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commit/galaxy-central: jgoecks: Trackster: refactoring to use dataset attributes rather than .dataset_id and .hda_ldda
by commits-noreply＠bitbucket.org 30 Apr '13

30 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a27856f42a61/ Changeset: a27856f42a61 User: jgoecks Date: 2013-04-30 15:12:18 Summary: Trackster: refactoring to use dataset attributes rather than .dataset_id and .hda_ldda Affected #: 1 file diff -r f8d07c98812903dc98de2665874a2c31b65b84da -r a27856f42a616378bf5b152a06707d1d8c24e66d static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1534,7 +1534,7 @@ if (this.overview_drawable) { // If drawable to be set as overview is already in overview, do nothing. // Otherwise, remove overview. - if (this.overview_drawable.dataset_id === drawable.dataset_id) { + if (this.overview_drawable.dataset.id === drawable.dataset.id) { return; } this.overview_viewport.find(".track").remove(); @@ -1712,7 +1712,7 @@ tool.run( // URL params. { - target_dataset_id: this.track.dataset_id, + target_dataset_id: this.track.dataset.id, action: 'rerun', tool_id: tool.id }, @@ -1741,7 +1741,7 @@ }), url_params = { - target_dataset_id: this.track.dataset_id, + target_dataset_id: this.track.dataset.id, action: 'rerun', tool_id: this.id, regions: [ @@ -2249,8 +2249,6 @@ // Attribute init. // this.dataset = new data.Dataset(obj_dict.dataset); - this.dataset_id = this.dataset.get('id'); - this.hda_ldda = this.dataset.get('hda_ldda'); this.dataset_check_type = 'converted_datasets_state'; this.data_url_extra_params = {}; this.data_query_wait = ('data_query_wait' in obj_dict ? obj_dict.data_query_wait : DEFAULT_DATA_QUERY_WAIT); @@ -2395,8 +2393,8 @@ window.location.href = galaxy_paths.get('sweepster_url') + "?" + $.param({ - dataset_id: track.dataset_id, - hda_ldda: track.hda_ldda, + dataset_id: track.dataset.id, + hda_ldda: track.dataset.get('hda_ldda'), regions: JSON.stringify(new Backbone.Collection(regions).toJSON()) }); }, @@ -2420,7 +2418,7 @@ ], can_draw: function() { - if ( this.dataset_id && Drawable.prototype.can_draw.call(this) ) { + if ( this.dataset.id && Drawable.prototype.can_draw.call(this) ) { return true; } return false; @@ -2444,8 +2442,6 @@ set_dataset: function(dataset) { this.dataset = dataset; this.data_manager.set('dataset', dataset); - this.dataset_id = dataset.get('id'); - this.hda_ldda = dataset.get('hda_ldda'); }, /** @@ -2601,7 +2597,7 @@ // Tracks with no dataset id are handled differently. // FIXME: is this really necessary? // - if (!track.dataset_id) { + if (!track.dataset.id) { return; } @@ -2609,7 +2605,7 @@ // about track status. var init_deferred = $.Deferred(), params = { - hda_ldda: track.hda_ldda, + hda_ldda: track.dataset.get('hda_ldda'), data_type: this.dataset_check_type, chrom: track.view.chrom, retry: retry @@ -2771,8 +2767,8 @@ return { "track_type": this.get_type(), "name": this.name, - "hda_ldda": this.hda_ldda, - "dataset_id": this.dataset_id, + "hda_ldda": this.dataset.get('hda_ldda'), + "dataset_id": this.dataset.id, "prefs": this.prefs, "mode": this.mode, "filters": this.filters_manager.to_dict(), @@ -3200,7 +3196,7 @@ // Reset data URL when dataset indexing has completed/when not pending. var ss_deferred = new util.ServerStateDeferred({ url: self.dataset_state_url, - url_params: {dataset_id : self.dataset_id, hda_ldda: self.hda_ldda}, + url_params: {dataset_id : self.dataset.id, hda_ldda: self.dataset.get('hda_ldda')}, interval: self.data_query_wait, // Set up deferred to check dataset state until it is not pending. success_fn: function(result) { return result !== "pending"; } @@ -3651,7 +3647,7 @@ */ set_min_value: function(new_val) { this.prefs.min_value = new_val; - $('#linetrack_' + this.dataset_id + '_minval').text(this.prefs.min_value); + $('#linetrack_' + this.dataset.id + '_minval').text(this.prefs.min_value); this.tile_cache.clear(); this.request_draw(); }, @@ -3661,7 +3657,7 @@ */ set_max_value: function(new_val) { this.prefs.max_value = new_val; - $('#linetrack_' + this.dataset_id + '_maxval').text(this.prefs.max_value); + $('#linetrack_' + this.dataset.id + '_maxval').text(this.prefs.max_value); this.tile_cache.clear(); this.request_draw(); }, @@ -3671,7 +3667,7 @@ track.vertical_range = undefined; return $.getJSON( track.dataset.url(), { data_type: 'data', stats: true, chrom: track.view.chrom, low: 0, - high: track.view.max_high, hda_ldda: track.hda_ldda }, function(result) { + high: track.view.max_high, hda_ldda: track.dataset.get('hda_ldda') }, function(result) { track.container_div.addClass( "line-track" ); var data = result.data; if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) { @@ -3689,8 +3685,8 @@ // FIXME: we should probably only save this when the user explicately sets it // since we lose the ability to compute it on the fly (when changing // chromosomes for example). - $('#track_' + track.dataset_id + '_minval').val(track.prefs.min_value); - $('#track_' + track.dataset_id + '_maxval').val(track.prefs.max_value); + $('#track_' + track.dataset.id + '_minval').val(track.prefs.min_value); + $('#track_' + track.dataset.id + '_maxval').val(track.prefs.max_value); } track.vertical_range = track.prefs.max_value - track.prefs.min_value; track.total_frequency = data.total_frequency; @@ -3710,7 +3706,7 @@ } }, help_text: "Set min value" - }).addClass('yaxislabel bottom').attr("id", 'linetrack_' + track.dataset_id + '_minval') + }).addClass('yaxislabel bottom').attr("id", 'linetrack_' + track.dataset.id + '_minval') .prependTo(track.container_div), max_label = $("<div/>").text(round(track.prefs.max_value, 3)).make_text_editable({ num_cols: 6, @@ -3722,7 +3718,7 @@ } }, help_text: "Set max value" - }).addClass('yaxislabel top').attr("id", 'linetrack_' + track.dataset_id + '_maxval') + }).addClass('yaxislabel top').attr("id", 'linetrack_' + track.dataset.id + '_maxval') .prependTo(track.container_div); }); }, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add more granular lists of writable repositories for the current user: repositories with missing tool test components, repositories with failing tool tests and repositories with no failing tool tests.
