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[hg] galaxy 2381: Handle the addition of new tool parameters bet...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dae0313bf5bb changeset: 2381:dae0313bf5bb user: James Taylor <james(a)jamestaylor.org> date: Wed Apr 29 13:46:02 2009 -0400 description: Handle the addition of new tool parameters better in the workflow editor. Default values will be filled in and a message displayed to the user 7 file(s) affected in this change: lib/galaxy/tools/__init__.py lib/galaxy/tools/parameters/grouping.py lib/galaxy/web/controllers/workflow.py lib/galaxy/workflow/modules.py static/scripts/galaxy.workflow_editor.canvas.js templates/workflow/editor.mako tools/maf/interval2maf.xml diffs (252 lines): diff -r 22b08d47f7ba -r dae0313bf5bb lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Apr 29 11:53:22 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Apr 29 13:46:02 2009 -0400 @@ -676,25 +676,7 @@ """ context = ExpressionContext( state, context ) for input in inputs.itervalues(): - if isinstance( input, Repeat ): - # Repeat elements are always initialized to have 0 units. - state[ input.name ] = [] - elif isinstance( input, Conditional ): - # State for a conditional is a plain dictionary. - s = state[ input.name ] = {} - # Get the default value for the 'test element' and use it - # to determine the current case - test_value = input.test_param.get_initial_value( trans, context ) - current_case = input.get_current_case( test_value, trans ) - # Store the current case in a special value - s['__current_case__'] = current_case - # Store the value of the test element - s[ input.test_param.name ] = test_value - # Recursively fill in state for selected case - self.fill_in_new_state( trans, input.cases[current_case].inputs, s, context ) - else: - # `input` is just a plain parameter, get its default value - state[ input.name ] = input.get_initial_value( trans, context ) + state[ input.name ] = input.get_initial_value( trans, context ) def get_param_html_map( self, trans, page=0, other_values={} ): """ @@ -1057,6 +1039,41 @@ def params_from_strings( self, params, app, ignore_errors=False ): return params_from_strings( self.inputs, params, app, ignore_errors ) + + + def check_and_update_param_values( self, values, trans ): + """ + Check that all parameters have values, and fill in with default + values where neccesary. This could be called after loading values + from a database in case new parameters have been added. + """ + messages = [] + self.check_and_update_param_values_helper( self.inputs, values, trans, messages ) + return messages + + def check_and_update_param_values_helper( self, inputs, values, trans, messages, context=None, prefix="" ): + """ + Recursive helper for `check_and_update_param_values_helper` + """ + context = ExpressionContext( values, context ) + for input in inputs.itervalues(): + # No value, insert the default + if input.name not in values: + messages.append( prefix + input.label ) + values[input.name] = input.get_initial_value( trans, context ) + # Value, visit recursively as usual + else: + if isinstance( input, Repeat ): + for i, d in enumerate( values[ input.name ] ): + rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 ) + self.check_and_update_param_values_helper( input.inputs, d, trans, messages, context, rep_prefix ) + elif isinstance( input, Conditional ): + group_values = values[ input.name ] + current = group_values["__current_case__"] + self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix ) + else: + # Regular tool parameter, no recursion needed + pass def handle_unvalidated_param_values( self, input_values, app ): """ diff -r 22b08d47f7ba -r dae0313bf5bb lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Wed Apr 29 11:53:22 2009 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Wed Apr 29 13:46:02 2009 -0400 @@ -3,6 +3,7 @@ """ from basic import ToolParameter +from galaxy.util.expressions import ExpressionContext class Group( object ): def __init__( self ): @@ -19,6 +20,11 @@ into the preferred value form. """ return value + def get_initial_value( self, trans, context ): + """ + Return the initial state/value for this group + """ + raise TypeError( "Not implemented" ) class Repeat( Group ): type = "repeat" @@ -65,7 +71,9 @@ if isinstance( input, ToolParameter ): callback( new_prefix, input, d[input.name], parent = d ) else: - input.visit_inputs( new_prefix, d[input.name], callback ) + input.visit_inputs( new_prefix, d[input.name], callback ) + def get_initial_value( self, trans, context ): + return [] class Conditional( Group ): type = "conditional" @@ -109,6 +117,22 @@ callback( prefix, input, value[input.name], parent = value ) else: input.visit_inputs( prefix, value[input.name], callback ) + def get_initial_value( self, trans, context ): + # State for a conditional is a plain dictionary. + rval = {} + # Get the default value for the 'test element' and use it + # to determine the current case + test_value = self.test_param.get_initial_value( trans, context ) + current_case = self.get_current_case( test_value, trans ) + # Store the current case in a special value + rval['__current_case__'] = current_case + # Store the value of the test element + rval[ self.test_param.name ] = test_value + # Fill in state for selected case + child_context = ExpressionContext( rval, context ) + for child_input in self.cases[current_case].inputs.itervalues(): + rval[ child_input.name ] = child_input.get_initial_value( trans, child_context ) + return rval class ConditionalWhen( object ): def __init__( self ): diff -r 22b08d47f7ba -r dae0313bf5bb lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py Wed Apr 29 11:53:22 2009 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Wed Apr 29 13:46:02 2009 -0400 @@ -300,9 +300,16 @@ data = {} data['name'] = workflow.name data['steps'] = {} + data['upgrade_messages'] = {} # For each step, rebuild the form and encode the state for step in workflow.steps: + # Load from database representation module = module_factory.from_workflow_step( trans, step ) + # Fix any missing parameters + upgrade_message = module.check_and_update_state() + if upgrade_message: + data['upgrade_messages'][step.order_index] = upgrade_message + # Pack atrributes into plain dictionary step_dict = { 'id': step.order_index, 'type': module.type, @@ -312,7 +319,7 @@ 'tool_errors': module.get_errors(), 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), - 'form_html': module.get_config_form() + 'form_html': module.get_config_form(), } # Connections input_conn_dict = {} @@ -324,6 +331,7 @@ step_dict['position'] = step.position # Add to return value data['steps'][step.order_index] = step_dict + print data['upgrade_messages'] return data @web.json diff -r 22b08d47f7ba -r dae0313bf5bb lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py Wed Apr 29 11:53:22 2009 -0400 +++ b/lib/galaxy/workflow/modules.py Wed Apr 29 13:46:02 2009 -0400 @@ -60,6 +60,13 @@ pass def get_config_form( self ): raise TypeError( "Abstract method" ) + + def check_and_update_state( self ): + """ + If the state is not in sync with the current implementation of the + module, try to update. Returns a list of messages to be displayed + """ + pass ## ---- Run time --------------------------------------------------------- @@ -236,7 +243,11 @@ return value, error # Update state using incoming values errors = self.tool.update_state( self.trans, self.tool.inputs, self.state.inputs, incoming, item_callback=item_callback ) - self.errors = errors