- galaxy-dev - lists.galaxyproject.org

new tool: calculate frequencies
by Assaf Gordon 22 Feb '10

22 Feb '10

Hi, Attached is a tool to calculate frequencies/distribution of values in a column (similar to "histogram" tool, but without plotting the chart). The tool allows finer control of the output, by setting min,max,bin-width or number-of-bins. This allows calculating distribution of multiple datasets, then comparing them or plotting them all together with the plotting tool. Also available for download here: http://cancan.cshl.edu/labmembers/gordon/files/calculate_frequncies.tar.bz2 comments are welcomed, -gordon

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GMOD Logo Program
by Dave Clements, GMOD Help Desk 22 Feb '10

22 Feb '10

Hello all, Need a logo that tells people what your web site, database or GMOD component is about? If your resource needs a logo then the GMOD Logo Program (http://gmod.org/wiki/GMOD_Logo_Program) can help. I am pleased to announce the first call for participation in the GMOD Logo Program. This program is for GMOD users and developers that would like have a custom designed logo for their web site, database or GMOD component. The program pairs GMOD community members with students in advanced design classes at colleges and universities. This spring we will be working with a class at Linn-Benton Community College. Participants will meet several times (remotely) over a 3 week period, with the end result being a new logo for your resource. Participation is limited to non-profits, and costs US$75. If you are interested, please see http://gmod.org/wiki/GMOD_Logo_Program for additional details and requirements, and an application form. The program is accepting applications until March 1. Thanks, Dave Clements GMOD Help Desk PS: This program was inspired by ZFIN's success with its logo (see http://zfin.org) ZFIN's excellent logo was created by working with a design class at the University of Oregon. -- Please keep responses on the list! http://gmod.org/wiki/2010_GMOD_Summer_School_-_Americas http://gmod.org/wiki/GMOD_Logo_Program http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback

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Exception when a tool has repeat, select and label options
by Assaf Gordon 19 Feb '10

19 Feb '10

Hello, First, thanks for fixing the boolean testing bug. We're having strange exception thrown in some of our tools, when a tool has a <repeat> section, a selection-box parameter and an output label. That might sound strange, but I've narrowed it down and it's (almost) definitely caused by the combination of those three. I know you don't use the "label" option in the public Galaxy, but we use it in many of our tools, and for some it simply doesn't work. Attached are three simple tools: tool_without_label: has a <repeat> parameter, a selection-box parameter, no 'label' in the <output>. works ok. tool_without_select: has a <repeat> parameter, a text parameter (instead of a selection box), and a label in the <output>. works ok. tool_with_label: has all three items: a <repeat>, a selection-box, and a label. Executing this tool throws an exception: ======================= URL: http://localhost:8080/tool_runner/index File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/WebError-0.8a-py2.5.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/gordon/temp/galaxy/eggs/py2.5-noplatform/Paste-1.6-py2.5.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/gordon/temp/galaxy/lib/galaxy/web/framework/base.py', line 125 in __call__ body = method( trans, **kwargs ) File '/home/gordon/temp/galaxy/lib/galaxy/web/controllers/tool_runner.py', line 53 in index template, vars = tool.handle_input( trans, params.__dict__ ) File '/home/gordon/temp/galaxy/lib/galaxy/tools/__init__.py', line 792 in handle_input out_data = self.execute( trans, incoming=params ) File '/home/gordon/temp/galaxy/lib/galaxy/tools/__init__.py', line 1064 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid ) File '/home/gordon/temp/galaxy/lib/galaxy/tools/actions/__init__.py', line 297 in execute for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): File '/home/gordon/temp/galaxy/lib/galaxy/tools/__init__.py', line 1067 in params_to_strings return params_to_strings( self.inputs, params, app ) File '/home/gordon/temp/galaxy/lib/galaxy/tools/parameters/__init__.py', line 80 in params_to_strings rval[ key ] = str( to_json_string( value ) ) File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/__init__.py', line 182 in dumps File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 312 in encode File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 262 in _iterencode File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 170 in _iterencode_list File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 265 in _iterencode File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 235 in _iterencode_dict File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 273 in _iterencode File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 279 in _iterencode_default File 'build/bdist.solaris-2.11-i86pc/egg/simplejson/encoder.py', line 300 in default TypeError: <galaxy.tools.SelectToolParameterWrapper object at 0x49a8d10> is not JSON serializable ======================= Any help/fix would be greatly appreciated. thanks! -gordon