by commits-noreply＠bitbucket.org 29 Apr '13

29 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8d07c988129/ Changeset: f8d07c988129 User: greg Date: 2013-04-29 23:09:44 Summary: Add more granular lists of writable repositories for the current user: repositories with missing tool test components, repositories with failing tool tests and repositories with no failing tool tests. Affected #: 8 files diff -r 8264c77e4f07c0dee932add796f5ee7ce02245b3 -r f8d07c98812903dc98de2665874a2c31b65b84da lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -77,19 +77,19 @@ # Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app ) webapp.mapper.resource( 'repository', - 'repositories', - controller='repositories', - collection={ 'get_repository_revision_install_info' : 'GET', - 'get_ordered_installable_revisions' : 'GET' }, - name_prefix='repository_', - path_prefix='/api', - parent_resources=dict( member_name='repository', collection_name='repositories' ) ) + 'repositories', + controller='repositories', + collection={ 'get_repository_revision_install_info' : 'GET', + 'get_ordered_installable_revisions' : 'GET' }, + name_prefix='repository_', + path_prefix='/api', + parent_resources=dict( member_name='repository', collection_name='repositories' ) ) webapp.mapper.resource( 'repository_revision', - 'repository_revisions', - controller='repository_revisions', - name_prefix='repository_revision_', - path_prefix='/api', - parent_resources=dict( member_name='repository_revision', collection_name='repository_revisions' ) ) + 'repository_revisions', + controller='repository_revisions', + name_prefix='repository_revision_', + path_prefix='/api', + parent_resources=dict( member_name='repository_revision', collection_name='repository_revisions' ) ) webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Fix failing functional test for dataset features.
by commits-noreply＠bitbucket.org 28 Apr '13

28 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8264c77e4f07/ Changeset: 8264c77e4f07 User: inithello Date: 2013-04-28 17:03:41 Summary: Fix failing functional test for dataset features. Affected #: 2 files diff -r 6638dbca87d3c7dfc4e5b0522eb4a17f124b5040 -r 8264c77e4f07c0dee932add796f5ee7ce02245b3 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -255,6 +255,13 @@ def get_latest_history( self ): return self.json_from_url( '/api/histories' )[ 0 ] + + def find_hda_by_dataset_name( self, name, history=None ): + if history is None: + history = self.get_history_from_api() + for hda in history: + if hda[ 'name' ] == name: + return hda def check_history_for_errors( self ): """Raises an exception if there are errors in a history""" diff -r 6638dbca87d3c7dfc4e5b0522eb4a17f124b5040 -r 8264c77e4f07c0dee932add796f5ee7ce02245b3 test/functional/test_dataset_features.py --- a/test/functional/test_dataset_features.py +++ b/test/functional/test_dataset_features.py @@ -1,7 +1,9 @@ from base.twilltestcase import TwillTestCase import base.test_db_util as test_db_util + class TestDatasetFeatures( TwillTestCase ): + def test_0000_initiate_users( self ): """Ensuring all required user accounts exist""" self.logout() @@ -16,14 +18,18 @@ self.new_history() latest_history = test_db_util.get_latest_history_for_user( admin_user ) assert latest_history is not None, "Problem retrieving latest_history from database" + def test_0005_initiate_data( self ): '''Ensure that data exists for this test suite.''' self.upload_file( '1.bed' ) + def test_0010_view_dataset_params( self ): '''Test viewing a dataset's parameters.''' - hda = test_db_util.get_latest_hda() - self.visit_url( '/datasets/%s/show_params' % self.security.encode_id( hda.hid ) ) + hda = self.find_hda_by_dataset_name( '1.bed' ) + assert hda is not None, 'Could not retrieve latest hda from history API.' + self.visit_url( '/datasets/%s/show_params' % hda[ 'id'] ) self.check_for_strings( strings_displayed=[ '1.bed', 'uploaded' ] ) + def test_0015_report_dataset_error( self ): '''Load and submit the report error form. This should show an error message, as the functional test instance should not be configured for email.''' hda = test_db_util.get_latest_hda() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Configuration API: include and standardize error handling, complete documentation
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6638dbca87d3/ Changeset: 6638dbca87d3 User: carlfeberhard Date: 2013-04-26 21:36:33 Summary: Configuration API: include and standardize error handling, complete documentation Affected #: 1 file diff -r a0877019caa1e1f6b4407d92eaa7c44f654d27df -r 6638dbca87d3c7dfc4e5b0522eb4a17f124b5040 lib/galaxy/webapps/galaxy/api/configuration.py --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -1,5 +1,6 @@ """ -API operations allowing clients to determine Galaxy instance's capabilities. +API operations allowing clients to determine Galaxy instance's capabilities +and configuration settings. """ from galaxy import web @@ -9,6 +10,7 @@ log = logging.getLogger( __name__ ) class ConfigurationController( BaseAPIController ): + # config attributes viewable by non-admin users EXPOSED_USER_OPTIONS = [ 'enable_unique_workflow_defaults', 'ftp_upload_site', @@ -19,6 +21,7 @@ 'terms_url', 'allow_user_dataset_purge', ] + # config attributes viewable by admin users EXPOSED_ADMIN_OPTIONS = [ 'library_import_dir', 'user_library_import_dir', @@ -30,12 +33,28 @@ @web.expose_api def index( self, trans, **kwd ): """ + GET /api/configuration + Return an object containing exposable configuration settings. + + Note: a