or None + self.errors = errors or None + + def check_and_update_state( self ): + return self.tool.check_and_update_param_values( self.state.inputs, self.trans ) + def add_dummy_datasets( self, connections=None): if connections: # Store onnections by input name diff -r 22b08d47f7ba -r dae0313bf5bb static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Wed Apr 29 11:53:22 2009 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Wed Apr 29 13:46:02 2009 -0400 @@ -255,6 +255,7 @@ if ( data.type ) { this.type = data.type; } + this.name = data.name; this.form_html = data.form_html; this.tool_state = data.tool_state; this.tool_errors = data.tool_errors; diff -r 22b08d47f7ba -r dae0313bf5bb templates/workflow/editor.mako --- a/templates/workflow/editor.mako Wed Apr 29 11:53:22 2009 -0400 +++ b/templates/workflow/editor.mako Wed Apr 29 13:46:02 2009 -0400 @@ -78,7 +78,18 @@ workflow.fit_canvas_to_nodes(); scroll_to_nodes(); canvas_manager.draw_overview(); - hide_modal(); + // Determine if any parameters were 'upgraded' and provide message + upgrade_message = "" + $.each( data['upgrade_messages'], function( k, v ) { + upgrade_message += ( "<li>Step " + ( parseInt(k) + 1 ) + ": " + workflow.nodes[k].name + " -- " + v.join( ", " ) ); + }); + if ( upgrade_message ) { + show_modal( "Workflow loaded with changes", + "Values were not found for the following parameters (possibly a result of tool upgrades), <br/> default values have been used. Please review the following parameters and then save.<ul>" + upgrade_message + "</ul>", + { "Continue" : hide_modal } ); + } else { + hide_modal(); + } }, beforeSubmit: function( data ) { show_modal( "Loading workflow", "progress" ); @@ -88,7 +99,9 @@ }); $(document).ajaxError( function ( e, x ) { - show_modal( "Server error", x.responseText, { "Ignore error" : hide_modal } ); + console.log( e, x ); + var message = x.responseText || x.statusText || "Could not connect to server"; + show_modal( "Server error", message, { "Ignore error" : hide_modal } ); return false; }); diff -r 22b08d47f7ba -r dae0313bf5bb tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml Wed Apr 29 11:53:22 2009 -0400 +++ b/tools/maf/interval2maf.xml Wed Apr 29 13:46:02 2009 -0400 @@ -6,6 +6,7 @@ #end if </command> <inputs> + <param type="text" name="TEST" label="Test" /> <param format="interval" name="input1" type="data" label="Choose intervals"> <validator type="unspecified_build" /> </param>

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[hg] galaxy 2385: PyTables and GeneTrack eggs. Still need to bu...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/add0911007d9 changeset: 2385:add0911007d9 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Apr 29 17:37:22 2009 -0400 description: PyTables and GeneTrack eggs. Still need to bundle up pychartdir. 2 file(s) affected in this change: dist-eggs.ini eggs.ini diffs (55 lines): diff -r cd1bcec32519 -r add0911007d9 dist-eggs.ini --- a/dist-eggs.ini Wed Apr 29 16:32:23 2009 -0400 +++ b/dist-eggs.ini Wed Apr 29 17:37:22 2009 -0400 @@ -24,9 +24,15 @@ py2.5-solaris-2.10-sun4u-ucs2 = v880.bx.psu.edu /depot/projects/pythons/solaris-2.10-sun4u-ucs2/bin/python2.5 [groups] -py2.4-linux = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4 -py2.5-linux = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 -linux = py2.4-linux py2.5-linux +py2.4-linux-i686 = py2.4-linux-i686-ucs2 py2.4-linux-i686-ucs4 +py2.4-linux-x86_64 = py2.4-linux-x86_64-ucs2 py2.4-linux-x86_64-ucs4 +py2.5-linux-i686 = py2.5-linux-i686-ucs2 py2.5-linux-i686-ucs4 +py2.5-linux-x86_64 = py2.5-linux-x86_64-ucs2 py2.5-linux-x86_64-ucs4 +py2.4-linux = py2.4-linux-i686 py2.4-linux-x86_64 +py2.5-linux = py2.5-linux-i686 py2.5-linux-x86_64 +linux-i686 = py2.4-linux-i686 py2.5-linux-i686 +linux-x86_64 = py2.4-linux-x86_64 py2.5-linux-x86_64 +linux = linux-i686 linux-x86_64 py2.4-macosx = py2.4-macosx-10.3-fat-ucs2 py2.5-macosx = py2.5-macosx-10.3-fat-ucs2 py2.5-macosx-10.5-i386-ucs2 macosx = py2.4-macosx py2.5-macosx diff -r cd1bcec32519 -r add0911007d9 eggs.ini --- a/eggs.ini Wed Apr 29 16:32:23 2009 -0400 +++ b/eggs.ini Wed Apr 29 17:37:22 2009 -0400 @@ -24,6 +24,7 @@ threadframe = 0.2 guppy = 0.1.8 numpy = 1.2.1 +tables = 2.1.1 [eggs:noplatform] Beaker = 0.5 @@ -51,6 +52,7 @@ wsgiref = 0.1.2 Babel = 0.9.4 wchartype = 0.1 +GeneTrack = 1.0.3 ; extra version information [tags] @@ -61,6 +63,7 @@ flup = .dev_r2311 bx_python = _dev_r4bf1f32e6b76 nose = .dev_r101 +tables = _hdf5_1.8.2_lzo_2.03_bzip2_1.0.5_static ; source location, necessary for scrambling [source] @@ -100,3 +103,5 @@ wsgiref = http://pypi.python.org/packages/source/w/wsgiref/wsgiref-0.1.2.zip Babel = http://ftp.edgewall.com/pub/babel/Babel-0.9.4.zip wchartype = http://ginstrom.com/code/wchartype-0.1.zip +tables = http://www.pytables.org/download/stable/tables-2.1.1.tar.gz ftp://ftp.hdfgroup.org/HDF5/current/src/hdf5-1.8.2.tar.gz http://www.oberhumer.com/opensource/lzo/download/lzo-2.03.tar.gz http://www.bzip.org/1.0.5/bzip2-1.0.5.tar.gz +GeneTrack = http://genetrack.googlecode.com/files/GeneTrack-1.0.3.zip http://dalchemy.com/opensource/formkit/FormKit_0.9b2.tar.gz

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[hg] galaxy 2383: Accidently commited a testing change, removed
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/656f1df80b46 changeset: 2383:656f1df80b46 user: James Taylor <james(a)jamestaylor.org> date: Wed Apr 29 14:47:18 2009 -0400 description: Accidently commited a testing change, removed 1 file(s) affected in this change: tools/maf/interval2maf.xml diffs (11 lines): diff -r 89541ac4983f -r 656f1df80b46 tools/maf/interval2maf.xml --- a/tools/maf/interval2maf.xml Wed Apr 29 13:56:59 2009 -0400 +++ b/tools/maf/interval2maf.xml Wed Apr 29 14:47:18 2009 -0400 @@ -6,7 +6,6 @@ #end if </command> <inputs> - <param type="text" name="TEST" label="Test" /> <param format="interval" name="input1" type="data" label="Choose intervals"> <validator type="unspecified_build" /> </param>

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[hg] galaxy 2382: Fix for reporting job errors - somehow necessa...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/89541ac4983f changeset: 2382:89541ac4983f user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Apr 29 13:56:59 2009 -0400 description: Fix for reporting job errors - somehow necessary imported stuff got eliminated. 1 file(s) affected in this change: lib/galaxy/web/controllers/dataset.py diffs (24 lines): diff -r dae0313bf5bb -r 89541ac4983f lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Wed Apr 29 13:46:02 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Wed Apr 29 13:56:59 2009 -0400 @@ -1,7 +1,7 @@ -import logging, os, mimetypes, smtplib +import logging, os, sets, string, shutil, re, socket, mimetypes, smtplib from galaxy.web.base.controller import * -from galaxy import web, model +from galaxy import util, datatypes, jobs, web, model from cgi import escape, FieldStorage from email.MIMEText import MIMEText @@ -89,8 +89,8 @@ s.sendmail( frm, [ to ], msg.as_string() ) s.close() return trans.show_ok_message( "Your error report has been sent" ) - except: - return trans.show_error_message( "An error occurred sending the report by email" ) + except Exception, e: + return trans.show_error_message( "An error occurred sending the report by email: %s" % str( e ) ) @web.expose def default(self, trans, dataset_id=None, **kwd):

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[hg] galaxy 2379: Fix for issubtype in workflow editor, would ca...