2 2

Sqlite to MYSQL conversion in galaxy
by Roy Weckiewicz 19 Feb '10

19 Feb '10

---------- Forwarded message ---------- From: Roy Weckiewicz <roystefan(a)gmail.com> Date: Fri, Feb 19, 2010 at 1:31 PM Subject: Re: [galaxy-dev] Sqlite to MYSQL conversion in galaxy To: Nate Coraor <nate(a)bx.psu.edu> Thanks again Nate, I just tried the one you sent me - it seems I just have a database revision issue: Traceback (most recent call last): File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/web/buildapp.py", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/app.py", line 28, in __init__ create_or_verify_database( db_url, self.config.database_engine_options ) File "/Users/rsw3284/Downloads/galaxy-0c07212afc00/lib/galaxy/model/migrate/check.py", line 72, in create_or_verify_database raise Exception( "Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually" ) Exception: Your database is older than hg revision 1464:c7acaa1bb88f and will need to be updated manually Rgds, Roy Weckiewicz On Fri, Feb 19, 2010 at 1:28 PM, Nate Coraor <nate(a)bx.psu.edu> wrote: > Roy Weckiewicz wrote: > > What's strange is that eventhough the file name on the egg is >> MySQL*fat-ucs2.egg the error still reports the file in question as >> MySQL*fat.egg -- I've tried renaming the egg to match the original file, but >> it didn't seem to make a difference. Furthermore, when I run.sh, the program >> will create a directory in home called .python-eggs/ containing the >> _MySQL.so file, among other things - Will I have to add a different URL to >> the eggs.ini to keep it from re-downloading the old file? >> > > Ah, sorry, that egg relies on some uncommitted patches. I've rebuilt it > using a clean checkout, could you try this one instead?: > > > http://www.bx.psu.edu/~nate/galaxy/MySQL_python-1.2.2_5.0.67_static-py2.5-m… > > Thanks, > --nate > -- Roy Weckiewicz Texas A&M University -- Roy Weckiewicz Texas A&M University

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Sqlite to MYSQL conversion in galaxy
by Roy Weckiewicz 19 Feb '10

19 Feb '10

Hello, I am trying to configure a local galaxy server using a MYSQL database instead of the standard sqlite3. I'm using OSX and have been attempting (unsuccessfully) to convert the sqlite database (universe.sql) to mysql format. Basically, I am in need of the database table schema for mysql. I noticed on your web page that you host a mysql server at: genome-mysql.cse.ucsc.edu -- would it be possible to do some sort of mysqldump or mysqlhotcopy in order to download the table schema, so that I could upload them into my local mysql installation? I've tried using Sqlite3 to dump the contents of universe.sql, but there are numerous syntax differences that need to be addressed before it will load successfully into my mysql database. Do you have any suggestions on how to either migrate the database from sqlite3 to MYSQL (via script or program), or create the mysql database from scratch and just import the correct table schema? Any help would be appreciated. MYSQL: Ver 14.14 Distrib 5.1.37, for apple-darwin9.5.0 (i386) using readline 5.1 Python 2.5.1 Rgds, Roy Weckiewicz. -- Roy Weckiewicz Texas A&M University