more complete list is returned if the user is an admin. """ - config = trans.app.config - options = self._get_options( config, self.EXPOSED_USER_OPTIONS ) - if trans.user_is_admin(): - options.update( self._get_options( config, self.EXPOSED_ADMIN_OPTIONS ) ) - return options + try: + config = trans.app.config + options = self._get_options( config, self.EXPOSED_USER_OPTIONS ) + if trans.user_is_admin(): + options.update( self._get_options( config, self.EXPOSED_ADMIN_OPTIONS ) ) + return options + + except Exception, exception: + log.error( 'could not get configuration: %s', str( exception ), exc_info=True ) + trans.response.status = 500 + return { 'error': str( exception ) } def _get_options( self, config, keys ): + """ + Build and return a subset of the config dictionary restricted to the + list `keys`. + + The attribute value will default to None if not available. + """ return dict( [ (key, getattr( config, key, None ) ) for key in keys ] ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Functional tests: update test_history_functions 060 to use the new json variable name in history.mako
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0877019caa1/ Changeset: a0877019caa1 User: carlfeberhard Date: 2013-04-26 21:26:33 Summary: Functional tests: update test_history_functions 060 to use the new json variable name in history.mako Affected #: 1 file diff -r 365d31607a569575ac666d142556403fe82d693a -r a0877019caa1e1f6b4407d92eaa7c44f654d27df test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py +++ b/test/functional/test_history_functions.py @@ -656,7 +656,7 @@ if hda[ 'id' ] == self.security.encode_id( hda_2_bed.id ): return ( not hda[ 'accessible' ] ) return False - self.check_history_json( r'\bhdas\s*=\s*(.*);', hda_2_bed_is_inaccessible ) + self.check_history_json( r'\bhdaJson\s*=\s*(.*);', hda_2_bed_is_inaccessible ) # Admin users can view all datasets ( using the history/view feature ), so make sure 2.bed is accessible to the admin self.logout() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: Browser tests: allow for use of test admin user, test configuration API, begin tests of user API
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/365d31607a56/ Changeset: 365d31607a56 User: carlfeberhard Date: 2013-04-26 21:17:08 Summary: Browser tests: allow for use of test admin user, test configuration API, begin tests of user API Affected #: 7 files diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -48,9 +48,17 @@ global datatypes_registry datatypes_registry = d_registry + class User( object, APIItem ): + """ + Data for a Galaxy user or admin and relations to their + histories, credentials, and roles. + """ + # attributes that will be accessed and returned when calling get_api_value( view='collection' ) api_collection_visible_keys = ( 'id', 'email' ) + # attributes that will be accessed and returned when calling get_api_value( view='element' ) api_element_visible_keys = ( 'id', 'email', 'username', 'total_disk_usage', 'nice_total_disk_usage' ) + def __init__( self, email=None, password=None ): self.email = email self.password = password @@ -61,45 +69,78 @@ # Relationships self.histories = [] self.credentials = [] + #? self.roles = [] def set_password_cleartext( self, cleartext ): - """Set 'self.password' to the digest of 'cleartext'.""" + """ + Set user password to the digest of `cleartext`. + """ self.password = new_secure_hash( text_type=cleartext ) + def check_password( self, cleartext ): - """Check if 'cleartext' matches 'self.password' when hashed.""" + """ + Check if `cleartext` matches user password when hashed. + """ return self.password == new_secure_hash( text_type=cleartext ) + def all_roles( self ): + """ + Return a unique list of Roles associated with this user or any of their groups. + """ roles = [ ura.role for ura in self.roles ] for group in [ uga.group for uga in self.groups ]: for role in [ gra.role for gra in group.roles ]: if role not in roles: roles.append( role ) return roles + def get_disk_usage( self, nice_size=False ): + """ + Return byte count of disk space used by user or a human-readable + string if `nice_size` is `True`. + """ rval = 0 if self.disk_usage is not None: rval = self.disk_usage if nice_size: rval = galaxy.datatypes.data.nice_size( rval ) return rval + def set_disk_usage( self, bytes ): + """ + Manually set the disk space used by a user to `bytes`. + """ self.disk_usage = bytes + total_disk_usage = property( get_disk_usage, set_disk_usage ) + @property def nice_total_disk_usage( self ): + """ + Return byte count of disk space used in a human-readable string. + """ return self.get_disk_usage( nice_size=True ) + def calculate_disk_usage( self ): + """ + Return byte count total of disk space used by all non-purged, non-library + HDAs in non-purged histories. + """ + # maintain a list so that we don't double count dataset_ids = [] total = 0 # this can be a huge number and can run out of memory, so we avoid the mappers db_session = object_session( self ) for history in db_session.query( History ).enable_eagerloads( False ).filter_by( user_id=self.id, purged=False ).yield_per( 1000 ): for hda in db_session.query( HistoryDatasetAssociation ).enable_eagerloads( False ).filter_by( history_id=history.id, purged=False ).yield_per( 1000 ): + #TODO: def hda.counts_toward_disk_usage(): + # return ( not self.dataset.purged and not self.dataset.library_associations ) if not hda.dataset.id in dataset_ids and not hda.dataset.purged and not hda.dataset.library_associations: dataset_ids.append( hda.dataset.id ) total += hda.dataset.get_total_size() return total + class Job( object ): """ A job represents a request to run a tool given input datasets, tool diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a lib/galaxy/webapps/galaxy/api/configuration.py --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -2,30 +2,29 @@ API operations allowing clients to determine Galaxy instance's capabilities. """ -import logging from galaxy import web from galaxy.web.base.controller import BaseAPIController +import logging log = logging.getLogger( __name__ ) - class ConfigurationController( BaseAPIController ): EXPOSED_USER_OPTIONS = [ - 'enable_unique_workflow_defaults', - 'ftp_upload_site', - 'ftp_upload_dir', - 'wiki_url', - 'support_url', - 'logo_url', - 'terms_url', - 'allow_user_dataset_purge', + 'enable_unique_workflow_defaults', + 'ftp_upload_site', + 'ftp_upload_dir', + 'wiki_url', + 'support_url', + 'logo_url', + 'terms_url', + 'allow_user_dataset_purge', ] EXPOSED_ADMIN_OPTIONS = [ - 'library_import_dir', - 'user_library_import_dir', - 'allow_library_path_paste', - 'allow_user_creation', - 'allow_user_deletion', + 'library_import_dir', + 'user_library_import_dir', + 'allow_library_path_paste', + 'allow_user_creation', + 'allow_user_deletion', ] @web.expose_api diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a test/casperjs/api-configuration-tests.js --- /dev/null +++ b/test/casperjs/api-configuration-tests.js @@ -0,0 +1,121 @@ +/* Utility to load a specific page and output html, page text, or a screenshot + * Optionally wait for some time, text, or dom selector + */ +try { + //...if there's a better way - please let me know, universe + var scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} +spaceghost.start(); + +// =================================================================== SET UP +var utils = require( 'utils' ); + +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} +spaceghost.user.loginOrRegisterUser( email, password ); + +function hasKeys( object, keysArray ){ + if( !utils.isObject( object ) ){ return false; } + for( var i=0; i<keysArray.length; i += 1 ){ + if( !object.hasOwnProperty( keysArray[i] ) ){ + spaceghost.debug( 'key not found: ' + keysArray[i] ); + return false; + } + } + return true; +} + +function compareObjs( obj1, where ){ + for( var key in where ){ + if( where.hasOwnProperty( key ) ){ + if( !obj1.hasOwnProperty( key ) ){ return false; } + if( obj1[ key ] !== where[ key ] ){ return false; } + } + } + return true; +} + +function findObject( objectArray, where, start ){ + start = start || 0; + for( var i=start; i<objectArray.length; i += 1 ){ + if( compareObjs( objectArray[i], where ) ){ return objectArray[i]; } + } + return null; +} + +// =================================================================== TESTS +var normKeys = [ + 'enable_unique_workflow_defaults', + 'ftp_upload_site', + 'ftp_upload_dir', + 'wiki_url', + 'support_url', + 'logo_url', + 'terms_url', + 'allow_user_dataset_purge' + ], + adminKeys = normKeys.concat([ + 'library_import_dir', + 'user_library_import_dir', + 'allow_library_path_paste', + 'allow_user_creation', + 'allow_user_deletion' + ]); + + +// ------------------------------------------------------------------------------------------- INDEX +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + + this.test.comment( 'index should get a (shortened) list of configuration settings ' + + 'when requested by a normal user' ); + var configIndex = this.api.configuration.index(); + this.debug( this.jsonStr( configIndex ) ); + this.test.assert( utils.isObject( configIndex ), "index returned an object" ); + this.test.assert( hasKeys( configIndex, normKeys ), 'Has the proper keys' ); + +}); +spaceghost.user.logout(); + +// ------------------------------------------------------------------------------------------- INDEX (admin) +spaceghost.tryStepsCatch( function tryAdminLogin(){ + spaceghost.user.loginAdmin(); +}); + +//}, function failedLoginRegister(){ +// this.info( 'Admin level configuration API tests not run: no admin account available' ); +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + + if( spaceghost.user.userIsAdmin() ){ + this.test.comment( 'index should get a (full) list of configuration settings ' + + 'when requested by an admin user' ); + configIndex = this.api.configuration.index(); + this.debug( this.jsonStr( configIndex ) ); + this.test.assert( utils.isObject( configIndex ), "index returned an object" ); + this.test.assert( hasKeys( configIndex, adminKeys ), 'Has the proper keys' ); + + } else { + this.info( 'Admin level configuration API tests not run: no admin account available' ); + } +}); + +// =================================================================== +spaceghost.run( function(){ +}); diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a test/casperjs/api-user-tests.js --- /dev/null +++ b/test/casperjs/api-user-tests.js @@ -0,0 +1,105 @@ +/* Utility to load a specific page and output html, page text, or a screenshot + * Optionally wait for some time, text, or dom selector + */ +try { + //...if there's a better way - please let me know, universe + var scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} +spaceghost.start(); + +// =================================================================== SET UP +var utils = require( 'utils' ); + +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} +spaceghost.user.loginOrRegisterUser( email, password ); + +function hasKeys( object, keysArray ){ + if( !utils.isObject( object ) ){ return false; } + for( var i=0; i<keysArray.length; i += 1 ){ + if( !object.hasOwnProperty( keysArray[i] ) ){ + spaceghost.debug( 'key not found: ' + keysArray[i] ); + return false; + } + } + return true; +} + +function compareObjs( obj1, where ){ + for( var key in where ){ + if( where.hasOwnProperty( key ) ){ + if( !obj1.hasOwnProperty( key ) ){ return false; } + if( obj1[ key ] !