galaxy testing on 'repeat' elements
Hi, Our team is now testing our integrated tools under galaxy testing framework. At present, we are trying to test the '<repeat>' elements in one of our tools, e.g. <repeat name="replicates" title="Replicate"> <param name="tfile" type="data" label="Treatment file"/> <param name="cfile" type="data" label="Control file"/> </repeat> we tried add the following section into the <test> tag and ran the test, but did not make it. <test> <param name="tfile" value="ma2c_treatment_ce4.pair" /> <param name="tfile" value="ma2c_treatment_ce5.pair" /> </test> after searching all over the internet, we were not able to come up with any solution (maybe we missed). I dont know if it proper to ask you a question like this. but we are kinda desprated for this issue. Could you please kindly tell us, how to write the test section when there are two or more 'replicates' inputed? Appreciate so much. Regards Yi
Yi, Yes, it is totally fine to ask questions like this. To answer your question, unfortunately, there is a weakness in the testing framework that limits the way repeat elements can be tested, but I believe the testing you want to do can be done. The only way to test a tool with a repeat element is with a test that includes exactly one _set_ for each repeat. (When you run the tool, you could include 0, 1, or more than 1 sets, but you can only test with 1.) In your case, you have a repeat element that requires two files, as follows: <repeat name="replicates" title="Replicate"> <param name="tfile" type="data" label="Treatment file"/> <param name="cfile" type="data" label="Control file"/> </repeat> So your test should include something like: <test> ... <param name="tfile" value="ma2c_treatment_ce4.pair" /> <param name="cfile" value="controlfile.name" /> ... </test> Both files need to be included and only one pair (set) can be. The parameter names in the test should exactly match the names in the input parameter declaration. Note that the syntax for the command line should refer to the repeat items something like this: #for $r in $replicates ${r.tfile} ${r.cfile} #end for If you want to see a simple example, tools/filters/sorter.xml has a fairly complex repeat element with multiple items and tests that run. Let us know if you have any other questions. Regards, Kelly On Oct 18, 2010, at 11:39 AM, WANGYi wrote:
Hi,
Our team is now testing our integrated tools under galaxy testing framework.
At present, we are trying to test the '<repeat>' elements in one of our tools, e.g. <repeat name="replicates" title="Replicate"> <param name="tfile" type="data" label="Treatment file"/> <param name="cfile" type="data" label="Control file"/> </repeat>
we tried add the following section into the <test> tag and ran the test, but did not make it. <test> <param name="tfile" value="ma2c_treatment_ce4.pair" /> <param name="tfile" value="ma2c_treatment_ce5.pair" /> </test>
after searching all over the internet, we were not able to come up with any solution (maybe we missed).
I dont know if it proper to ask you a question like this. but we are kinda desprated for this issue. Could you please kindly tell us, how to write the test section when there are two or more 'replicates' inputed?
Appreciate so much.
Regards Yi _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi, The search for requests is giving me the following error. Interesting because if I use the Advanced Search works well. Do you have any ideas where I should look? Other than this, I pretty much have a working version for Tracking Samples via Galaxy. We are mounting our run directory directly to the server running galaxy so at this point we do not need to transfer anything. To connect a sample to the tracking system, we might use a data library with a local path to that sample. Seems reasonable? Thanks in advance. Victor AttributeError: 'StateColumn' object has no attribute 'get_filter' Source Template Extra Data Traceback Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'StateColumn' object has no attribute 'get_filter' URL: http://mir-13:8087/requests_admin/list?f-deleted=False&f-state=New&f-name=All&f-desc=All&sort=-update_time&async=false&page=1&f-free-text-search=cells& Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:145 in __call__ view body = method( trans, **kwargs ) Module galaxy.web.framework:139 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.requests_admin:343 in list view return self.request_grid( trans, **kwd ) Module galaxy.web.framework.helpers.grids:138 in __call__ view query = column.filter( trans, trans.user, query, column_filter ) Module galaxy.web.framework.helpers.grids:593 in filter view clause_list.append( column.get_filter( trans, user, column_filter ) ) AttributeError: 'StateColumn' object has no attribute 'get_filter'
Extra Features
Display the lines of code near each part of the traceback Show a debug prompt to allow you to directly debug the code at the traceback Re-GET Page
On Oct 18, 2010, at 12:40 PM, Kelly Vincent wrote:
Yi,
Yes, it is totally fine to ask questions like this.
To answer your question, unfortunately, there is a weakness in the testing framework that limits the way repeat elements can be tested, but I believe the testing you want to do can be done. The only way to test a tool with a repeat element is with a test that includes exactly one _set_ for each repeat. (When you run the tool, you could include 0, 1, or more than 1 sets, but you can only test with 1.)