3 7

boolean testing problems
by Assaf Gordon 19 Feb '10

19 Feb '10

Hi, I really appreciate your help with this, and I'm sorry to keep bothering you about the boolean thing, but: It seems the recent successive changes to the boolean parameter are conflicting with one another (some changes made to the testing framework and others to the rest of galaxy). At changeset 3402:bb50ac713feb (before the whole boolean issue start), testing "gpos_concat_1" works OK - single tests the succeeds (and only tests the "true" case). At changeset 3410:4a416d872806 (which fixed the boolean in the testing framework), testing "gpos_concat_1" works OK - with two tests, checking both "true" and "false" cases. But changeset 3411:0c07212afc00 (which fixed the boolean bug not related to testing framework) broke the testing framework entirely: testing "gpos_concat_1" fails on both tests (together with all my tools which have a boolean parameter, even if those tests worked before). -gordon

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[hg] galaxy 3413: lims: added feature to to transfer folders fro...
by Greg Von Kuster 19 Feb '10

19 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/bbff5050cfd2 changeset: 3413:bbff5050cfd2 user: rc date: Thu Feb 18 11:50:19 2010 -0500 description: lims: added feature to to transfer folders from a sequencer diffstat: lib/galaxy/web/controllers/requests_admin.py | 63 ++++++++++++++------------- 1 files changed, 32 insertions(+), 31 deletions(-) diffs (94 lines): diff -r e05cdf1205bc -r bbff5050cfd2 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Thu Feb 18 11:26:39 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Thu Feb 18 11:50:19 2010 -0500 @@ -1146,7 +1146,7 @@ for index in range(len(sample.request.samples)): # check for empty bar code if not barcode.strip(): - msg = 'Please fill the barcode for sample <b>%s</b>.' % samples[index].name + msg = 'Please fill the barcode for sample <b>%s</b>.' % sample.name break # check all the saved bar codes all_samples = trans.sa_session.query( trans.app.model.Sample ) @@ -1401,9 +1401,19 @@ sample_id=trans.security.encode_id(sample.id), msg=msg, messagetype='error', folder_path=folder_path )) - files = output.split()[2:] - return files - + return output.split()[2:] + + def __get_files_in_dir(self, trans, sample, folder_path): + tmpfiles = self.__get_files(trans, sample, folder_path) + for tf in tmpfiles: + if tf[-1] == os.sep: + self.__get_files_in_dir(trans, sample, os.path.join(folder_path, tf)) + else: + sample.dataset_files.append([os.path.join(folder_path, tf), + sample.transfer_status.NOT_STARTED]) + trans.sa_session.add( sample ) + trans.sa_session.flush() + return @web.expose @web.require_admin def get_data(self, trans, **kwd): @@ -1460,19 +1470,24 @@ sample=sample, dataset_files=sample.dataset_files) elif params.get( 'start_transfer_button', False ): - for f in files_list: - if f[-1] == os.sep: - # the selected item is a folder so transfer all the - # folder contents - sample.dataset_files.append([os.path.join(folder_path, f), - sample.transfer_status.NOT_STARTED]) - else: - sample.dataset_files.append([os.path.join(folder_path, f), - sample.transfer_status.NOT_STARTED]) - trans.sa_session.add( sample ) - trans.sa_session.flush() - return self.__start_datatx(trans, sample) - + folder_files = [] + if len(files_list): + for f in files_list: + if f[-1] == os.sep: + # the selected item is a folder so transfer all the + # folder contents + self.__get_files_in_dir(trans, sample, os.path.join(folder_path, f)) + else: + sample.dataset_files.append([os.path.join(folder_path, f), + sample.transfer_status.NOT_STARTED]) + trans.sa_session.add( sample ) + trans.sa_session.flush() + return self.__start_datatx(trans, sample) + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='show_datatx_page', + sample_id=trans.security.encode_id(sample.id), + folder_path=folder_path)) + def __setup_datatx_user(self, trans, library, folder): ''' This method sets up the datatx user: @@ -1562,20 +1577,6 @@ dataset_index=index, cmd=cmd) dtt.start() -# # set the transfer status -# sample.dataset_files[index][1] = sample.transfer_status.IN_PROGRESS -# trans.sa_session.add( sample ) -# trans.sa_session.flush() -# try: -# retcode = subprocess.call(cmd) -# except Exception, e: -# error_msg = dfile.split('/')[-1] + ": Data transfer failed. " + str(e) + "<br/>" -# return trans.response.send_redirect( web.url_for( controller='requests_admin', -# action='show_datatx_page', -# sample_id=trans.security.encode_id(sample.id), -# folder_path=os.path.dirname(dfile), -# messagetype='error', -# msg=error_msg)) # set the sample state to the last state if sample.current_state().id != sample.request.type.states[-1].id: event = trans.app.model.SampleEvent(sample, sample.request.type.states[-1],