== where[ key ] ){ return false; } + } + } + return true; +} + +function findObject( objectArray, where, start ){ + start = start || 0; + for( var i=start; i<objectArray.length; i += 1 ){ + if( compareObjs( objectArray[i], where ) ){ return objectArray[i]; } + } + return null; +} + +// =================================================================== TESTS +var workflowSummaryKeys = [ + 'id', 'model_class', 'name', 'published', 'tags', 'url' + ], + workflowDetailKeys = workflowSummaryKeys.concat([ + 'inputs', 'steps' + ]); + + +spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ + + // ------------------------------------------------------------------------------------------- INDEX + this.test.comment( 'index should get a list of users' ); + var userIndex = this.api.users.index(); + this.debug( this.jsonStr( userIndex ) ); + this.test.assert( utils.isArray( userIndex ), "index returned an array: length " + userIndex.length ); + + // need a way to import/create a user here for testing + if( userIndex.length <= 0 ){ + log.warn( 'No users available' ); + return; + } + this.test.assert( userIndex.length >= 1, 'Has at least one user' ); + + //TODO: index( deleted ) + + // ------------------------------------------------------------------------------------------- SHOW + this.test.comment( 'show should get detailed data about the user with the given id' ); + var userShow = this.api.users.show( userIndex[0].id ); + this.debug( this.jsonStr( userShow ) ); + + //TODO: show( current ) + //TODO: show( deleted ) + + // ------------------------------------------------------------------------------------------- CREATE + + // ------------------------------------------------------------------------------------------- MISC +}); + +// =================================================================== +spaceghost.run( function(){ +}); diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a test/casperjs/modules/api.js --- a/test/casperjs/modules/api.js +++ b/test/casperjs/modules/api.js @@ -18,10 +18,12 @@ this.encodedIdExpectedLength = 16; this.jQueryLocation = '../../static/scripts/libs/jquery/jquery.js'; + this.configuration = new ConfigurationAPI( this ); this.histories = new HistoriesAPI( this ); this.hdas = new HDAAPI( this ); this.tools = new ToolsAPI( this ); this.workflows = new WorkflowsAPI( this ); + this.users = new UsersAPI( this ); }; exports.API = API; @@ -121,6 +123,28 @@ }; +// =================================================================== CONFIGURATION +var ConfigurationAPI = function ConfigurationAPI( api ){ + this.api = api; +}; +ConfigurationAPI.prototype.toString = function toString(){ + return this.api + '.ConfigurationAPI'; +}; + +// ------------------------------------------------------------------- +ConfigurationAPI.prototype.urlTpls = { + index : 'api/configuration' +}; + +ConfigurationAPI.prototype.index = function index( deleted ){ + this.api.spaceghost.info( 'configuration.index' ); + + return this.api._ajax( this.urlTpls.index, { + data : {} + }); +}; + + // =================================================================== HISTORIES var HistoriesAPI = function HistoriesAPI( api ){ this.api = api; @@ -140,7 +164,7 @@ }; HistoriesAPI.prototype.index = function index( deleted ){ - this.api.spaceghost.info( 'history.index: ' + (( deleted )?( 'w deleted' ):( '(wo deleted)' )) ); + this.api.spaceghost.info( 'histories.index: ' + (( deleted )?( 'w deleted' ):( '(wo deleted)' )) ); deleted = deleted || false; return this.api._ajax( this.urlTpls.index, { @@ -149,7 +173,7 @@ }; HistoriesAPI.prototype.show = function show( id, deleted ){ - this.api.spaceghost.info( 'history.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); + this.api.spaceghost.info( 'histories.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); id = ( id === 'most_recently_used' )?( id ):( this.api.ensureId( id ) ); deleted = deleted || false; @@ -159,7 +183,7 @@ }; HistoriesAPI.prototype.create = function create( payload ){ - this.api.spaceghost.info( 'history.create: ' + this.api.spaceghost.jsonStr( payload ) ); + this.api.spaceghost.info( 'histories.create: ' + this.api.spaceghost.jsonStr( payload ) ); // py.payload <-> ajax.data payload = this.api.ensureObject( payload ); @@ -170,7 +194,7 @@ }; HistoriesAPI.prototype.delete_ = function delete_( id, purge ){ - this.api.spaceghost.info( 'history.delete: ' + [ id, (( purge )?( '(purge!)' ):( '' )) ] ); + this.api.spaceghost.info( 'histories.delete: ' + [ id, (( purge )?( '(purge!)' ):( '' )) ] ); // py.payload <-> ajax.data var payload = ( purge )?