galaxy-dev October 2009

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[hg] galaxy 2815: Only allow 'uload files' option when replacing...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/80d4b33c85ca changeset: 2815:80d4b33c85ca user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Oct 01 15:07:22 2009 -0400 description: Only allow 'uload files' option when replacing a dataset with a new version, more code merging, a few bugs fixes and additional functional tests for libraries. 11 file(s) affected in this change: lib/galaxy/web/controllers/library.py lib/galaxy/web/controllers/library_admin.py lib/galaxy/web/controllers/library_common.py templates/admin/library/browse_library.mako templates/admin/library/ldda_info.mako templates/admin/library/upload.mako templates/library/browse_library.mako templates/library/ldda_info.mako templates/library/upload.mako test/base/twilltestcase.py test/functional/test_security_and_libraries.py diffs (673 lines): diff -r b45a5a51c7d1 -r 80d4b33c85ca lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Thu Oct 01 14:01:53 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Thu Oct 01 15:07:22 2009 -0400 @@ -568,64 +568,31 @@ msg=util.sanitize_text( msg ), messagetype='error' ) ) lddas.append( ldda ) - if params.get( 'update_roles_button', False ): - if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \ - trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ): - permissions = {} - for k, v in trans.app.model.Dataset.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - for ldda in lddas: - # Set the DATASET permissions on the Dataset - trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) - ldda.dataset.refresh() - permissions = {} - for k, v in trans.app.model.Library.permitted_actions.items(): - in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] - permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles - for ldda in lddas: - # Set the LIBRARY permissions on the LibraryDataset - # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions - trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) - ldda.library_dataset.refresh() - # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation - trans.app.security_agent.set_all_library_permissions( ldda, permissions ) - ldda.refresh() - msg = 'Permissions and roles have been updated on %d datasets' % len( lddas ) - messagetype = 'done' - else: - msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name - messagetype = 'error' - return trans.fill_template( "/library/ldda_permissions.mako", - ldda=lddas, - library_id=library_id, - msg=msg, - messagetype=messagetype ) + if params.get( 'update_roles_button', False ): if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \ trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ): - # Ensure that the permissions across all library items are identical, otherwise we can't update them together. - check_list = [] + permissions = {} + for k, v in trans.app.model.Dataset.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( params.get( k + '_in', [] ) ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles for ldda in lddas: - permissions = [] - # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation - # will always be the same as the permissions on the associated LibraryDataset, so we only need to - # check one Library object - for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ): - if library_permission.action not in permissions: - permissions.append( library_permission.action ) - for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ): - if dataset_permission.action not in permissions: - permissions.append( dataset_permission.action ) - permissions.sort() - if not check_list: - check_list = permissions - if permissions != check_list: - msg = 'The datasets you selected do not have identical permissions, so they can not be updated together' - trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - obj_id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) + # Set the DATASET permissions on the Dataset + trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, permissions ) + ldda.dataset.refresh() + permissions = {} + for k, v in trans.app.model.Library.permitted_actions.items(): + in_roles = [ trans.app.model.Role.get( x ) for x in util.listify( kwd.get( k + '_in', [] ) ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + for ldda in lddas: + # Set the LIBRARY permissions on the LibraryDataset + # NOTE: the LibraryDataset and LibraryDatasetDatasetAssociation will be set with the same permissions + trans.app.security_agent.set_all_library_permissions( ldda.library_dataset, permissions ) + ldda.library_dataset.refresh() + # Set the LIBRARY permissions on the LibraryDatasetDatasetAssociation + trans.app.security_agent.set_all_library_permissions( ldda, permissions ) + ldda.refresh() + msg = 'Permissions and roles have been updated on %d datasets' % len( lddas ) + messagetype = 'done' else: msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name messagetype = 'error' @@ -634,6 +601,39 @@ library_id=library_id, msg=msg, messagetype=messagetype ) + if trans.app.security_agent.can_manage_library_item( user, roles, ldda ) and \ + trans.app.security_agent.can_manage_dataset( roles, ldda.dataset ): + # Ensure that the permissions across all library items are identical, otherwise we can't update them together. + check_list = [] + for ldda in lddas: + permissions = [] + # Check the library level permissions - the permissions on the LibraryDatasetDatasetAssociation + # will always be the same as the permissions on the associated LibraryDataset, so we only need to + # check one Library object + for library_permission in trans.app.security_agent.get_library_dataset_permissions( ldda.library_dataset ): + if library_permission.action not in permissions: + permissions.append( library_permission.action ) + for dataset_permission in trans.app.security_agent.get_dataset_permissions( ldda.dataset ): + if dataset_permission.action not in permissions: + permissions.append( dataset_permission.action ) + permissions.sort() + if not check_list: + check_list = permissions + if permissions != check_list: + msg = 'The datasets you selected do not have identical permissions, so they can not be updated together' + trans.response.send_redirect( web.url_for( controller='library', + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + else: + msg = "You are not authorized to change the permissions of dataset '%s'" % ldda.name + messagetype = 'error' + return trans.fill_template( "/library/ldda_permissions.mako", + ldda=lddas, + library_id=library_id, + msg=msg, + messagetype=messagetype ) @web.expose def upload_library_dataset( self, trans, library_id, folder_id, **kwd ): params = util.Params( kwd ) @@ -652,8 +652,11 @@ replace_dataset = trans.app.model.LibraryDataset.get( params.get( 'replace_id', None ) ) if not last_used_build: last_used_build = replace_dataset.library_dataset_dataset_association.dbkey + # Don't allow multiple datasets to be uploaded when replacing a dataset with a new version + upload_option = 'upload_file' else: replace_dataset = None + upload_option = params.get( 'upload_option', 'upload_file' ) user, roles = trans.get_user_and_roles() if trans.app.security_agent.can_add_library_item( user, roles, folder ) or \ ( replace_dataset and trans.app.security_agent.can_modify_library_item( user, roles, replace_dataset ) ): @@ -666,15 +669,14 @@ else: template_id = 'None' widgets = [] - upload_option = params.get( 'upload_option', 'upload_file' ) created_outputs = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans, - controller='library', - library_id=library_id, - folder_id=folder_id, - template_id=template_id, - widgets=widgets, - replace_dataset=replace_dataset, - **kwd ) + controller='library', + library_id=library_id, + folder_id=folder_id, + template_id=template_id, + widgets=widgets, + replace_dataset=replace_dataset, + **kwd ) if created_outputs: ldda_id_list = [ str( v.id ) for v in created_outputs.values() ] total_added = len( created_outputs.values() ) @@ -860,35 +862,6 @@ msg=msg, messagetype=messagetype ) @web.expose - def download_dataset_from_folder(self, trans, obj_id, library_id=None, **kwd): - """Catches the dataset id and displays file contents as directed""" - # id must refer to a LibraryDatasetDatasetAssociation object - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id ) - if not ldda.dataset: - msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( obj_id ) - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - obj_id=library_id, - msg=msg, - messagetype='error' ) ) - mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) - trans.response.set_content_type( mime ) - fStat = os.stat( ldda.file_name ) - trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = ldda.name - fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( obj_id ), fname ) - try: - return open( ldda.file_name ) - except: - msg = 'This dataset contains no content' - return trans.response.send_redirect( web.url_for( controller='library', - action='browse_library', - obj_id=library_id, - msg=msg, - messagetype='error' ) ) - @web.expose def datasets( self, trans, library_id, ldda_ids='', **kwd ): # This method is used by the select list labeled "Perform action on selected datasets" # on the analysis library browser. diff -r b45a5a51c7d1 -r 80d4b33c85ca lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Thu Oct 01 14:01:53 2009 -0400 +++ b/lib/galaxy/web/controllers/library_admin.py Thu Oct 01 15:07:22 2009 -0400 @@ -673,8 +673,11 @@ replace_dataset = trans.app.model.LibraryDataset.get( int( replace_id ) ) if not last_used_build: last_used_build = replace_dataset.library_dataset_dataset_association.dbkey + # Don't allow multiple datasets to be uploaded when replacing a dataset with a new version + upload_option = 'upload_file' else: replace_dataset = None + upload_option = params.get( 'upload_option', 'upload_file' ) if params.get( 'runtool_btn', False ) or params.get( 'ajax_upload', False ): # See if we have any inherited templates, but do not inherit contents. info_association, inherited = folder.get_info_association( inherited=True ) @@ -684,15 +687,14 @@ else: template_id = 'None' widgets = [] - upload_option = params.get( 'upload_option', 'upload_file' ) created_outputs = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans, - controller='library_admin', - library_id=library_id, - folder_id=folder_id, - template_id=template_id, - widgets=widgets, - replace_dataset=replace_dataset, - **kwd ) + controller='library_admin', + library_id=library_id, + folder_id=folder_id, + template_id=template_id, + widgets=widgets, + replace_dataset=replace_dataset, + **kwd ) if created_outputs: total_added = len( created_outputs.values() ) if replace_dataset: @@ -851,36 +853,6 @@ messagetype=messagetype ) @web.expose @web.require_admin - def download_dataset_from_folder(self, trans, obj_id, library_id=None, **kwd): - """Catches the dataset id and displays file contents as directed""" - # id must refer to a LibraryDatasetDatasetAssociation object - ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id ) - if not ldda.dataset: - msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( obj_id ) - return trans.response.send_redirect( web.url_for( controller='library_admin', - action='browse_library', - obj_id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) - trans.response.set_content_type( mime ) - fStat = os.stat( ldda.file_name ) - trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) - valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' - fname = ldda.name - fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] - trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( obj_id ), fname ) - try: - return open( ldda.file_name ) - except: - msg = 'This dataset contains no content' - return trans.response.send_redirect( web.url_for( controller='library_admin', - action='browse_library', - obj_id=library_id, - msg=util.sanitize_text( msg ), - messagetype='error' ) ) - @web.expose - @web.require_admin def datasets( self, trans, library_id, **kwd ): # This method is used by the select list labeled "Perform action on selected datasets" # on the admin library browser. diff -r b45a5a51c7d1 -r 80d4b33c85ca lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Thu Oct 01 14:01:53 2009 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Thu Oct 01 15:07:22 2009 -0400 @@ -181,6 +181,35 @@ return None, err_redirect, msg return uploaded_datasets, None, None @web.expose + def download_dataset_from_folder( self, trans, cntrller, obj_id, library_id=None, **kwd ): + """Catches the dataset id and displays file contents as directed""" + # id must refer to a LibraryDatasetDatasetAssociation object + ldda = trans.app.model.LibraryDatasetDatasetAssociation.get( obj_id ) + if not ldda.dataset: + msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( obj_id ) + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() ) + trans.response.set_content_type( mime ) + fStat = os.stat( ldda.file_name ) + trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ldda.name + fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] + trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( obj_id ), fname ) + try: + return open( ldda.file_name ) + except: + msg = 'This dataset contains no content' + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_library', + obj_id=library_id, + msg=util.sanitize_text( msg ), + messagetype='error' ) ) + @web.expose def info_template( self, trans, cntrller, library_id, response_action='library', obj_id=None, folder_id=None, ldda_id=None, **kwd ): # Only adding a new templAte to a library or folder is currently allowed. Editing an existing template is # a future enhancement. The