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[hg] galaxy 3415: lims:
by Greg Von Kuster 19 Feb '10

19 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/52edc83ed81c changeset: 3415:52edc83ed81c user: rc date: Thu Feb 18 21:38:49 2010 -0500 description: lims: - added data directory field in sequencer info - UI changes on samples page diffstat: lib/galaxy/web/controllers/requests_admin.py | 9 +++++++-- templates/admin/requests/create_request_type.mako | 4 ++++ templates/admin/requests/show_request.mako | 12 ++++++++---- templates/admin/requests/view_request_type.mako | 4 ++++ templates/requests/show_request.mako | 11 +++++++---- 5 files changed, 30 insertions(+), 10 deletions(-) diffs (164 lines): diff -r c280939fd48d -r 52edc83ed81c lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Thu Feb 18 17:04:43 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Thu Feb 18 21:38:49 2010 -0500 @@ -1370,10 +1370,14 @@ status='error', message="Invalid sample ID", **kwd) ) + if sample.request.type.datatx_info.get('data_dir', ''): + folder_path = util.restore_text( sample.request.type.datatx_info.get('data_dir', '') ) + else: + folder_path = util.restore_text( params.get( 'folder_path', '' ) ) return trans.fill_template( '/admin/requests/get_data.mako', sample=sample, dataset_files=sample.dataset_files, msg=msg, messagetype=messagetype, files=[], - folder_path=util.restore_text( params.get( 'folder_path', '' ) )) + folder_path=folder_path ) def __get_files(self, trans, sample, folder_path): ''' This method retrieves the filenames to be transfer from the remote host. @@ -1687,7 +1691,8 @@ # data transfer info rt.datatx_info = dict(host=util.restore_text( params.get( 'host', '' ) ), username=util.restore_text( params.get( 'username', '' ) ), - password=util.restore_text( params.get( 'password', '' ) )) + password=util.restore_text( params.get( 'password', '' ) ), + data_dir=util.restore_text( params.get( 'data_dir', '' ) )) trans.sa_session.add( rt ) trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', diff -r c280939fd48d -r 52edc83ed81c templates/admin/requests/create_request_type.mako --- a/templates/admin/requests/create_request_type.mako Thu Feb 18 17:04:43 2010 -0500 +++ b/templates/admin/requests/create_request_type.mako Thu Feb 18 21:38:49 2010 -0500 @@ -66,6 +66,10 @@ <input type="password" name="password" value="" size="40"/> </div> <div class="form-row"> + <label>Data directory:</label> + <input type="text" name="data_dir" value="" size="40"/> + </div> + <div class="form-row"> <div style="float: left; width: 250px; margin-right: 10px;"> <input type="hidden" name="new" value="submitted" size="40"/> </div> diff -r c280939fd48d -r 52edc83ed81c templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Thu Feb 18 17:04:43 2010 -0500 +++ b/templates/admin/requests/show_request.mako Thu Feb 18 21:38:49 2010 -0500 @@ -43,7 +43,7 @@ </script> <style type="text/css"> .msg_head { - padding: 10px 0px; + padding: 0px 0px; cursor: pointer; } @@ -134,7 +134,7 @@ <th>Data Library</th> <th>Folder</th> %if request.submitted() or request.complete(): - <th>Dataset(s)</th> + <th>Dataset(s) Transfered</th> %endif <th></th> </tr> @@ -252,7 +252,7 @@ <div class="toolForm"> <div class="form-row"> <div class="msg_list"> - <h4 class="msg_head">Request Information</h4> + <h4 class="msg_head"><u>Request Information</u></h4> <div class="msg_body"> %for index, rd in enumerate(request_details): <div class="form-row"> @@ -282,11 +282,14 @@ </div> </div> +<br/> + <%def name="render_grid( grid_index, grid_name, fields_dict )"> + <br/> <div class="msg_list"> %if grid_name: - <h4 class="msg_head">${grid_name}</h4> + <h4 class="msg_head"><u>${grid_name}</u></h4> %else: <h4>Grid ${grid_index}</h4> %endif @@ -346,6 +349,7 @@ <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate(request.type.sample_form.layout): ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_index ) )} + <br/> %endfor %else: <label>There are no samples.</label> diff -r c280939fd48d -r 52edc83ed81c templates/admin/requests/view_request_type.mako --- a/templates/admin/requests/view_request_type.mako Thu Feb 18 17:04:43 2010 -0500 +++ b/templates/admin/requests/view_request_type.mako Thu Feb 18 21:38:49 2010 -0500 @@ -58,6 +58,10 @@ <input type="password" name="password" value="${request_type.datatx_info['password']}" size="40"/> </div> <div class="form-row"> + <label>Data directory:</label> + <input type="text" name="data_dir" value="${request_type.datatx_info.get('data_dir', '')}" size="40"/> + </div> + <div class="form-row"> <input type="submit" name="save_changes" value="Save changes"/> </div> </form> diff -r c280939fd48d -r 52edc83ed81c templates/requests/show_request.mako --- a/templates/requests/show_request.mako Thu Feb 18 17:04:43 2010 -0500 +++ b/templates/requests/show_request.mako Thu Feb 18 21:38:49 2010 -0500 @@ -44,7 +44,7 @@ </script> <style type="text/css"> .msg_head { - padding: 15px 0px; + padding: 0px 0px; cursor: pointer; } @@ -124,7 +124,7 @@ <th>Data Library</th> <th>Folder</th> %if request.submitted() or request.complete(): - <th>Dataset(s)</th> + <th>Dataset(s) Transfered</th> %endif <th></th> </tr> @@ -240,7 +240,7 @@ <div class="toolForm"> <div class="form-row"> <div class="msg_list"> - <h4 class="msg_head">Request Information</h4> + <h4 class="msg_head"><u>Request Information</u></h4> <div class="msg_body"> %for index, rd in enumerate(request_details): <div class="form-row"> @@ -269,11 +269,13 @@ </div> </div> </div> +<br/> <%def name="render_grid( grid_index, grid_name, fields_dict )"> + <br/> <div class="msg_list"> %if grid_name: - <h4 class="msg_head">${grid_name}</h4> + <h4 class="msg_head"><u>${grid_name}</u></h4> %else: <h4>Grid ${grid_index}</h4> %endif @@ -333,6 +335,7 @@ <% trans.sa_session.refresh( request.type.sample_form ) %> %for grid_index, grid_name in enumerate(request.type.sample_form.layout): ${render_grid( grid_index, grid_name, request.type.sample_form.fields_of_grid( grid_index ) )} + <br/> %endfor %else: <label>There are no samples.</label>