by Greg Von Kuster 30 Apr '09

30 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5a4aac327bad changeset: 2379:5a4aac327bad user: James Taylor <james(a)jamestaylor.org> date: Wed Apr 29 10:27:57 2009 -0400 description: Fix for issubtype in workflow editor, would cause problems drawing connections for types with no inheritence relationships 1 file(s) affected in this change: static/scripts/galaxy.workflow_editor.canvas.js diffs (12 lines): diff -r e0534b25c282 -r 5a4aac327bad static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Tue Apr 28 15:32:44 2009 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Wed Apr 29 10:27:57 2009 -0400 @@ -645,7 +645,7 @@ function issubtype( child, parent ) { child = ext_to_type[child]; parent = ext_to_type[parent]; - return ( parent in type_to_type[child] ); + return ( type_to_type[child] ) && ( parent in type_to_type[child] ); }; function populate_datatype_info( data ) {

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[hg] galaxy 2378: Updated bx-python.
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/e0534b25c282 changeset: 2378:e0534b25c282 user: guru date: Tue Apr 28 15:32:44 2009 -0400 description: Updated bx-python. 1 file(s) affected in this change: eggs.ini diffs (19 lines): diff -r 635d97a3a228 -r e0534b25c282 eggs.ini --- a/eggs.ini Tue Apr 28 14:18:21 2009 -0400 +++ b/eggs.ini Tue Apr 28 15:32:44 2009 -0400 @@ -59,13 +59,13 @@ MySQL_python = _5.0.67_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r130f083b56b9 +bx_python = _dev_r4bf1f32e6b76 nose = .dev_r101 ; source location, necessary for scrambling [source] numpy = http://downloads.sourceforge.net/numpy/numpy-1.2.1.tar.gz -bx_python = http://bitbucket.org/james_taylor/bx-python/get/130f083b56b9.bz2 +bx_python = http://bitbucket.org/james_taylor/bx-python/get/4bf1f32e6b76.bz2 Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar… DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://mysql.mirrors.pair.com/Downloads/MySQL-5.0/mysql-5.0.67.tar.gz

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[hg] galaxy 2377: Fix a problem with dynamic selects depending o...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/635d97a3a228 changeset: 2377:635d97a3a228 user: James Taylor <james(a)jamestaylor.org> date: Tue Apr 28 14:18:21 2009 -0400 description: Fix a problem with dynamic selects depending on other dynamic selects when setting values at runtime in workflows 2 file(s) affected in this change: lib/galaxy/tools/__init__.py lib/galaxy/tools/parameters/basic.py diffs (43 lines): diff -r 87885ab394a0 -r 635d97a3a228 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Tue Apr 28 09:44:35 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Tue Apr 28 14:18:21 2009 -0400 @@ -686,12 +686,12 @@ # to determine the current case test_value = input.test_param.get_initial_value( trans, context ) current_case = input.get_current_case( test_value, trans ) - # Recursively fill in state for selected case - self.fill_in_new_state( trans, input.cases[current_case].inputs, s, context ) # Store the current case in a special value s['__current_case__'] = current_case # Store the value of the test element s[ input.test_param.name ] = test_value + # Recursively fill in state for selected case + self.fill_in_new_state( trans, input.cases[current_case].inputs, s, context ) else: # `input` is just a plain parameter, get its default value state[ input.name ] = input.get_initial_value( trans, context ) diff -r 87885ab394a0 -r 635d97a3a228 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Tue Apr 28 09:44:35 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Tue Apr 28 14:18:21 2009 -0400 @@ -569,6 +569,11 @@ def value_to_basic( self, value, app ): if isinstance( value, UnvalidatedValue ): return { "__class__": "UnvalidatedValue", "value": value.value } + elif isinstance( value, RuntimeValue ): + # Need to handle runtime value's ourself since delegating to the + # parent method causes the value to be turned into a string, which + # breaks multiple selection + return { "__class__": "RuntimeValue" } return value def value_from_basic( self, value, app, ignore_errors=False ): if isinstance( value, dict ) and value["__class__"] == "UnvalidatedValue": @@ -598,6 +603,9 @@ dep_value = context[ dep_name ] # Dependency on a dataset that does not yet exist if isinstance( dep_value, DummyDataset ): + return True + # Dependency on a value that has not been checked + if isinstance( dep_value, UnvalidatedValue ): return True # Dependency on a value that does not yet exist if isinstance( dep_value, RuntimeValue ):

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[hg] galaxy 2376: Can now optionally create a new group with the...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/87885ab394a0 changeset: 2376:87885ab394a0 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Apr 28 09:44:35 2009 -0400 description: Can now optionally create a new group with the same name as a role when creating the role, along with more cleanup on the various users / groups / roles templates. 9 file(s) affected in this change: lib/galaxy/web/controllers/admin.py templates/admin/dataset_security/deleted_groups.mako templates/admin/dataset_security/deleted_roles.mako templates/admin/dataset_security/group.mako templates/admin/dataset_security/group_create.mako templates/admin/dataset_security/role.mako templates/admin/dataset_security/role_create.mako templates/admin/dataset_security/user.mako templates/admin/user/create.mako diffs (485 lines): diff -r 7fd4f748b0ca -r 87885ab394a0 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Mon Apr 27 16:30:08 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Tue Apr 28 09:44:35 2009 -0400 @@ -60,6 +60,7 @@ description = util.restore_text( params.description ) in_users = util.listify( params.get( 'in_users', [] ) ) in_groups = util.listify( params.get( 'in_groups', [] ) ) + create_group_for_role = params.get( 'create_group_for_role', 'no' ) if not name or not description: msg = "Enter a valid name and a description" elif trans.app.model.Role.filter( trans.app.model.Role.table.c.name==name ).first(): @@ -76,7 +77,14 @@ for group in [ trans.app.model.Group.get( x ) for x in in_groups ]: gra = trans.app.model.GroupRoleAssociation( group, role ) gra.flush() - msg = "Role '%s' has been created with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) ) + if create_group_for_role == 'yes': + # Create the group + group = trans.app.model.Group( name=name ) + group.flush() + msg = "Group '%s' has been created, and role '%s' has been created with %d associated users and %d associated groups" % \ + ( group.name, role.name, len( in_users ), len( in_groups ) ) + else: + msg = "Role '%s' has been created