({ purge: true }):({}); @@ -182,7 +206,7 @@ HistoriesAPI.prototype.undelete = function undelete( id ){ //throw ( 'unimplemented' ); - this.api.spaceghost.info( 'history.undelete: ' + id ); + this.api.spaceghost.info( 'histories.undelete: ' + id ); return this.api._ajax( utils.format( this.urlTpls.undelete, this.api.ensureId( id ) ), { type : 'POST' @@ -190,7 +214,7 @@ }; HistoriesAPI.prototype.update = function create( id, payload ){ - this.api.spaceghost.info( 'history.update: ' + id + ',' + this.api.spaceghost.jsonStr( payload ) ); + this.api.spaceghost.info( 'histories.update: ' + id + ',' + this.api.spaceghost.jsonStr( payload ) ); // py.payload <-> ajax.data id = this.api.ensureId( id ); @@ -269,6 +293,7 @@ }); }; + // =================================================================== TOOLS var ToolsAPI = function HDAAPI( api ){ this.api = api; @@ -319,6 +344,7 @@ // }); //}; + // =================================================================== WORKFLOWS var WorkflowsAPI = function WorkflowsAPI( api ){ this.api = api; @@ -394,3 +420,88 @@ }); }; + +// =================================================================== USERS +var UsersAPI = function UsersAPI( api ){ + this.api = api; +}; +UsersAPI.prototype.toString = function toString(){ + return this.api + '.UsersAPI'; +}; + +// ------------------------------------------------------------------- +//NOTE: lots of admin only functionality in this section +UsersAPI.prototype.urlTpls = { + index : 'api/users', + show : 'api/users/%s', + create : 'api/users', + delete_ : 'api/users/%s', + undelete: 'api/users/deleted/%s/undelete', + update : 'api/users/%s' +}; + +UsersAPI.prototype.index = function index( deleted ){ + this.api.spaceghost.info( 'users.index: ' + (( deleted )?( 'w deleted' ):( '(wo deleted)' )) ); + + deleted = deleted || false; + return this.api._ajax( this.urlTpls.index, { + data : { deleted: deleted } + }); +}; + +UsersAPI.prototype.show = function show( id, deleted ){ + this.api.spaceghost.info( 'users.show: ' + [ id, (( deleted )?( 'w deleted' ):( '' )) ] ); + + id = ( id === 'current' )?( id ):( this.api.ensureId( id ) ); + deleted = deleted || false; + return this.api._ajax( utils.format( this.urlTpls.show, id ), { + data : { deleted: deleted } + }); +}; + +UsersAPI.prototype.create = function create( payload ){ + this.api.spaceghost.info( 'users.create: ' + this.api.spaceghost.jsonStr( payload ) ); + + // py.payload <-> ajax.data + payload = this.api.ensureObject( payload ); + return this.api._ajax( utils.format( this.urlTpls.create ), { + type : 'POST', + data : payload + }); +}; + +UsersAPI.prototype.delete_ = function delete_( id, purge ){ + this.api.spaceghost.info( 'users.delete: ' + [ id, (( purge )?( '(purge!)' ):( '' )) ] ); + + // py.payload <-> ajax.data + var payload = ( purge )?({ purge: true }):({}); + return this.api._ajax( utils.format( this.urlTpls.delete_, this.api.ensureId( id ) ), { + type : 'DELETE', + data : payload + }); +}; + +UsersAPI.prototype.undelete = function undelete( id ){ + //throw ( 'unimplemented' ); + this.api.spaceghost.info( 'users.undelete: ' + id ); + + return this.api._ajax( utils.format( this.urlTpls.undelete, this.api.ensureId( id ) ), { + type : 'POST' + }); +}; + +UsersAPI.prototype.update = function create( id, payload ){ + this.api.spaceghost.info( 'users.update: ' + id + ',' + this.api.spaceghost.jsonStr( payload ) ); + + // py.payload <-> ajax.data + id = this.api.ensureId( id ); + payload = this.api.ensureObject( payload ); + url = utils.format( this.urlTpls.update, id ); + + return this.api._ajax( url, { + type : 'PUT', + data : payload + }); +}; + + diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -134,7 +134,7 @@ this._submitLogin( email, password ); spaceghost.withMainPanel( function mainAfterLogin(){ - if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) != -1 ){ + if( spaceghost.getCurrentUrl().search( spaceghost.data.selectors.loginPage.url_regex ) !== -1 ){ var messageInfo = spaceghost.getElementInfo( spaceghost.data.selectors.messages.all ); if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ this.warning( 'Login failed: ' + messageInfo.text ); @@ -171,6 +171,7 @@ User.prototype.logout = function logout(){ var spaceghost = this.spaceghost; spaceghost.thenOpen( spaceghost.baseUrl, function(){ + this.info( 'user logging out' ); //TODO: handle already logged out spaceghost.clickLabel( spaceghost.data.labels.masthead.menus.user ); spaceghost.clickLabel( spaceghost.data.labels.masthead.userMenu.logout ); @@ -196,6 +197,63 @@ return spaceghost; }; +// ------------------------------------------------------------------- Admin +/** Gets the admin user data from spaceghost if set and checks the universe_wsgi.ini file for the email. + * @returns {Object|null} the admin data object (email, pasword, username) + * or null if no admin is set in both the universe_wsgi.ini and spaceghost. + */ +User.prototype.getAdminData = function getAdminData(){ + //TODO: this might be better inside sg + // check for the setting in sg and the universe_wsgi.ini file + var adminData = this.spaceghost.options.adminUser, + iniAdminEmails = this.spaceghost.getUniverseSetting( 'admin_users' ); + iniAdminEmails = ( iniAdminEmails )?( iniAdminEmails.split( ',' ) ):( null ); + + //TODO: seems like we only need the wsgi setting - that's the only thing we can't change + if( adminData ){ + if( iniAdminEmails.indexOf( adminData.email ) !