1 0

[hg] galaxy 3416: Re-fix new functional test support for setting...
by Greg Von Kuster 19 Feb '10

19 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/d995557d383b changeset: 3416:d995557d383b user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Feb 19 10:01:33 2010 -0500 description: Re-fix new functional test support for setting check boxes and boolean tool params to false, and fix a broken functional test in the security and libraries suite. diffstat: lib/galaxy/web/controllers/library_common.py | 24 ++++++++++---------- templates/library/common/browse_library.mako | 4 +- templates/library/common/common.mako | 2 +- test-data/gops_concat_out2.bed | 10 ++++---- test/base/twilltestcase.py | 31 ++++++++++++++++--------- test/functional/test_security_and_libraries.py | 13 ++++------ 6 files changed, 45 insertions(+), 39 deletions(-) diffs (228 lines): diff -r 52edc83ed81c -r d995557d383b lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Thu Feb 18 21:38:49 2010 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Fri Feb 19 10:01:33 2010 -0500 @@ -1067,7 +1067,6 @@ # use act_on_multiple_datasets( self, trans, cntrller, library_id, ldda_ids='', **kwd ) since it does what we need kwd['do_action'] = 'zip' return self.act_on_multiple_datasets( trans, cntrller, library_id, ldda_ids=id, **kwd ) - else: mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) trans.response.set_content_type( mime ) @@ -1198,15 +1197,16 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) show_deleted = util.string_as_bool( params.get( 'show_deleted', False ) ) + action = params.get( 'do_action', None ) if not ldda_ids: msg = "You must select at least one dataset" messagetype = 'error' - elif not params.do_action: + elif not action: msg = "You must select an action to perform on selected datasets" messagetype = 'error' else: ldda_ids = util.listify( ldda_ids ) - if params.do_action == 'add': + if action == 'add': history = trans.get_history() total_imported_lddas = 0 msg = '' @@ -1223,7 +1223,7 @@ trans.sa_session.add( history ) trans.sa_session.flush() msg += "%i dataset(s) have been imported into your history. " % total_imported_lddas - elif params.do_action == 'manage_permissions': + elif action == 'manage_permissions': # We need the folder containing the LibraryDatasetDatasetAssociation(s) ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_ids[0] ) ) trans.response.send_redirect( web.url_for( controller='library_common', @@ -1235,7 +1235,7 @@ show_deleted=show_deleted, msg=util.sanitize_text( msg ), messagetype=messagetype ) ) - elif params.do_action == 'delete': + elif action == 'delete': for ldda_id in ldda_ids: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) ldda.deleted = True @@ -1245,18 +1245,18 @@ else: error = False try: - if params.do_action == 'zip': + if action == 'zip': # Can't use mkstemp - the file must not exist first tmpd = tempfile.mkdtemp() - tmpf = os.path.join( tmpd, 'library_download.' + params.do_action ) + tmpf = os.path.join( tmpd, 'library_download.' + action ) if ziptype == '64': archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) else: archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) - elif params.do_action == 'tgz': + elif action == 'tgz': archive = util.streamball.StreamBall( 'w|gz' ) - elif params.do_action == 'tbz': + elif action == 'tbz': archive = util.streamball.StreamBall( 'w|bz2' ) except (OSError, zipfile.BadZipFile): error = True @@ -1321,7 +1321,7 @@ msg = "Unable to create archive for download, please report this error" messagetype = 'error' if not error: - if params.do_action == 'zip': + if action == 'zip': archive.close() tmpfh = open( tmpf ) # clean up now @@ -1335,11 +1335,11 @@ messagetype = 'error' if not error: trans.response.set_content_type( "application/x-zip-compressed" ) - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % params.do_action + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % action return tmpfh else: trans.response.set_content_type( "application/x-tar" ) - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % params.do_action + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryFiles.%s" % action archive.wsgi_status = trans.response.wsgi_status() archive.wsgi_headeritems = trans.response.wsgi_headeritems() return archive.stream diff -r 52edc83ed81c -r d995557d383b templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako Thu Feb 18 21:38:49 2010 -0500 +++ b/templates/library/common/browse_library.mako Fri Feb 19 10:01:33 2010 -0500 @@ -472,12 +472,12 @@ %if cntrller in [ 'library', 'requests' ]: ${self.render_folder( 'library', library.root_folder, 0, created_ldda_ids, trans.security.encode_id( library.id ), hidden_folder_ids, tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} %if not library.deleted: - ${render_actions_on_multiple_items( 'library', default_action=default_action )} + ${render_actions_on_multiple_items()} %endif %elif cntrller in [ 'library_admin', 'requests_admin' ]: ${self.render_folder( 'library_admin', library.root_folder, 0, created_ldda_ids, trans.security.encode_id( library.id ), [], tracked_datasets, show_deleted=show_deleted, parent=None, row_counter=row_counter, root_folder=True )} %if not library.deleted and not show_deleted: - ${render_actions_on_multiple_items( 'library_admin' )} + ${render_actions_on_multiple_items()} %endif %endif </table> diff -r 52edc83ed81c -r d995557d383b templates/library/common/common.mako --- a/templates/library/common/common.mako Thu Feb 18 21:38:49 2010 -0500 +++ b/templates/library/common/common.mako Fri Feb 19 10:01:33 2010 -0500 @@ -356,7 +356,7 @@ %endif </%def> -<%def name="render_actions_on_multiple_items( cntrller, default_action=None )"> +<%def name="render_actions_on_multiple_items()"> <tfoot> <tr> <td colspan="4" style="padding-left: 42px;"> diff -r 52edc83ed81c -r d995557d383b test-data/gops_concat_out2.bed --- a/test-data/gops_concat_out2.bed Thu Feb 18 21:38:49 2010 -0500 +++ b/test-data/gops_concat_out2.bed Fri Feb 19 10:01:33 2010 -0500 @@ -63,8 +63,8 @@ chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - -chr1 4348187 4348589 3.70 4.90 2.55 -chr1 4488177 4488442 4.03 5.77 1.92 -chr1 4774091 4774440 8.07 8.33 7.82 -chr1 4800122 4800409 6.40 7.35 5.44 -chr1 4878925 4879277 2.18 0.28 4.93 +chr1 4348187 4348589 . . + +chr1 4488177 4488442 . . + +chr1 4774091 4774440 . . + +chr1 4800122 4800409 . . + +chr1 4878925 4879277 . . + diff -r 52edc83ed81c -r d995557d383b test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu Feb 18 21:38:49 2010 -0500 +++ b/test/base/twilltestcase.py Fri Feb 19 10:01:33 2010 -0500 @@ -862,17 +862,14 @@ # Copied from form_builder.CheckboxField if value == True: return True - if isinstance( value, basestring ) and value.lower() in ( "yes", "true", "on" ): - return True - # This may look strange upon initial inspection, but see the comments in the get_html() method - # above for clarification. Basically, if value is not True, then it will always be a list with - # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not - # checked, then value will be only