:319 in render_context >> **kwargs) Module mako.runtime:692 in _render_context >> _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template >> callable_(context, *args, **kwargs) Module _base_mako:42 in render_body >> __M_writer(unicode(next.body())) Module _dataset_large_file_mako:45 in render_body >> __M_writer(filters.html_escape(unicode( unicode( truncated_data, 'utf-8' ) >> ))) UnicodeDecodeError: 'utf8' codec can't decode byte 0xb9 in position 15: invalid start byte ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] migration error
This isn't an issue with postgresql or mysql; they don't use a temporary table for table alterations. Can you open up the sqlite database if you still have it and see what the contents of the migrate_tmp table were? They'll be a copy of a prior migrated table, I'm just curious what from -- it should have been cleaned up previously in the event of successful migrations. My hunch is that previously various scripts threw a lot of errors for mysql and so this table wasn't automatically cleaned up after after the execution of one of those migration scripts, but the old version of sqlalchemy-migrate didn't care if it existed or not and would overwrite it, while the new version is more reticent to delete the table (which is probably more reasonable, should you need to recover data after an unsuccessful migration). In any event, to fix it, you'll want to make sure that the contents of that migrate_tmp table aren't something you want and drop it, downgrade to 114, then upgrade to 115 again. If I can recreate this I'll work on a more reasonable solution. Dannon On Thu, May 9, 2013 at 6:12 AM, Peter Cock wrote: > On Thu, May 9, 2013 at 11:03 AM, Peter Cock > wrote: > > On Wed, May 8, 2013 at 10:19 PM, Dannon Baker > wrote: > >> > >> Hey Robert, > >> > >> I assume this is sqlite? And, when you say you ran this without any > >> existing database -- was this was a completely new clone of galaxy, or > did > >> you update a prior installation and delete database/universe.sqlite > manually > >> before running? > >> > >> -Dannon > > > > Hi guys, > > > > I've just hit this bug too, using SQLite on a working development machine > > which was running with schema 114 until I grabbed the latest > galaxy-central > > just now, revision 80ab774559f8405a46082286c6cf35db420db002 > > > > $ sh manage_db.sh upgrade > > 114 -> 115... > > Altering password column failed > > Traceback (most recent call last): > > File > "lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py", > > line 15, in upgrade > > user.c.password.alter(type=String(255)) > > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py", > > line 491, in alter > > return alter_column(self, *p, **k) > > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py", > > line 136, in alter_column > > engine._run_visitor(visitorcallable, delta) > > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > > line 2302, in _run_visitor > > conn._run_visitor(visitorcallable, element, **kwargs) > > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > > line 1972, in _run_visitor > > **kwargs).traverse_single(element) > > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py", > > line 53, in traverse_single > > ret = super(AlterTableVisitor, self).traverse_single(elem) > > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/visitors.py", > > line 106, in traverse_single > > return meth(obj, **kw) > > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py", > > line 53, in visit_column > > self.recreate_table(table,column,delta) > > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py", > > line 36, in recreate_table > > self.execute() > > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py", > > line 42, in execute > > return self.connection.execute(self.buffer.getvalue()) > > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > > line 1449, in execute > > params) > > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > > line 1628, in _execute_text > > statement, parameters > > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > > line 1698, in _execute_context > > context) > > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > > line 1691, in _execute_context > > context) > > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", > > line 331, in do_execute > > cursor.execute(statement, parameters) > > OperationalError: (OperationalError) there is already another table or > > index with this name: migration_tmp 'ALTER TABLE galaxy_user RENAME TO > > migration_tmp' () > > done > > > > Presumably one of the previous migration scripts has left an old > > migration_tmp table in place? > > Note th
Re: [galaxy-dev] Getting example_watch_folder.py to work...
Hey Neil,
A user browsing that history wouldn't automatically get the updates (unless
the history was already refreshing for some reason), but they definitely
would upon refresh. Glad you got the rest working!
-Dannon
On Thu, May 9, 2013 at 2:02 AM, wrote:
> Hi all,
>
> I finally resolved the issue I’ll mention it here to help anyone
> else who has the same issue. In “Edit” mode on the workflow you add the
> “Workflow control->Inputs” to use the api.