with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) ) trans.response.send_redirect( web.url_for( controller='admin', action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) ) trans.response.send_redirect( web.url_for( controller='admin', action='create_role', msg=util.sanitize_text( msg ), messagetype='error' ) ) out_users = [] @@ -201,23 +209,12 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - # Build a list of tuples which are roles followed by lists of groups and users - # [ ( role, [ group, group, group ], [ user, user ] ), ( role, [ group, group ], [ user ] ) ] - roles_groups_users = [] roles = trans.app.model.Role.query() \ .filter( trans.app.model.Role.table.c.deleted==True ) \ .order_by( trans.app.model.Role.table.c.name ) \ .all() - for role in roles: - groups = [] - for gra in role.groups: - groups.append( trans.app.model.Group.get( gra.group_id ) ) - users = [] - for ura in role.users: - users.append( trans.app.model.User.get( ura.user_id ) ) - roles_groups_users.append( ( role, groups, users ) ) return trans.fill_template( '/admin/dataset_security/deleted_roles.mako', - roles_groups_users=roles_groups_users, + roles=roles, msg=msg, messagetype=messagetype ) @web.expose @@ -398,23 +395,12 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - # Build a list of tuples which are groups followed by lists of members and roles - # [ ( group, [ member, member, member ], [ role, role ] ), ( group, [ member, member ], [ role ] ) ] - groups_members_roles = [] groups = trans.app.model.Group.query() \ .filter( trans.app.model.Group.table.c.deleted==True ) \ .order_by( trans.app.model.Group.table.c.name ) \ .all() - for group in groups: - members = [] - for uga in group.members: - members.append( trans.app.model.User.get( uga.user_id ) ) - roles = [] - for gra in group.roles: - roles.append( trans.app.model.Role.get( gra.role_id ) ) - groups_members_roles.append( ( group, members, roles ) ) return trans.fill_template( '/admin/dataset_security/deleted_groups.mako', - groups_members_roles=groups_members_roles, + groups=groups, msg=msg, messagetype=messagetype ) @web.expose @@ -627,8 +613,8 @@ msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) users = trans.app.model.User.filter( and_( trans.app.model.User.table.c.deleted==True, trans.app.model.User.table.c.purged==False ) ) \ - .order_by( trans.app.model.User.table.c.email ) \ - .all() + .order_by( trans.app.model.User.table.c.email ) \ + .all() return trans.fill_template( '/admin/user/deleted_users.mako', users=users, msg=msg, messagetype=messagetype ) @web.expose @web.require_admin diff -r 7fd4f748b0ca -r 87885ab394a0 templates/admin/dataset_security/deleted_groups.mako --- a/templates/admin/dataset_security/deleted_groups.mako Mon Apr 27 16:30:08 2009 -0400 +++ b/templates/admin/dataset_security/deleted_groups.mako Tue Apr 28 09:44:35 2009 -0400 @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> ## Render a row -<%def name="render_row( group, members, roles, ctr, anchored, curr_anchor )"> +<%def name="render_row( group, ctr, anchored, curr_anchor )"> %if ctr % 2 == 1: <tr class="odd_row"> %else: @@ -17,18 +17,10 @@ </div> </td> <td> - <ul> - %for user in members: - <li>${user.email}</li> - %endfor - </ul> + ${len( group.members )} </td> <td> - <ul> - %for role in roles: - <li>${role.name}</li> - %endfor - </ul> + ${len( group.roles )} %if not anchored: <a name="${curr_anchor}"></a> <div style="float: right;"><a href="#TOP">top</a></div> @@ -43,12 +35,12 @@ ${render_msg( msg, messagetype )} %endif -%if len( groups_members_roles ) == 0: +%if len( groups ) == 0: There are no deleted Galaxy groups %else: <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> <% - render_quick_find = len( groups_members_roles ) > 50 + render_quick_find = len( groups ) > 50 ctr = 0 %> %if render_quick_find: @@ -69,34 +61,29 @@ %endif <tr class="header"> <td>Name</td> - <td>Members</td> + <td>Users</td> <td>Roles</td> </tr> - %for ctr, group_tuple in enumerate( groups_members_roles ): - <% - group = group_tuple[0] - members = group_tuple[1] - roles = group_tuple[2] - %> + %for ctr, group in enumerate( groups ): %if render_quick_find and not group.name.upper().startswith( curr_anchor ): <% anchored = False %> %endif %if render_quick_find and group.name.upper().startswith( curr_anchor ): %if not anchored: - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} %endif %elif render_quick_find: %for anchor in anchors[ anchor_loc: ]: %if group.name.upper().startswith( anchor ): %if not anchored: <% curr_anchor = anchor %> - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} %endif <% anchor_loc = anchors.index( anchor ) @@ -105,7 +92,7 @@ %endif %endfor %else: - ${render_row( group, members, roles, ctr, True, '' )} + ${render_row( group, ctr, True, '' )} %endif %endfor </table> diff -r 7fd4f748b0ca -r 87885ab394a0 templates/admin/dataset_security/deleted_roles.mako --- a/templates/admin/dataset_security/deleted_roles.mako Mon Apr 27 16:30:08 2009 -0400 +++ b/templates/admin/dataset_security/deleted_roles.mako Tue Apr 28 09:44:35 2009 -0400 @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> ## Render a row -<%def name="render_row( role, groups, users, ctr, anchored, curr_anchor )"> +<%def name="render_row( role, ctr, anchored, curr_anchor )"> %if ctr % 2 == 1: <tr class="odd_row"> %else: @@ -16,19 +16,13 @@ <a class="action-button" href="${h.url_for( action='purge_role', role_id=role.id )}">Purge</a> </div> </td> + <td>${role.description}</td> + <td>${role.type}</td> <td> - <ul> - %for group in groups: - <li>${group.name}</li> - %endfor - </ul> + ${len( role.users )} </td> <td> - <ul> - %for user in users: - <li>${user.email}</li> - %endfor - </ul> + ${len( role.groups )} %if not anchored: <a name="${curr_anchor}"></a> <div style="float: right;"><a href="#TOP">top</a></div> @@ -43,12 +37,12 @@ ${render_msg( msg, messagetype )} %endif -%if len( roles_groups_users ) == 0: +%if len( roles ) == 0: There are no deleted Galaxy roles %else: <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> <% - render_quick_find = len( roles_groups_users ) > 50 + render_quick_find = len( roles ) > 50 ctr = 0 %> %if render_quick_find: @@ -69,34 +63,31 @@ %endif <tr class="header"> <td>Name</td> - <td>Associated Groups</td> - <td>Associated Users</td> + <td>Description</td> + <td>Type</td> + <td>Users</td> + <td>Groups</td> </tr> - %for ctr, role_tuple in enumerate( roles_groups_users ): - <% - role = role_tuple[0] - groups = role_tuple[1] - users = role_tuple[2] - %> + %for ctr, role in enumerate( roles ): %if render_quick_find and not role.name.upper().startswith( curr_anchor ): <% anchored = False %> %endif %if render_quick_find and role.name.upper().startswith( curr_anchor ): %if not anchored: - ${render_row( role, groups, users, ctr, anchored, curr_anchor )} + ${render_row( role, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( role, groups, users, ctr, anchored, curr_anchor )} + ${render_row( role, ctr, anchored, curr_anchor )} %endif %elif render_quick_find: %for anchor in anchors[ anchor_loc: ]: %if role.name.upper().startswith( anchor ): %if not anchored: <% curr_anchor = anchor %> - ${render_row( role, groups, users, ctr, anchored, curr_anchor )} + ${render_row( role, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( role, groups, users, ctr, anchored, curr_anchor )} + ${render_row( role, ctr, anchored, curr_anchor )} %endif <% anchor_loc = anchors.index( anchor ) @@ -105,7 +96,7 @@ %endif %endfor %else: - ${render_row( role, groups, users, ctr, True, '' )} + ${render_row( role, ctr, True, '' )} %endif %endfor </table> diff -r 7fd4f748b0ca -r 87885ab394a0 templates/admin/dataset_security/group.mako --- a/templates/admin/dataset_security/group.mako Mon Apr 27 16:30:08 2009 -0400 +++ b/templates/admin/dataset_security/group.mako Tue Apr 28 09:44:35 2009 -0400 @@ -53,24 +53,24 @@ <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='group', group_id=group.id )}" method="post" > <div class="form-row"> <div style="float: left; margin-right: 10px;"> - Roles associated with '${group.name}'<br/> + <label>Roles associated with '${group.name}'</label> ${render_select( "in_roles", in_roles )}<br/> <input type="submit" id="roles_remove_button" value=">>"/> </div> <div> - Roles not associated with '${group.name}'<br/> + <label>Roles not associated with '${group.name}'</label> ${render_select( "out_roles", out_roles )}<br/> <input type="submit" id="roles_add_button" value="<<"/> </div> </div> <div class="form-row"> <div style="float: left; margin-right: 10px;"> - Users associated with '${group.name}'<br/> + <label>Users associated with '${group.name}'</label> ${render_select( "in_users", in_users )}<br/> <input type="submit" id="users_remove_button" value=">>"/> </div> <div> - Users not associated with '${group.name}'<br/> + <label>Users not associated with '${group.name}'</label> ${render_select( "out_users", out_users )}<br/> <input type="submit" id="users_add_button" value="<<"/> </div> diff -r 7fd4f748b0ca -r 87885ab394a0 templates/admin/dataset_security/group_create.mako --- a/templates/admin/dataset_security/group_create.mako Mon Apr 27 16:30:08 2009 -0400 +++ b/templates/admin/dataset_security/group_create.mako Tue Apr 28 09:44:35 2009 -0400 @@ -52,28 +52,29 @@ <div class="toolFormBody"> <form name="associate_group_role_user" id="associate_group_role_user" action="${h.url_for( action='create_group' )}" method="post" > <div class="form-row"> - Name: <input name="name" type="textfield" value="" size=40"/> + <label>Name:</label> + <input name="name" type="textfield" value="" size=40"/> </div> <div class="form-row"> <div style="float: left; margin-right: 10px;"> - Groups associated with new role<br/> + <label>Groups associated with new role</label> ${render_select( "in_roles", in_roles )}<br/> <input type="submit" id="roles_remove_button" value=">>"/> </div> <div> - Groups not associated with new role<br/> + <label>Groups not associated with new role</label> ${render_select( "out_roles", out_roles )}<br/> <input type="submit" id="roles_add_button" value="<<"/> </div> </div> <div class="form-row"> <div style="float: left; margin-right: 10px;"> - Users associated with new role<br/> + <label>Users associated with new role</label> ${render_select( "in_users", in_users )}<br/> <input type="submit" id="users_remove_button" value=">>"/> </div> <div> - Users not associated with new role<br/> + <label>Users not associated with new role</label> ${render_select( "out_users", out_users )}<br/> <input type="submit" id="users_add_button" value="<<"/> </div> diff -r 7fd4f748b0ca -r 87885ab394a0 templates/admin/dataset_security/role.mako --- a/templates/admin/dataset_security/role.mako Mon Apr 27 16:30:08 2009 -0400 +++ b/templates/admin/dataset_security/role.mako Tue Apr 28 09:44:35 2009 -0400 @@ -53,24 +53,24 @@ <form name="associate_role_user_group" id="associate_role_user_group" action="${h.url_for( action='role', role_id=role.id )}" method="post" > <div class="form-row"> <div style="float: left; margin-right: 10px;"> - Users associated with '${role.name}'<br/> + <label>Users associated with '${role.name}'</label> ${render_select( "in_users", in_users )}<br/> <input type="submit" id="users_remove_button" value=">>"/> </div> <div> - Users not associated with '${role.name}'<br/> + <label>Users not associated with '${role.name}'</label> ${render_select( "out_users", out_users )}<br/> <input type="submit" id="users_add_button" value="<<"/> </div> </div> <div class="form-row"> <div style="float: left; margin-right: 10px;"> - Groups associated with '${role.name}'<br/> + <label>Groups associated with '${role.name}'</label> ${render_select( "in_groups", in_groups )}<br/> <input type="submit" id="groups_remove_button" value=">>"/> </div> <div> - Groups not associated with '${role.name}'<br/> + <label>Groups not associated with '${role.name}'</label> ${render_select( "out_groups", out_groups )}<br/> <input type="submit" id="groups_add_button" value="<<"/> </div> diff -r 7fd4f748b0ca -r 87885ab394a0 templates/admin/dataset_security/role_create.mako --- a/templates/admin/dataset_security/role_create.mako Mon Apr 27 16:30:08 2009 -0400 +++ b/templates/admin/dataset_security/role_create.mako Tue Apr 28 09:44:35 2009 -0400 @@ -52,32 +52,39 @@ <div class="toolFormBody"> <form name="associate_role_group_user" id="associate_role_group_user" action="${h.url_for( action='create_role' )}" method="post" > <div class="form-row"> - Name: <input name="name" type="textfield" value="" size=40"/> - Description: <input name="description" type="textfield" value="" size=40"/> + <label>Name:</label> + <input name="name" type="textfield" value="" size=40"/> + </div> + <div class="form-row"> + <label>Description:</label> + <input name="description" type="textfield" value="" size=40"/> </div> <div class="form-row"> <div style="float: left; margin-right: 10px;"> - Groups associated with new role<br/> + <label>Groups associated with new role</label> ${render_select( "in_groups", in_groups )}<br/> <input type="submit" id="groups_remove_button" value=">>"/> </div> <div> - Groups not associated with new role<br/> + <label>Groups not associated with new role</label> ${render_select( "out_groups", out_groups )}<br/> <input type="submit" id="groups_add_button" value="<<"/> </div> </div> <div class="form-row"> <div style="float: left; margin-right: 10px;"> - Users associated with new role<br/> + <label>Users associated with new role</label> ${render_select( "in_users", in_users )}<br/> <input type="submit" id="users_remove_button" value=">>"/> </div> <div> - Users not associated with new role<br/> + <label>Users not associated with new role</label> ${render_select( "out_users", out_users )}<br/> <input type="submit" id="users_add_button" value="<<"/> </div> + </div> + <div class="form-row"> + <input