the hidden field. - return isinstance( value, list ) and len( value ) == 2 + if isinstance( value, list ): + value = value[0] + return isinstance( value, basestring ) and value.lower() in ( "yes", "true", "on" ) try: checkbox = control.get() checkbox.selected = is_checked( control_value ) except Exception, e1: + print "Attempting to set checkbox selected value threw exception: ", e1 # if there's more than one checkbox, probably should use the behaviour for # ClientForm.ListControl ( see twill code ), but this works for now... for elem in control_value: @@ -885,6 +882,7 @@ try: tc.fv( f.name, control.name, str( elem ) ) except Exception, e2: + print "Attempting to set control '", control.name, "' to value '", elem, "' threw exception: ", e2 # Galaxy truncates long file names in the dataset_collector in ~/parameters/basic.py if len( elem ) > 30: elem_name = '%s..%s' % ( elem[:17], elem[-11:] ) @@ -1654,11 +1652,22 @@ self.home() def download_archive_of_library_files( self, cntrller, library_id, ldda_ids, format ): self.home() - self.visit_url( "%s/library_common/browse_library?cntrller=%s&id=%s" % ( self.url, cntrller, library_id ) ) + # Here it would be ideal to have twill set form values and submit the form, but + # twill barfs on that due to the recently introduced page wrappers around the contents + # of the browse_library.mako template which enable panel layout when visiting the + # page from an external URL. By "barfs", I mean that twill somehow loses hod on the + # cntrller param. We'll just simulate the form submission by building the URL manually. + # Here's the old, better approach... + #self.visit_url( "%s/library_common/browse_library?cntrller=%s&id=%s" % ( self.url, cntrller, library_id ) ) + #for ldda_id in ldda_ids: + # tc.fv( "1", "ldda_ids", ldda_id ) + #tc.fv( "1", "do_action", format ) + #tc.submit( "action_on_datasets_button" ) + # Here's the new approach... + url = "%s/library_common/act_on_multiple_datasets?cntrller=%s&library_id=%s&do_action=%s" % ( self.url, cntrller, library_id, format ) for ldda_id in ldda_ids: - tc.fv( "1", "ldda_ids", ldda_id ) - tc.fv( "1", "do_action", format ) - tc.submit( "action_on_datasets_button" ) + url += "&ldda_ids=%s" % ldda_id + self.visit_url( url ) tc.code( 200 ) archive = self.write_temp_file( self.last_page(), suffix=format ) self.home() diff -r 52edc83ed81c -r d995557d383b test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Thu Feb 18 21:38:49 2010 -0500 +++ b/test/functional/test_security_and_libraries.py Fri Feb 19 10:01:33 2010 -0500 @@ -1596,18 +1596,15 @@ self.home() self.logout() self.login( email=admin_user.email ) - """ - TODO: debug this, somebody recently broke it def test_167_download_archive_of_library_files( self ): - Testing downloading an archive of files from the library + """Testing downloading an archive of files from the library""" for format in ( 'tbz', 'tgz', 'zip' ): - archive = self.download_archive_of_library_files( 'library', - self.security.encode_id( library_one.id ), - ( self.security.encode_id( ldda_one.id ), self.security.encode_id( ldda_two.id ) ), - format ) + archive = self.download_archive_of_library_files( cntrller='library', + library_id=self.security.encode_id( library_one.id ), + ldda_ids=[ self.security.encode_id( ldda_one.id ), self.security.encode_id( ldda_two.id ) ], + format=format ) self.check_archive_contents( archive, ( ldda_one, ldda_two ) ) os.remove( archive ) - """ def test_170_mark_group_deleted( self ): """Testing marking a group as deleted""" # Logged in as admin_user