In your case, you have a repeat element that requires two files, as follows: <repeat name="replicates" title="Replicate"> <param name="tfile" type="data" label="Treatment file"/> <param name="cfile" type="data" label="Control file"/> </repeat> So your test should include something like: <test> ... <param name="tfile" value="ma2c_treatment_ce4.pair" /> <param name="cfile" value="controlfile.name" /> ... </test> Both files need to be included and only one pair (set) can be. The parameter names in the test should exactly match the names in the input parameter declaration. Note that the syntax for the command line should refer to the repeat items something like this: #for $r in $replicates ${r.tfile} ${r.cfile} #end for
If you want to see a simple example, tools/filters/sorter.xml has a fairly complex repeat element with multiple items and tests that run.
Let us know if you have any other questions.
Regards, Kelly
On Oct 18, 2010, at 11:39 AM, WANGYi wrote:
Hi,
Our team is now testing our integrated tools under galaxy testing framework.
At present, we are trying to test the '<repeat>' elements in one of our tools, e.g. <repeat name="replicates" title="Replicate"> <param name="tfile" type="data" label="Treatment file"/> <param name="cfile" type="data" label="Control file"/> </repeat>
we tried add the following section into the <test> tag and ran the test, but did not make it. <test> <param name="tfile" value="ma2c_treatment_ce4.pair" /> <param name="tfile" value="ma2c_treatment_ce5.pair" /> </test>
after searching all over the internet, we were not able to come up with any solution (maybe we missed).
I dont know if it proper to ask you a question like this. but we are kinda desprated for this issue. Could you please kindly tell us, how to write the test section when there are two or more 'replicates' inputed?
Appreciate so much.
Regards Yi _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Victor, The search on the sequencing requests page has been fixed. It should work if you do an update from galaxy-central or you may wait till the next galaxy-dist release. rc On Oct 18, 2010, at 3:51 PM, Victor Ruotti wrote:
Hi, The search for requests is giving me the following error. Interesting because if I use the Advanced Search works well. Do you have any ideas where I should look? Other than this, I pretty much have a working version for Tracking Samples via Galaxy. We are mounting our run directory directly to the server running galaxy so at this point we do not need to transfer anything. To connect a sample to the tracking system, we might use a data library with a local path to that sample. Seems reasonable?
Thanks in advance. Victor AttributeError: 'StateColumn' object has no attribute 'get_filter'
Section Links
Source Template Extra Data Traceback Hi, I'm source! Extra Data
CGI Variables CONTENT_LENGTH '0' HTTP_ACCEPT 'application/xml,application/xhtml+xml,text/ html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5' HTTP_ACCEPT_ENCODING 'gzip, deflate' HTTP_ACCEPT_LANGUAGE 'en-us' HTTP_CONNECTION 'keep-alive' HTTP_COOKIE 'galaxysession = c6ca0ddb55be603a9d10856f5a7750a46606c5ee2c7c9708d522a267a74384365d964a7f30438d18 ' HTTP_HOST 'mir-13:8087' HTTP_REFERER 'http://mir-13:8087/requests_admin/list' HTTP_USER_AGENT 'Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10_6_4; en-us) AppleWebKit/533.18.1 (KHTML, like Gecko) Version/5.0.2 Safari/ 533.18.5' PATH_INFO '/requests_admin/list' QUERY_STRING 'f-deleted=False&f-state=New&f-name=All&f- desc=All&sort=-update_time&async=false&page=1&f-free-text- search=cells&' REMOTE_ADDR '192.168.120.169' REQUEST_METHOD 'GET' SERVER_NAME '192.168.100.13' SERVER_PORT '8087' SERVER_PROTOCOL 'HTTP/1.1' Extra Data
WSGI Variables application <paste.debug.prints.PrintDebugMiddleware object at 0x1a2ec150> paste.cookies (<SimpleCookie: galaxysession = 'c6ca0ddb55be603a9d10856f5a7750a46606c5ee2c7c9708d522a267a74384365d964a7f30438d18 '>, 'galaxysession = c6ca0ddb55be603a9d10856f5a7750a46606c5ee2c7c9708d522a267a74384365d964a7f30438d18 ') paste.evalexception <weberror.evalexception.middleware.EvalException object at 0x1a6c3110> paste.evalexception.debug_count 1287428209 paste.expected_exceptions [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions <paste.httpexceptions.HTTPExceptionHandler object at 0x1a2dadd0> paste.httpserver.thread_pool <paste.httpserver.ThreadPool object at 0x167f8490> paste.printdebug_listeners [<cStringIO.StringO object at 0x1b13c810>, <open file '<stderr>', mode 'w' at 0x2af73d376210>] paste.recursive.forward <paste.recursive.Forwarder from /> paste.recursive.include <paste.recursive.Includer from /> paste.recursive.include_app_iter <paste.recursive.IncluderAppIter from /> paste.recursive.script_name '' paste.remove_printdebug <function remove_printdebug at 0x1b193050> paste.throw_errors True weberror.evalexception <weberror.evalexception.middleware.EvalException object at 0x1a6c3110> weberror.evalexception.debug_count 1287428209 webob._parsed_query_vars (MultiDict([('f-deleted', 'False'), ('f- state', 'New'), ('f-name', 'All'), ('f-desc', 'All'), ('sort', '- update_time'), ('async', 'false'), ('page', '1'), ('f-free-text- search', 'cells')]), 'f-deleted=False&f-state=New&f-name=All&f- desc=All&sort=-update_time&async=false&page=1&f-free-text- search=cells&') wsgi process 'Multithreaded' No Template information available.