== -1 ){ return adminData; } + + // if not set in options, but there are entries in the ini and a default admin pass: + // return the first email with the default pass + // Hopefully this is no less secure than the user/pwd in twilltestcase + } else if( iniAdminEmails.length && this.spaceghost.options.adminPassword ){ + return { email: iniAdminEmails[0], password: this.spaceghost.options.adminPassword }; + } + + return null; +}; + +/** Logs in the admin user (if available) as the current user. + * Note: logs out any other current users. + * @throws {GalaxyError} err if specified user is not admin or no admin found + * @returns {SpaceGhost} the spaceghost instance (for chaining) + */ +User.prototype.loginAdmin = function loginAdmin(){ + this.spaceghost.then( function(){ + var adminData = this.user.getAdminData(); + if( !adminData ){ + throw new this.GalaxyError( 'No admin users found' ); + } + this.info( 'logging in administrator' ); + return this.user.loginOrRegisterUser( adminData.email, adminData.password ); + }); +}; + +/** Is the currently logged in user an admin? + * @returns {Boolean} true if the currently logged in user is admin, false if not. + */ +User.prototype.userIsAdmin = function userIsAdmin(){ + // simple test of whether the Admin tab is displayed in the masthead + return this.spaceghost.jumpToTop( function(){ + if( this.visible( this.data.selectors.masthead.adminLink ) ){ + return true; + } + return false; + }); +}; + + +// ------------------------------------------------------------------- Utility /** Gets a psuedo-random (unique?) email based on the time stamp. * Helpful for testing registration. * @param {String} username email user (defaults to 'test') @@ -207,3 +265,4 @@ domain = domain || 'test.test'; return username + Date.now() + '@' + domain; }; + diff -r 98cd1bcb36f129e8fed213687deccd7701ab047a -r 365d31607a569575ac666d142556403fe82d693a test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -47,7 +47,17 @@ } utils.inherits( SpaceGhost, Casper ); -//console.debug( 'CasperError:' + CasperError ); +/** String representation + * @returns {String} + */ +SpaceGhost.prototype.toString = function(){ + var currentUrl = ''; + try { + currentUrl = this.getCurrentUrl(); + } catch( err ){} + return 'SpaceGhost(' + currentUrl + ')'; +}; + // ------------------------------------------------------------------- included libs //??: can we require underscore, etc. from the ../../static/scripts/lib? @@ -157,9 +167,14 @@ //htmlOnError : { defaultsTo: false, flag: 'error-html', help: 'output page html on a page error' } //htmlOnFail : { defaultsTo: false, flag: 'fail-html', help: 'output page html on a test failure' }, //screenOnFail : { defaultsTo: false, flag: 'fail-screen', help: 'capture a screenshot on a test failure' } - logNamespace : { defaultsTo: false, flag: 'log-namespace', help: 'filter log messages to this namespace' } + logNamespace : { defaultsTo: false, flag: 'log-namespace', help: 'filter log messages to this namespace' }, + + adminUser : { defaultsTo: null, flag: 'admin', help: 'JSON string with email and password of admin' } }; + // no switches/hardcoded options: + this.options.adminPassword = 'testuser'; + // --url parameter required (the url of the server to test with) if( !this.cli.has( 'url' ) ){ this.die( 'Test server URL is required - ' + @@ -237,6 +252,13 @@ this._setLogNamespaceFilter( this.options.logNamespace ); } + /** email and password JSON string for admin user */ + this.options.adminUser = CLI_OPTIONS.adminUser.defaultsTo; + if( this.cli.has( CLI_OPTIONS.adminUser.flag ) ){ + this.options.adminUser = JSON.parse( this.cli.get( CLI_OPTIONS.adminUser.flag ) ); + this.warning( 'Using admin user from CLI: ' + this.jsonStr( this.options.adminUser ) ); + } + }; /** Suppress the normal output from the casper object (echo, errors) @@ -1002,6 +1024,7 @@ } }; +// ------------------------------------------------------------------- debugging /** JSON formatter */ SpaceGhost.prototype.jsonStr = function( obj ){ @@ -1036,17 +1059,7 @@ return this.errors[( this.errors.length - 1 )]; }; -/** String representation - * @returns {String} - */ -SpaceGhost.prototype.toString = function(){ - var currentUrl = ''; - try { - currentUrl = this.getCurrentUrl(); - } catch( err ){} - return 'SpaceGhost(' + currentUrl + ')'; -}; - +// ------------------------------------------------------------------- file system /** Load and parse a JSON file into an object. * @param {String} filepath filepath relative to the current scriptDir * @returns {Object} the object parsed @@ -1078,6 +1091,34 @@ return fs.write( filepath, this.getHTML( selector, outer ), 'w' ); }; +/** Read and search a file for the given regex. + * @param {String} filepath filepath relative to the current scriptDir + * @param {Regex} searchFor regex to search for + * @returns {Object} search results + */ +SpaceGhost.prototype.searchFile = function searchFile( filepath, regex ){ + //precondition: filepath is relative to script dir + filepath = this.options.scriptDir + filepath; + var read = fs.read( filepath ); + return read.match( regex ); +}; + +/** Read a configuration setting from the universe_wsgi.ini file. + * @param {String} iniKey the setting key to find + * @returns {String} value from file for iniKey (or null if not found or commented out) + */ +SpaceGhost.prototype.getUniverseSetting = function getUniverseSetting( iniKey ){ + var iniFilepath = '../../universe_wsgi.ini', + regex = new RegExp( '^([#]*)\\\s*' + iniKey + '\\\s*=\\\s*(.*)$', 'm' ), + match = this.searchFile( iniFilepath, regex ); + this.debug( 'regex: ' + regex ); + // if nothing found or found and first group (the ini comment char) is not empty + if( match === null || match[1] || !match[2] ){ + return null; + } + return match[2]; +}; + // =================================================================== TEST DATA /** General use selectors, labels, and text. Kept here to allow a centralized location. @@ -1105,6 +1146,7 @@ }, masthead : { + adminLink : '#masthead a[href="/admin"]', userMenu : { userEmail : 'a #user-email', userEmail_xpath : '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: More compatibility with main tool shed.