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[hg] galaxy 3414: Make page 'View' option use same URL as shared...
by Greg Von Kuster 19 Feb '10

19 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c280939fd48d changeset: 3414:c280939fd48d user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Feb 18 17:04:43 2010 -0500 description: Make page 'View' option use same URL as shared/accessible/published page does so that relative URLs behave the same in both contexts. This change addresses the issue raised by the temporarily broken hyperlink on the Bushman page. diffstat: lib/galaxy/web/controllers/page.py | 2 +- lib/galaxy/web/framework/helpers/grids.py | 5 +++++ 2 files changed, 6 insertions(+), 1 deletions(-) diffs (27 lines): diff -r bbff5050cfd2 -r c280939fd48d lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Thu Feb 18 11:50:19 2010 -0500 +++ b/lib/galaxy/web/controllers/page.py Thu Feb 18 17:04:43 2010 -0500 @@ -44,7 +44,7 @@ grids.GridAction( "Add new page", dict( action='create' ) ) ] operations = [ - grids.GridOperation( "View", allow_multiple=False, url_args=dict( action='display') ), + grids.DisplayByUsernameAndSlugGridOperation( "View", allow_multiple=False ), grids.GridOperation( "Edit name/id", allow_multiple=False, url_args=dict( action='edit') ), grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ), grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), diff -r bbff5050cfd2 -r c280939fd48d lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Thu Feb 18 11:50:19 2010 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Thu Feb 18 17:04:43 2010 -0500 @@ -541,6 +541,11 @@ return self.condition( item ) else: return True + +class DisplayByUsernameAndSlugGridOperation( GridOperation ): + """ Operation to display an item by username and slug. """ + def get_url_args( self, item ): + return { 'action' : 'display_by_username_and_slug', 'username' : item.user.username, 'slug' : item.slug } class GridAction( object ): def __init__( self, label=None, url_args=None ):

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