response_action param is the name of the method to which this method will redirect diff -r b45a5a51c7d1 -r 80d4b33c85ca templates/admin/library/browse_library.mako --- a/templates/admin/library/browse_library.mako Thu Oct 01 14:01:53 2009 -0400 +++ b/templates/admin/library/browse_library.mako Thu Oct 01 15:07:22 2009 -0400 @@ -137,7 +137,7 @@ <a class="action-button" href="${h.url_for( controller='library_admin', action='ldda_manage_permissions', library_id=library.id, folder_id=folder.id, obj_id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> %if ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', obj_id=ldda.id, library_id=library.id )}">Download this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', cntrller='library_admin', obj_id=ldda.id, library_id=library.id )}">Download this dataset</a> %endif <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a> </div> diff -r b45a5a51c7d1 -r 80d4b33c85ca templates/admin/library/ldda_info.mako --- a/templates/admin/library/ldda_info.mako Thu Oct 01 14:01:53 2009 -0400 +++ b/templates/admin/library/ldda_info.mako Thu Oct 01 15:07:22 2009 -0400 @@ -47,7 +47,7 @@ <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=ldda.library_dataset.folder.id, replace_id=ldda.library_dataset.id )}">Upload a new version of this dataset</a> %endif %if ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', obj_id=ldda.id, library_id=library_id )}">Download this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', cntrller='library_admin', obj_id=ldda.id, library_id=library_id )}">Download this dataset</a> %endif %if not library.deleted and not ldda.library_dataset.folder.deleted and not ldda.library_dataset.deleted: <a class="action-button" confirm="Click OK to remove dataset '${ldda.name}'?" href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library_id, folder_id=ldda.library_dataset.folder.id, library_item_id=ldda.library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a> diff -r b45a5a51c7d1 -r 80d4b33c85ca templates/admin/library/upload.mako --- a/templates/admin/library/upload.mako Thu Oct 01 14:01:53 2009 -0400 +++ b/templates/admin/library/upload.mako Thu Oct 01 15:07:22 2009 -0400 @@ -12,17 +12,20 @@ %> <b>Create new data library datasets</b> -<a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a> -<div popupmenu="upload-librarydataset--popup"> - <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a> - %if trans.app.config.library_import_dir and os.path.exists( trans.app.config.library_import_dir ): - <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a> - %endif - %if trans.app.config.allow_library_path_paste: - <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_paths' )}">Upload files from filesystem paths</a> - %endif - <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a> -</div> +%if replace_dataset in [ None, 'None' ]: + ## Don't allow multiple datasets to be uploaded when replacing a dataset with a new version + <a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="upload-librarydataset--popup"> + <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a> + %if trans.app.config.library_import_dir and os.path.exists( trans.app.config.library_import_dir ): + <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a> + %endif + %if trans.app.config.allow_library_path_paste: + <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_paths' )}">Upload files from filesystem paths</a> + %endif + <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a> + </div> +%endif <br/><br/> <ul class="manage-table-actions"> <li> diff -r b45a5a51c7d1 -r 80d4b33c85ca templates/library/browse_library.mako --- a/templates/library/browse_library.mako Thu Oct 01 14:01:53 2009 -0400 +++ b/templates/library/browse_library.mako Thu Oct 01 15:07:22 2009 -0400 @@ -178,7 +178,7 @@ %endif %if ldda.has_data: <a class="action-button" href="${h.url_for( controller='library', action='datasets', library_id=library.id, ldda_ids=str( ldda.id ), do_action='add' )}">Import this dataset into your current history</a> - <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', obj_id=ldda.id, library_id=library.id )}">Download this dataset</a> + <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', cntrller='library', obj_id=ldda.id, library_id=library.id )}">Download this dataset</a> %endif </div> </td> diff -r b45a5a51c7d1 -r 80d4b33c85ca templates/library/ldda_info.mako --- a/templates/library/ldda_info.mako Thu Oct 01 14:01:53 2009 -0400 +++ b/templates/library/ldda_info.mako Thu Oct 01 15:07:22 2009 -0400 @@ -53,7 +53,7 @@ %endif %if ldda.has_data: <a