Error Traceback:
View as: Interactive | Text | XML (full) ⇝ AttributeError: 'StateColumn' object has no attribute 'get_filter' URL: http://mir-13:8087/requests_admin/list?f-deleted=False&f- state=New&f-name=All&f-desc=All&sort=- update_time&async=false&page=1&f-free-text-search=cells& Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:145 in __call__ view body = method( trans, **kwargs ) Module galaxy.web.framework:139 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.web.controllers.requests_admin:343 in list view return self.request_grid( trans, **kwd ) Module galaxy.web.framework.helpers.grids:138 in __call__ view query = column.filter( trans, trans.user, query, column_filter ) Module galaxy.web.framework.helpers.grids:593 in filter view clause_list.append( column.get_filter( trans, user,
column_filter ) ) AttributeError: 'StateColumn' object has no attribute 'get_filter'
Display the lines of code near each part of the traceback Show a debug prompt to allow you to directly debug the code at the
Extra Features traceback Re-GET Page
On Oct 18, 2010, at 12:40 PM, Kelly Vincent wrote:
Yi,
Yes, it is totally fine to ask questions like this.
To answer your question, unfortunately, there is a weakness in the testing framework that limits the way repeat elements can be tested, but I believe the testing you want to do can be done. The only way to test a tool with a repeat element is with a test that includes exactly one _set_ for each repeat. (When you run the tool, you could include 0, 1, or more than 1 sets, but you can only test with 1.)
In your case, you have a repeat element that requires two files, as follows: <repeat name="replicates" title="Replicate"> <param name="tfile" type="data" label="Treatment file"/> <param name="cfile" type="data" label="Control file"/> </repeat> So your test should include something like: <test> ... <param name="tfile" value="ma2c_treatment_ce4.pair" /> <param name="cfile" value="controlfile.name" /> ... </test> Both files need to be included and only one pair (set) can be. The parameter names in the test should exactly match the names in the input parameter declaration. Note that the syntax for the command line should refer to the repeat items something like this: #for $r in $replicates ${r.tfile} ${r.cfile} #end for
If you want to see a simple example, tools/filters/sorter.xml has a fairly complex repeat element with multiple items and tests that run.
Let us know if you have any other questions.
Regards, Kelly
On Oct 18, 2010, at 11:39 AM, WANGYi wrote:
Hi,
Our team is now testing our integrated tools under galaxy testing framework.
At present, we are trying to test the '<repeat>' elements in one of our tools, e.g. <repeat name="replicates" title="Replicate"> <param name="tfile" type="data" label="Treatment file"/> <param name="cfile" type="data" label="Control file"/> </repeat>
we tried add the following section into the <test> tag and ran the test, but did not make it. <test> <param name="tfile" value="ma2c_treatment_ce4.pair" /> <param name="tfile" value="ma2c_treatment_ce5.pair" /> </test>
after searching all over the internet, we were not able to come up with any solution (maybe we missed).
I dont know if it proper to ask you a question like this. but we are kinda desprated for this issue. Could you please kindly tell us, how to write the test section when there are two or more 'replicates' inputed?
Appreciate so much.
Regards Yi _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi, I installed both rpy and rpy2 following the directions in their documentation. I no longer get the error cant find the rpy module. But now it looks as there is an error in from the python program, histogram.py Any ideas? Thanks, Victor An error occurred running this job: global name 'array' is not defined
Okay, Adding one line in the histogram.py script fixed it. a = r.c(a) r.pdf( out_fname, 8, 8 ) a = r.c(a) r.hist( a, probability=True, main=title, xlab=xlab, breaks=breaks ) On Oct 19, 2010, at 11:16 AM, Victor Ruotti wrote:
Hi, I installed both rpy and rpy2 following the directions in their documentation. I no longer get the error cant find the rpy module.
But now it looks as there is an error in from the python program, histogram.py
Any ideas? Thanks, Victor
An error occurred running this job: global name 'array' is not defined
participants (4)
-
Kelly Vincent -
Ramkrishna Chakrabarty -
Victor Ruotti -
WANGYi