>
> ** **
>
> Final question
>
> Everything gets created and stored in the database, but the history column
> on the left of the browser doesn’t get updated. Can user see if the task
> has completed successfully and all files uploaded from the browser?
>
> ** **
>
> Thanks
>
> Neil
>
> ** **
>
> *From:* Burdett, Neil (ICT Centre, Herston - RBWH)
> *Sent:* Thursday, 9 May 2013 2:56 PM
>
> *To:* galaxy-dev@lists.bx.psu.edu
> *Subject:* Getting example_watch_folder.py to work...
>
> ** **
>
> Hi,
>
>I'm still struggling to get the example_watch_folder.py to work. So
> any help much appreciated.
>
> I've created a simple workflow, which essentially opens a text file and
> then writes out the data to a html file.
>
> My xml file:
>
> Test
> $__root_dir__/tools/copy/copy.pl
> --input_image "$inputImage"
> --output_html "$output"
>
>
>
> />
>
>
>
>
>
> Copy Tool
>
>
>
>
> And copy.pl:
> #!/usr/bin/perl
> use strict;
> use warnings;
> use Getopt::Long;
> my $input_image ;
> my $output_html ;
>
> # Get options from command line (i.e. galaxy)
> my $result = GetOptions ( "input_image=s" => \$input_image,
> "output_html=s" => \$output_html )
> or die "Bad options";
>
> print "input_image is: $input_image\n";
>
> open FILE,"$input_image" or die $!;
> my @lines = ;
> close FILE;
> my $numOfLines = scalar @lines;
>
>
> # Create the output HTML, with links to the files and the square gif.
> #
> open HTML, ">", $output_html
> or die "Failed to create output HTML file '$output_html': $! ";
>
> print HTML<
>
>
> iframe {
> border: 0px;
> background: #ee ;
> }
>
>
>
> Copy Files tool
> Generated $numOfLines files
> EOF
>
> # Put direct links to each output file
> foreach my $sub_filename ( @lines )
> {
> print HTML "Direct link to the $sub_filename file.\n";
> }
>
> print HTML "\n";
>
> print HTML "\n" ;
>
> close HTML ;
>
> So pretty basic.
>
> I run:
> ./example_watch_folder.py cce1b01926646d548f6ddc32ff01aa2e
> http://140.253.78.234/galaxy/api/ /home/galaxy/data_input
> /home/galaxy/data_output "My API Import" f2db41e1fa331b3e
>
> and get the following output:
> {'outputs': ['a799d38679e985db'], 'history': '33b43b4e7093c91f'}
>
> I can see the sample.txt file I placed in the /home/galaxy/data_input has
> been put into the database:
> /home/galaxy/galaxy-dist/database/files/000/dataset_8.dat
>
> and:
>
> http://140.253.78.234/galaxy/api/libraries/f2db41e1fa331b3e/contents/1cd8e2f6b131e891
> shows the file has been uploaded:
>
> {
>
> "data_type": "txt",
>
> "date_uploaded": "2013-05-09T04:41:10.579602",
>
> "file_name": "/home/galaxy/galaxy-dist/database/files/000/dataset_8.dat",
>
>
> "file_size": 76,
>
> "genome_build": "?",
>
> "id": "1cd8e2f6b131e891",
>
> "ldda_id": "1cd8e2f6b131e891",
>
> "message": "",
>
> "metadata_data_lines": 8,
>
> "metadata_dbkey": "?",
>
> "misc_blurb": "8 lines",
>
> "misc_info": "uploaded txt file",
>
> "model_class": "LibraryDataset",
>
> "name": "sam2.txt",
>
> "template_data": {},
>
> "uploaded_by": "t...@test.com",
>
> "uuid": null
>
> }
>
> However, looking in the histories:
> http://140.253.78.234/galaxy/api/histories/33b43b4e7093c91f/contents/a799d38679e985db
>
> The output file is zero as the input file can not be found as shown below in
> bold ...