type="checkbox" name="create_group_for_role" value="yes" />Create a new group of the same name for this role </div> <div class="form-row"> <input type="submit" name="create_role_button" value="Save"/> diff -r 7fd4f748b0ca -r 87885ab394a0 templates/admin/dataset_security/user.mako --- a/templates/admin/dataset_security/user.mako Mon Apr 27 16:30:08 2009 -0400 +++ b/templates/admin/dataset_security/user.mako Tue Apr 28 09:44:35 2009 -0400 @@ -53,24 +53,24 @@ <form name="associate_user_role_group" id="associate_user_role_group" action="${h.url_for( action='user', user_id=user.id )}" method="post" > <div class="form-row"> <div style="float: left; margin-right: 10px;"> - Roles associated with '${user.email}'<br/> + <label>Roles associated with '${user.email}'</label> ${render_select( "in_roles", in_roles )}<br/> <input type="submit" id="roles_remove_button" value=">>"/> </div> <div> - Roles not associated with '${user.email}'<br/> + <label>Roles not associated with '${user.email}'</label> ${render_select( "out_roles", out_roles )}<br/> <input type="submit" id="roles_add_button" value="<<"/> </div> </div> <div class="form-row"> <div style="float: left; margin-right: 10px;"> - Groups associated with '${user.email}'<br/> + <label>Groups associated with '${user.email}'</label> ${render_select( "in_groups", in_groups )}<br/> <input type="submit" id="groups_remove_button" value=">>"/> </div> <div> - Groups not associated with '${user.email}'<br/> + <label>Groups not associated with '${user.email}'</label> ${render_select( "out_groups", out_groups )}<br/> <input type="submit" id="groups_add_button" value="<<"/> </div> diff -r 7fd4f748b0ca -r 87885ab394a0 templates/admin/user/create.mako --- a/templates/admin/user/create.mako Mon Apr 27 16:30:08 2009 -0400 +++ b/templates/admin/user/create.mako Tue Apr 28 09:44:35 2009 -0400 @@ -6,7 +6,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">Create account</div> + <div class="toolFormTitle">Create user account</div> <div class="toolFormBody"> <form name="form" action="${h.url_for( controller='admin', action='create_new_user' )}" method="post" > <div class="form-row">

1 0

[hg] galaxy 2374: Display only the number of associations on the...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d0c905db68db changeset: 2374:d0c905db68db user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Apr 27 16:03:44 2009 -0400 description: Display only the number of associations on the main users, groups, roles pages rather than the associated objects - much faster display times. Also a tweek to my last fix for the column_maker tool. 6 file(s) affected in this change: lib/galaxy/web/controllers/admin.py templates/admin/dataset_security/groups.mako templates/admin/dataset_security/roles.mako templates/admin/dataset_security/users.mako test/base/twilltestcase.py tools/stats/column_maker.py diffs (483 lines): diff -r 22118cf46b0a -r d0c905db68db lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Mon Apr 27 13:33:47 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon Apr 27 16:03:44 2009 -0400 @@ -280,23 +280,12 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - # Build a list of tuples which are groups followed by lists of members and roles - # [ ( group, [ member, member, member ], [ role, role ] ), ( group, [ member, member ], [ role ] ) ] - groups_members_roles = [] groups = trans.app.model.Group.query() \ .filter( trans.app.model.Group.table.c.deleted==False ) \ .order_by( trans.app.model.Group.table.c.name ) \ .all() - for group in groups: - members = [] - for uga in group.members: - members.append( trans.app.model.User.get( uga.user_id ) ) - roles = [] - for gra in group.roles: - roles.append( trans.app.model.Role.get( gra.role_id ) ) - groups_members_roles.append( ( group, members, roles ) ) return trans.fill_template( '/admin/dataset_security/groups.mako', - groups_members_roles=groups_members_roles, + groups=groups, msg=msg, messagetype=messagetype ) @web.expose @@ -647,20 +636,9 @@ params = util.Params( kwd ) msg = util.restore_text( params.get( 'msg', '' ) ) messagetype = params.get( 'messagetype', 'done' ) - # Build a list of tuples which are users followed by lists of groups and roles - # [ ( user, [ group, group, group ], [ role, role ] ), ( user, [ group, group ], [ role ] ) ] - users_groups_roles = [] users = trans.app.model.User.filter( trans.app.model.User.table.c.deleted==False ).order_by( trans.app.model.User.table.c.email ).all() - for user in users: - groups = [] - for uga in user.groups: - groups.append( trans.app.model.Group.get( uga.group_id ) ) - roles = [] - for ura in user.non_private_roles: - roles.append( trans.app.model.Role.get( ura.role_id ) ) - users_groups_roles.append( ( user, groups, roles ) ) return trans.fill_template( '/admin/dataset_security/users.mako', - users_groups_roles=users_groups_roles, + users=users, allow_user_deletion=trans.app.config.allow_user_deletion, msg=msg, messagetype=messagetype ) @@ -702,91 +680,6 @@ out_groups=out_groups, msg=msg, messagetype=messagetype ) - # Utility methods to enable removal of associations - redirects are key - @web.expose - @web.require_admin - def remove_group_from_role( self, trans, **kwd ): - params = util.Params( kwd ) - group_id = int( params.group_id ) - group = trans.app.model.Group.get( group_id ) - role_id = int( params.role_id ) - role = trans.app.model.Role.get( role_id ) - gra = trans.app.model.GroupRoleAssociation.filter( and_( trans.app.model.GroupRoleAssociation.table.c.group_id==group_id, - trans.app.model.GroupRoleAssociation.table.c.role_id==role_id ) ).first() - gra.delete() - gra.flush() - msg = "Group '%s' removed from role '%s'" % ( group.name, role.name ) - trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def remove_group_from_user( self, trans, **kwd ): - params = util.Params( kwd ) - group_id = int( params.group_id ) - group = trans.app.model.Group.get( group_id ) - user_id = int( params.user_id ) - user = trans.app.model.User.get( user_id ) - uga = trans.app.model.UserGroupAssociation.filter( and_( trans.app.model.UserGroupAssociation.table.c.group_id==group_id, - trans.app.model.UserGroupAssociation.table.c.user_id==user_id ) ).first() - uga.delete() - uga.flush() - msg = "Group '%s' removed from user '%s'" % ( group.name, user.email ) - trans.response.send_redirect( web.url_for( action='users', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def remove_role_from_group( self, trans, **kwd ): - params = util.Params( kwd ) - role_id = int( params.role_id ) - role = trans.app.model.Role.get( role_id ) - group_id = int( params.group_id ) - group = trans.app.model.Group.get( group_id ) - gra = trans.app.model.GroupRoleAssociation.filter( and_( trans.app.model.GroupRoleAssociation.table.c.role_id==role_id, - trans.app.model.GroupRoleAssociation.table.c.group_id==group_id ) ).first() - gra.delete() - gra.flush() - msg = "Role '%s' removed from group '%s'" % ( role.name, group.name ) - trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def remove_role_from_user( self, trans, **kwd ): - params = util.Params( kwd ) - user_id = int( params.user_id ) - user = trans.app.model.User.get( user_id ) - role_id = int( params.role_id ) - role = trans.app.model.Role.get( role_id ) - ura = trans.app.model.UserRoleAssociation.filter( and_( trans.app.model.UserRoleAssociation.table.c.user_id==user_id, - trans.app.model.UserRoleAssociation.table.c.role_id==role_id ) ).first() - ura.delete() - ura.flush() - msg = "Role '%s' removed from user '%s'" % ( role.name, user.email ) - trans.response.send_redirect( web.url_for( action='users', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def remove_user_from_group( self, trans, **kwd ): - params = util.Params( kwd ) - user_id = int( params.user_id ) - user = trans.app.model.User.get( user_id ) - group_id = int( params.group_id ) - group = trans.app.model.Group.get( group_id ) - uga = trans.app.model.UserGroupAssociation.filter( and_( trans.app.model.UserGroupAssociation.table.c.user_id==user_id, - trans.app.model.UserGroupAssociation.table.c.group_id==group_id ) ).first() - uga.delete() - uga.flush() - msg = "User '%s' removed from group '%s'" % ( user.email, group.name ) - trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) - @web.expose - @web.require_admin - def remove_user_from_role( self, trans, **kwd ): - params = util.Params( kwd ) - user_id = int( params.user_id ) - user = trans.app.model.User.get( user_id ) - role_id = int( params.role_id ) - role = trans.app.model.Role.get( role_id ) - ura = trans.app.model.UserRoleAssociation.filter( and_( trans.app.model.UserRoleAssociation.table.c.user_id==user_id, - trans.app.model.UserRoleAssociation.table.c.role_id==role_id ) ).first() - ura.delete() - ura.flush() - msg = "User '%s' removed from role '%s'" % ( user.email, role.name ) - trans.response.send_redirect( web.url_for( action='roles', msg=util.sanitize_text( msg ), messagetype='done' ) ) # Galaxy Library Stuff @web.expose diff -r 22118cf46b0a -r d0c905db68db templates/admin/dataset_security/groups.mako --- a/templates/admin/dataset_security/groups.mako Mon Apr 27 13:33:47 2009 -0400 +++ b/templates/admin/dataset_security/groups.mako Mon Apr 27 16:03:44 2009 -0400 @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> ## Render a row -<%def name="render_row( group, members, roles, ctr, anchored, curr_anchor )"> +<%def name="render_row( group, ctr, anchored, curr_anchor )"> %if ctr % 2 == 1: <tr class="odd_row"> %else: @@ -18,34 +18,10 @@ </div> </td> <td> - <ul> - %for user in members: - <li> - <a href="${h.url_for( controller='admin', action='user', user_id=user.id )}">${user.email}</a> - <a id="user-${user.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="user-${user.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_user_from_group', group_id=group.id, user_id=user.id )}">Remove user from group</a> - </div> - </li> - %endfor - </ul> + ${len( group.members )} </td> <td> - <ul> - %for role in roles: - <li> - %if not role.type == trans.app.model.Role.types.PRIVATE: - <a href="${h.url_for( controller='admin', action='role', role_id=role.id )}">${role.name}</a> - <a id="role-${role.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="role-${role.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_role_from_group', group_id=group.id, role_id=role.id )}">Remove role from group</a> - </div> - %else: - ${role.name} - %endif - </li> - %endfor - </ul> + ${len( group.roles )} %if not anchored: <a name="${curr_anchor}"></a> <div style="float: right;"><a href="#TOP">top</a></div> @@ -65,12 +41,12 @@ ${render_msg( msg, messagetype )} %endif -%if len( groups_members_roles ) == 0: +%if len( groups ) == 0: There are no Galaxy groups %else: <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> <% - render_quick_find = len( groups_members_roles ) > 50 + render_quick_find = len( groups ) > 50 ctr = 0 %> %if render_quick_find: @@ -91,34 +67,29 @@ %endif <tr class="header"> <td>Name</td> - <td>Associated Users</td> - <td>Associated Roles</td> + <td>Users</td> + <td>Roles</td> </tr> - %for ctr, group_tuple in enumerate( groups_members_roles ): - <% - group = group_tuple[0] - members = group_tuple[1] - roles = group_tuple[2] - %> + %for ctr, group in enumerate( groups ): %if render_quick_find and not group.name.upper().startswith( curr_anchor ): <% anchored = False %> %endif %if render_quick_find and group.name.upper().startswith( curr_anchor ): %if not anchored: - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} %endif %elif render_quick_find: %for anchor in anchors[ anchor_loc: ]: %if group.name.upper().startswith( anchor ): %if not anchored: <% curr_anchor = anchor %> - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( group, members, roles, ctr, anchored, curr_anchor )} + ${render_row( group, ctr, anchored, curr_anchor )} %endif <% anchor_loc = anchors.index( anchor ) @@ -127,7 +98,7 @@ %endif %endfor %else: - ${render_row( group, members, roles, ctr, True, '' )} + ${render_row( group, ctr, True, '' )} %endif %endfor </table> diff -r 22118cf46b0a -r d0c905db68db templates/admin/dataset_security/roles.mako --- a/templates/admin/dataset_security/roles.mako Mon Apr 27 13:33:47 2009 -0400 +++ b/templates/admin/dataset_security/roles.mako Mon Apr 27 16:03:44 2009 -0400 @@ -20,30 +20,10 @@ <td>${role.description}</td> <td>${role.type}</td> <td> - <ul> - %for ura in role.users: - <li> - <a href="${h.url_for( controller='admin', action='user', user_id=ura.user.id )}">${ura.user.email}</a> - <a id="user-${ura.user.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="user-${ura.user.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_role_from_user', role_id=role.id, user_id=ura.user.id )}">Remove user from role</a> - </div> - </li> - %endfor - </ul> + ${len( role.users )} </td> <td> - <ul> - %for gra in role.groups: - <li> - <a href="${h.url_for( controller='admin', action='group', group_id=gra.group.id )}">${gra.group.name}</a> - <a id="group-${gra.group.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="group-${gra.group.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_group_from_role', role_id=role.id, group_id=gra.group.id )}">Remove group from role</a> - </div> - </li> - %endfor - </ul> + ${len( role.groups )} %if not anchored: <a name="${curr_anchor}"></a> <div style="float: right;"><a href="#TOP">top</a></div> @@ -91,8 +71,8 @@ <td>Name</td> <td>Description</td> <td>Type</td> - <td>Associated Users</td> - <td>Associated Groups</td> + <td>Users</td> + <td>Groups</td> </tr> %for ctr, role in enumerate( roles ): %if render_quick_find and not role.name.upper().startswith( curr_anchor ): diff -r 22118cf46b0a -r d0c905db68db templates/admin/dataset_security/users.mako --- a/templates/admin/dataset_security/users.mako Mon Apr 27 13:33:47 2009 -0400 +++ b/templates/admin/dataset_security/users.mako Mon Apr 27 16:03:44 2009 -0400 @@ -2,7 +2,7 @@ <%namespace file="/message.mako" import="render_msg" /> ## Render a row -<%def name="render_row( user, groups, roles, ctr, anchored, curr_anchor )"> +<%def name="render_row( user, ctr, anchored, curr_anchor )"> %if ctr % 2 == 1: <tr class="odd_row"> %else: @@ -20,30 +20,10 @@ </div> </td> <td> - <ul> - %for group in groups: - <li> - <a href="${h.url_for( controller='admin', action='group', group_id=group.id )}">${group.name}</a> - <a id="group-${group.