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/98cd1bcb36f1/ Changeset: 98cd1bcb36f1 User: inithello Date: 2013-04-26 21:01:21 Summary: More compatibility with main tool shed. Affected #: 1 file diff -r b16126d45099c38563e4372b4a7f781d30e44bde -r 98cd1bcb36f129e8fed213687deccd7701ab047a test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -269,9 +269,11 @@ api_path = [ 'api', 'repository_revisions', metadata_revision_id ] api_url = get_api_url( base=tool_shed_url, parts=api_path ) repository_metadata = json_from_url( api_url ) - if repository_metadata[ 'tool_test_results' ] is None: - return {} - return repository_metadata[ 'tool_test_results' ] + tool_test_results = repository_metadata.get( 'tool_test_results', {} ) + # Compatibility code, remove before next release. + if not tool_test_results: + tool_test_results = repository_metadata.get( 'tool_test_errors', {} ) + return tool_test_results def json_from_url( url ): url_handle = urllib.urlopen( url ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Remove stderr from passed test display.
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b16126d45099/ Changeset: b16126d45099 User: inithello Date: 2013-04-26 17:22:27 Summary: Remove stderr from passed test display. Affected #: 2 files diff -r 4de773e06e148df80d85783b04408307ba277f00 -r b16126d45099c38563e4372b4a7f781d30e44bde lib/galaxy/webapps/tool_shed/util/container_util.py --- a/lib/galaxy/webapps/tool_shed/util/container_util.py +++ b/lib/galaxy/webapps/tool_shed/util/container_util.py @@ -160,9 +160,8 @@ class PassedTest( object ): """Passed tool tests object""" - def __init__( self, id=None, stderr=None, test_id=None, tool_id=None, tool_version=None ): + def __init__( self, id=None, test_id=None, tool_id=None, tool_version=None ): self.id = id - self.stderr = stderr self.test_id = test_id self.tool_id = tool_id self.tool_version = tool_version @@ -1027,7 +1026,6 @@ for passed_tests_dict in passed_tests_dicts: passed_test_id += 1 passed_test = PassedTest( id=passed_test_id, - stderr=passed_tests_dict.get( 'stderr', '' ), test_id=passed_tests_dict.get( 'test_id' '' ), tool_id=passed_tests_dict.get( 'tool_id', '' ), tool_version=passed_tests_dict.get( 'tool_version', '' ) ) diff -r 4de773e06e148df80d85783b04408307ba277f00 -r b16126d45099c38563e4372b4a7f781d30e44bde templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -618,7 +618,6 @@ <tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${passed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${passed_test.test_id | h}</td></tr> - <tr><td><b>Stderr:</b><br/>${passed_test.stderr | h}</td></tr></table></td></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Update rss feed per changes in tool test results dict.
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4de773e06e14/ Changeset: 4de773e06e14 User: inithello Date: 2013-04-26 17:16:16 Summary: Update rss feed per changes in tool test results dict. Affected #: 1 file diff -r 3c9b47aca3a5d25f23fcccfbc8e42d897dd39743 -r 4de773e06e148df80d85783b04408307ba277f00 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1122,10 +1122,11 @@ # Generate a citable URL for this repository with owner and changeset revision. repository_citable_url = suc.url_join( tool_shed_url, 'view', user.username, repository.name, metadata_row.changeset_revision ) title = 'Functional test results for changeset revision %s of %s' % ( metadata_row.changeset_revision, repository.name ) - tests_passed = len( metadata_row.tool_test_results.get( 'tests_passed', [] ) ) - tests_failed = len( metadata_row.tool_test_results.get( 'test_errors', [] ) ) - invalid_tests = len( metadata_row.tool_test_results.get( 'invalid_tests', [] ) ) - description = '%d tests passed, %d tests failed, %d tests determined to be invalid.' % ( tests_passed, tests_failed, invalid_tests ) + passed_tests = len( metadata_row.tool_test_results.get( 'passed_tests', [] ) ) + failed_tests = len( metadata_row.tool_test_results.get( 'failed_tests', [] ) ) + missing_test_components = len( metadata_row.tool_test_results.get( 'missing_test_components', [] ) ) + description = '%d tests passed, %d tests failed, %d tests missing test components.' % \ + ( passed_tests, failed_tests, missing_test_components ) # The guid attribute in an RSS feed's list of items allows a feed reader to choose not to show an item as updated # if the guid is unchanged. For functional test results, the citable URL is sufficiently unique to enable # that behavior. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Fix workflow display in tool shed.
by commits-noreply＠bitbucket.org 26 Apr '13

26 Apr '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3c9b47aca3a5/ Changeset: 3c9b47aca3a5 User: inithello Date: 2013-04-26 17:05:05 Summary: Fix workflow display in tool shed. Affected #: 1 file diff -r 01b7b48cc823a64f9ea9d35c144e9ac12b0d205b -r 3c9b47aca3a5d25f23fcccfbc8e42d897dd39743 templates/webapps/tool_shed/repository/view_workflow.mako --- a/templates/webapps/tool_shed/repository/view_workflow.mako +++ b/templates/webapps/tool_shed/repository/view_workflow.mako @@ -35,7 +35,7 @@ <%inherit file="${inherit(context)}"/><%def name="render_workflow( workflow_name, repository_metadata_id )"> - <% center_url = h.url_for( controller='repository', action='generate_workflow_image', workflow_name=tool_shed_encode( workflow_name ), repository_metadata_id=repository_metadata_id, repository_id=None ) %> + <% center_url = h.url_for( controller='repository', action='generate_workflow_image', workflow_name=tool_shed_encode( workflow_name ), repository_metadata_id=repository_metadata_id ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0