>
> {
>
> "accessible": true,
>
> "api_type": "file",
>
> "data_type": "html",
>
> "deleted": false,
>
> "display_apps": [],
>
> "display_types": [],
>
> "download_url":
> "/galaxy/api/histories/33b43b4e7093c91f/contents/a799d38679e985db/display",
>
>
> "file_ext": "html",
>
> "file_name": "/home/galaxy/galaxy-dist/database/files/000/dataset_9.dat",
>
>
> "file_size": 0,
>
> "genome_build": "?",
>
> "hid": 1,
>
> "history_id": "33b43b4e7093c91f",
>
> "id": "a799d38679e985db",
>
> "metadata_data_lines": null,
>
> "metadata_dbkey": "?",
>
> "misc_blurb": "error",
>
> *"misc_info": "Thu May 9 14:42:10 2013input_image is: None\nNo such file
> or directory at /home/galaxy/galaxy-dist/tools/copy/copy.pl line 27.\n", *
>
> "model_class": "HistoryDatasetAssociation",
Re: [galaxy-dev] Error in installing Galaxy.
On Thu, May 9, 2013 at 12:21 AM, sridhar srinivasan < sridhar2bioi...@gmail.com> wrote: > and it is working.. but i could'nt connect to the webpage > http://127.0.0.1:8080/ from another system in same network.. > > By default, galaxy will only be serving on 127.0.0.1 (localhost), which is a loopback and only accessible on the machine itself. Accessing 127.0.0.1 using another machine on the network is actually making requests to the machine you're trying that from, which I assume isn't running galaxy. In your universe_wsgi.ini, you can edit this via the 'host' setting. Just use 0.0.0.0 to listen to all connections. -Dannon ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Multiple values in tags for parameters
Hello all, I'm exploring a example where I would like to group some of the select values into a single clause. Currently it seems each value requires its own which leads to duplication and worse. For example, I'd like to do something like this: Single file - want sequences listed in ONE tabular file Union - want sequences listed in ANY of given tabular files Intersection - want sequences listed in ALL of given tabular files But instead I am forced to use: Single file - want sequences listed in ONE tabular file Union - want sequences listed in ANY of given tabular files Intersection - want sequences listed in ALL of given tabular files This has a major usability downside in that when the user switches from UNION to INTERSECTION, any previously entered values for the parameters are lost. Is this something that has already been enhanced, or is the wiki page accurate regarding the current inflexible behaviour? http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax I can see how to avoid the issue where by splitting this 3-way select into two separate parameters, but that feels more awkward. Thanks, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] migration error
On Thu, May 9, 2013 at 11:03 AM, Peter Cock wrote: > On Wed, May 8, 2013 at 10:19 PM, Dannon Baker wrote: >> >> Hey Robert, >> >> I assume this is sqlite? And, when you say you ran this without any >> existing database -- was this was a completely new clone of galaxy, or did >> you update a prior installation and delete database/universe.sqlite manually >> before running? >> >> -Dannon > > Hi guys, > > I've just hit this bug too, using SQLite on a working development machine > which was running with schema 114 until I grabbed the latest galaxy-central > just now, revision 80ab774559f8405a46082286c6cf35db420db002 > > $ sh manage_db.sh upgrade > 114 -> 115... > Altering password column failed > Traceback (most recent call last): > File "lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py", > line 15, in upgrade > user.c.password.alter(type=String(255)) > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py", > line 491, in alter > return alter_column(self, *p, **k) > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py", > line 136, in alter_column > engine._run_visitor(visitorcallable, delta) > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > line 2302, in _run_visitor > conn._run_visitor(visitorcallable, element, **kwargs) > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > line 1972, in _run_visitor > **kwargs).traverse_single(element) > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py", > line 53, in traverse_single > ret = super(AlterTableVisitor, self).traverse_single(elem) > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/visitors.py", > line 106, in traverse_single > return meth(obj, **kw) > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py", > line 53, in visit_column > self.recreate_table(table,column,delta) > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py", > line 36, in recreate_table > self.execute() > File > "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py", > line 42, in execute > return self.connection.execute(self.buffer.getvalue()) > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > line 1449, in execute > params) > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > line 1628, in _execute_text > statement, parameters > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > line 1698, in _execute_context > context) > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", > line 1691, in _execute_context > context) > File > "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", > line 331, in do_execute > cursor.execute(statement, parameters) > OperationalError: (OperationalError) there is already another table or > index with this name: migration_tmp 'ALTER TABLE galaxy_user RENAME TO > migration_tmp' () > done > > Presumably one of the previous migration scripts has left an old > migration_tmp table in place? Note that attempting to re-run the migration appeared to do nothing: $ sh manage_db.sh upgrade $ sh run.sh ... This isn't a big issue for my development machine, but it would seem that this migration step aborted halfway (having marked the schema as being updated to version 115), and did not roll back the database to the previous state labelled as version 114. If that happens just on SQLite that's tolerable, but if there is no transaction integrity used on MySQL or PostgreSQL the migration framework seems very fragile. Regards, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Shed test framework breaking where run_functional_tests.sh works
On Thu, May 9, 2013 at 10:59 AM, Peter Cock wrote: > > On Thu, May 9, 2013 at 10:49 AM, Peter Cock wrote: > > > > Hi Dave, > > > > As you hoped, these test now shows up on the tool page (as expected > > they are test failures - apparently my install script isn't quite right > > yet): > > > > ... > > > > This one is more interesting, and appears to be a problem with the > > test framework (both tests pass locally via run_functional_tests.sh): > > > > http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 > > Functional test results for changeset revision 16a1a5ae98e9 of seq_rename > > 0 tests passed, 2 tests failed, 0 tests missing test components. > > > > I'll raise that on a new thread, > > Here's the output from the (Test) Tool Shed where the tests fail: > > ... > > Both tests fail with the following assertion: > > AssertionError: Attempting to set field 'new_column' to value '['c2']' in form > 'tool_form' threw exception: cannot find value/label "c2" in list control > control: > If the above control is a DataToolparameter > whose data type class does not include a sniff() method, make sure to include > a proper 'ftype' attribute to the tag for the control within the tag > set. > > Both tests pass on my development machine run via: > > $ ./run_functional_tests.sh -id seq_rename > > The two tests are defined as follows - identical bar the style used for the > column > arguments - I was wondering if the Tool Shed testing was stricter about > numeric > column names, but that does not seem to be relevant: > > > > ftype="fasta" /> > value="four_human_proteins.rename.tabular" ftype="tabular" /> > > > file="four_human_proteins.rename.fasta" ftype="fasta" /> > > > ftype="fasta" /> > value="four_human_proteins.rename.tabular" ftype="tabular" /> > > > file="four_human_proteins.rename.fasta" ftype="fasta" /> > > > > I can retest with the latest galaxy-dist once this issue is resolved: > http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.htm Correction, I'm trying to update to the latest galaxy-central (I was using f8d07c98812903dc98de2665874a2c31b65b84da from 2013-04-29 where these tests pass). 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] migration error
On Wed, May 8, 2013 at 10:19 PM, Dannon Baker wrote: > > Hey Robert, > > I assume this is sqlite? And, when you say you ran this without any > existing database -- was this was a completely new clone of galaxy, or did > you update a prior installation and delete database/universe.sqlite manually > before running? > > -Dannon Hi guys, I've just hit this bug too, using SQLite on a working development machine which was running with schema 114 until I grabbed the latest galaxy-central just now, revision 80ab774559f8405a46082286c6cf35db420db002 $ sh manage_db.sh upgrade 114 -> 115... Altering password column failed Traceback (most recent call last): File "lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py", line 15, in upgrade user.c.password.alter(type=String(255)) File "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py", line 491, in alter return alter_column(self, *p, **k) File "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/schema.py", line 136, in alter_column engine._run_visitor(visitorcallable, delta) File "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 2302, in _run_visitor conn._run_visitor(visitorcallable, element, **kwargs) File "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1972, in _run_visitor **kwargs).traverse_single(element) File "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py", line 53, in traverse_single ret = super(AlterTableVisitor, self).traverse_single(elem) File "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/sql/visitors.py", line 106, in traverse_single return meth(obj, **kw) File "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py", line 53, in visit_column self.recreate_table(table,column,delta) File "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/databases/sqlite.py", line 36, in recreate_table self.execute() File "/mnt/galaxy/galaxy-central/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/changeset/ansisql.py", line 42, in execute return self.connection.execute(self.buffer.getvalue()) File "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1449, in execute params) File "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1628, in _execute_text statement, parameters File "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1698, in _execute_context context) File "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py", line 1691, in _execute_context context) File "/mnt/galaxy/galaxy-central/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py", line 331, in do_execute cursor.execute(statement, parameters) OperationalError: (OperationalError) there is already another table or index with this name: migration_tmp 'ALTER TABLE galaxy_user RENAME TO migration_tmp' () done Presumably one of the previous migration scripts has left an old migration_tmp table in place? 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool Shed test framework breaking where run_functional_tests.sh works
On Thu, May 9, 2013 at 10:49 AM, Peter Cock wrote: > > Hi Dave, > > As you hoped, these test now shows up on the tool page (as expected > they are test failures - apparently my install script isn't quite right yet): > > ... > > This one is more interesting, and appears to be a problem with the > test framework (both tests pass locally via run_functional_tests.sh): > > http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 > Functional test results for changeset revision 16a1a5ae98e9 of seq_rename > 0 tests passed, 2 tests failed, 0 tests missing test components. > > I'll raise that on a new thread, Here's the output from the (Test) Tool Shed where the tests fail: Tests that failed *Tool id:* seq_rename *Tool version:* seq_rename *Test:*test_tool_00 ( functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3 ) *Stderr:* *Traceback:* Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1320, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['2']' in form 'tool_form' threw exception: cannot find value/label "2" in list control control: If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the tag set.*Tool id:* seq_rename *Tool version:* seq_rename *Test:*test_tool_01 ( functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/seq_rename/seq_rename/0.0.3 ) *Stderr:* *Traceback:* Traceback (most recent call last): File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 171, in test_tool self.do_it( td, shed_tool_id=shed_tool_id ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 78, in do_it self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1320, in run_tool self.submit_form( **kwd ) File "/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py", line 1270, in submit_form raise AssertionError( errmsg ) AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the tag set. Both tests fail with the following assertion: AssertionError: Attempting to set field 'new_column' to value '['c2']' in form 'tool_form' threw exception: cannot find value/label "c2" in list control control: If the above control is a DataToolparameter whose data type class does not include a sniff() method, make sure to include a proper 'ftype' attribute to the tag for the control within the tag set. Both tests pass on my development machine run via: $ ./run_functional_tests.sh -id seq_rename The two tests are defined as follows - identical bar the style used for the column arguments - I was wondering if the Tool Shed testing was stricter about numeric column names, but that does not seem to be relevant: I can retest with the latest galaxy-dist once this issue is resolved: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014557.html 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Missing test results on (Test) Tool Shed
On Wed, May 8, 2013 at 2:09 PM, Dave Bouvier wrote: > Peter, > > A technical issue prevented the tests from automatically running. I've > resolved the issue and started a manual run, you should be seeing test > results within 2-3 hours. > >--Dave B. Hi Dave, As you hoped, these test now shows up on the tool page (as expected they are test failures - apparently my install script isn't quite right yet): http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5 Functional test results for changeset revision a66a914c39b5 of clinod 0 tests passed, 1 tests failed, 0 tests missing test components. http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/5644c28cf965 Functional test results for changeset revision 5644c28cf965 of effectivet3 0 tests passed, 2 tests failed, 0 tests missing test components. This one is more interesting, and appears to be a problem with the test framework (both tests pass locally via run_functional_tests.sh): http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9 Functional test results for changeset revision 16a1a5ae98e9 of seq_rename 0 tests passed, 2 tests failed, 0 tests missing test components. I'll raise that on a new thread, Peter (Sorry for resending this Dave, I left off the mailing list the first time) ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