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="group-${group.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_group_from_user', user_id=user.id, group_id=group.id )}">Remove group from user</a> - </div> - </li> - %endfor - </ul> + ${len( user.groups )} </td> <td> - <ul> - %for role in roles: - <li> - <a href="${h.url_for( controller='admin', action='role', role_id=role.id )}">${role.name}</a> - <a id="role-${role.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="role-${role.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin', action='remove_role_from_user', user_id=user.id, role_id=role.id )}">Remove role from user</a> - </div> - </li> - %endfor - </ul> + ${len( user.roles )} %if not anchored: <a name="${curr_anchor}"></a> <div style="float: right;"><a href="#TOP">top</a></div> @@ -65,12 +45,12 @@ ${render_msg( msg, messagetype )} %endif -%if len( users_groups_roles ) == 0: +%if len( users ) == 0: There are no Galaxy users %else: <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> <% - render_quick_find = len( users_groups_roles ) > 50 + render_quick_find = len( users ) > 50 ctr = 0 %> %if render_quick_find: @@ -91,34 +71,29 @@ %endif <tr class="header"> <td>Email</td> - <td>Associated Groups</td> - <td>Associated Roles</td> + <td>Groups</td> + <td>Roles</td> </tr> - %for ctr, user_tuple in enumerate( users_groups_roles ): - <% - user = user_tuple[0] - groups = user_tuple[1] - roles = user_tuple[2] - %> + %for ctr, user in enumerate( users ): %if render_quick_find and not user.email.upper().startswith( curr_anchor ): <% anchored = False %> %endif %if render_quick_find and user.email.upper().startswith( curr_anchor ): %if not anchored: - ${render_row( user, groups, roles, ctr, anchored, curr_anchor )} + ${render_row( user, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( user, groups, roles, ctr, anchored, curr_anchor )} + ${render_row( user, ctr, anchored, curr_anchor )} %endif %elif render_quick_find: %for anchor in anchors[ anchor_loc: ]: %if user.email.upper().startswith( anchor ): %if not anchored: <% curr_anchor = anchor %> - ${render_row( user, groups, roles, ctr, anchored, curr_anchor )} + ${render_row( user, ctr, anchored, curr_anchor )} <% anchored = True %> %else: - ${render_row( user, groups, roles, ctr, anchored, curr_anchor )} + ${render_row( user, ctr, anchored, curr_anchor )} %endif <% anchor_loc = anchors.index( anchor ) @@ -127,7 +102,7 @@ %endif %endfor %else: - ${render_row( user, groups, roles, ctr, True, '' )} + ${render_row( user, ctr, True, '' )} %endif %endfor </table> diff -r 22118cf46b0a -r d0c905db68db test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Apr 27 13:33:47 2009 -0400 +++ b/test/base/twilltestcase.py Mon Apr 27 16:03:44 2009 -0400 @@ -787,29 +787,6 @@ self.check_page_for_string( check_str ) self.home() - # Utility methods to test removal of associations - def remove_role_from_group( self, role_id, role_name, group_id, group_name ): - """Remove a role from a group""" - self.home() - self.visit_url( "%s/admin/remove_role_from_group?role_id=%s&group_id=%s" % ( self.url, role_id, group_id ) ) - check_str = "Role '%s' removed from group '%s'" % ( role_name, group_name ) - self.check_page_for_string( check_str ) - self.home() - def remove_user_from_group( self, user_id, email, group_id, group_name ): - """Remove a user from a group""" - self.home() - self.visit_url( "%s/admin/remove_user_from_group?user_id=%s&group_id=%s" % ( self.url, user_id, group_id ) ) - check_str = "User '%s' removed from group '%s'" % ( email, group_name ) - self.check_page_for_string( check_str ) - self.home() - def remove_user_from_role( self, user_id, email, role_id, role_name ): - """Remove a user from a role""" - self.home() - self.visit_url( "%s/admin/remove_user_from_role?user_id=%s&role_id=%s" % ( self.url, user_id, role_id ) ) - check_str = "User '%s' removed from role '%s'" % ( email, role_name ) - self.check_page_for_string( check_str ) - self.home() - # Library stuff def create_library( self, name='Library One', description='This is Library One' ): """Create a new library""" diff -r 22118cf46b0a -r d0c905db68db tools/stats/column_maker.py --- a/tools/stats/column_maker.py Mon Apr 27 13:33:47 2009 -0400 +++ b/tools/stats/column_maker.py Mon Apr 27 16:03:44 2009 -0400 @@ -13,10 +13,6 @@ sys.stderr.write( msg ) sys.exit() -data_err = "This tool can only be used with tab-delimited data." -columns_err = "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. " -column_types_err = "Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. " -invalid_metadata_err = "The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it. " inp_file = sys.argv[1] out_file = sys.argv[2] expr = sys.argv[3] @@ -24,16 +20,16 @@ try: in_columns = int( sys.argv[5] ) except: - stop_err( columns_err + data_err ) + stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." ) if in_columns < 2: # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method. - stop_err( columns_err + data_err ) + stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." ) try: in_column_types = sys.argv[6].split( ',' ) except: - stop_err( column_types_err + data_err ) + stop_err( "Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." ) if len( in_column_types ) != in_columns: - stop_err( invalid_metadata_err + data_err ) + stop_err( "The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it. This tool can only be used with tab-delimited data." ) # Unescape if input has been escaped mapped_str = {

1 0

[hg] galaxy 2373: Test dataset for 'Mask CpG sites' tool which I...
by Greg Von Kuster 29 Apr '09

29 Apr '09

details: http://www.bx.psu.edu/hg/galaxy/rev/22118cf46b0a changeset: 2373:22118cf46b0a user: guru date: Mon Apr 27 13:33:47 2009 -0400 description: Test dataset for 'Mask CpG sites' tool which I forgot to include in my last commit. 1 file(s) affected in this change: test-data/6_mask_noncpg.maf diffs (61 lines): diff -r ea9235523069 -r 22118cf46b0a test-data/6_mask_noncpg.maf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/6_mask_noncpg.maf Mon Apr 27 13:33:47 2009 -0400 @@ -0,0 +1,57 @@ +##maf version=1 +a score=356676.0 +s hg18.chr1 2817 1438 + 247249719 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