class="action-button" href="${h.url_for( controller='library', action='datasets', library_id=library_id, ldda_ids=str( ldda.id ), do_action='add' )}">Import this dataset into your current history</a> - <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', obj_id=ldda.id, library_id=library_id )}">Download this dataset</a> + <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', cntrller='library', obj_id=ldda.id, library_id=library_id )}">Download this dataset</a> %endif </div> </div> diff -r b45a5a51c7d1 -r 80d4b33c85ca templates/library/upload.mako --- a/templates/library/upload.mako Thu Oct 01 14:01:53 2009 -0400 +++ b/templates/library/upload.mako Thu Oct 01 15:07:22 2009 -0400 @@ -12,14 +12,17 @@ %> <b>Create new data library datasets</b> -<a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a> -<div popupmenu="upload-librarydataset--popup"> - <a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a> - %if trans.app.config.user_library_import_dir and os.path.exists( os.path.join( trans.app.config.user_library_import_dir, trans.user.email ) ): - <a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a> - %endif - <a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a> -</div> +%if replace_dataset in [ None, 'None' ]: + ## Don't allow multiple datasets to be uploaded when replacing a dataset with a new version + <a id="upload-librarydataset--popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="upload-librarydataset--popup"> + <a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_file' )}">Upload files</a> + %if trans.app.config.user_library_import_dir and os.path.exists( os.path.join( trans.app.config.user_library_import_dir, trans.user.email ) ): + <a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a> + %endif + <a class="action-button" href="${h.url_for( controller='library', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a> + </div> +%endif <br/><br/> <ul class="manage-table-actions"> <li> diff -r b45a5a51c7d1 -r 80d4b33c85ca test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu Oct 01 14:01:53 2009 -0400 +++ b/test/base/twilltestcase.py Thu Oct 01 15:07:22 2009 -0400 @@ -1144,14 +1144,15 @@ tc.fv( "1", "2", description ) # form field 1 is the field named name... tc.submit( "create_library_button" ) self.home() - def set_library_permissions( self, library_id, library_name, role_id, permissions_in, permissions_out ): + def set_library_permissions( self, library_id, library_name, role_ids_str, permissions_in, permissions_out ): + # role_ids_str must be a comma-separated string of role ids url = "library_admin/library?obj_id=%s&permissions=True&update_roles_button=Save" % ( library_id ) for po in permissions_out: key = '%s_out' % po - url ="%s&%s=%s" % ( url, key, str( role_id ) ) + url ="%s&%s=%s" % ( url, key, role_ids_str ) for pi in permissions_in: key = '%s_in' % pi - url ="%s&%s=%s" % ( url, key, str( role_id ) ) + url ="%s&%s=%s" % ( url, key, role_ids_str ) self.home() self.visit_url( "%s/%s" % ( self.url, url ) ) check_str = "Permissions updated for library '%s'" % library_name @@ -1276,17 +1277,16 @@ self.check_page_for_string( check_str ) self.library_wait( library_id ) self.home() - def set_library_dataset_permissions( self, library_id, folder_id, ldda_id, ldda_name, role_id, permissions_in, permissions_out ): + def set_library_dataset_permissions( self, library_id, folder_id, ldda_id, ldda_name, role_ids_str, permissions_in, permissions_out ): + # role_ids_str must be a comma-separated string of role ids url = "library_admin/ldda_manage_permissions?library_id=%s&folder_id=%s&obj_id=%s&update_roles_button=Save" % \ ( library_id, folder_id, ldda_id ) - #role_ids = util.listify( role_ids ) - #for role_id in role_ids: for po in permissions_out: key = '%s_out' % po - url ="%s&%s=%s" % ( url, key, str( role_id ) ) + url ="%s&%s=%s" % ( url, key, role_ids_str ) for pi in permissions_in: key = '%s_in' % pi - url ="%s&%s=%s" % ( url, key, str( role_id ) ) + url ="%s&%s=%s" % ( url, key, role_ids_str ) self.home() self.visit_url( "%s/%s" % ( self.url, url ) ) check_str = "Permissions have been updated on 1 datasets" diff -r b45a5a51c7d1 -r 80d4b33c85ca test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Thu Oct 01 14:01:53 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Thu Oct 01 15:07:22 2009 -0400 @@ -176,6 +176,7 @@ actions_in = [ 'manage permissions' ] permissions_out = [ 'DATASET_ACCESS' ] actions_out = [ 'access' ] + global regular_user2_private_role regular_user2_private_role = None for role in regular_user2.all_roles(): if role.name == regular_user2.email and role.description == 'Private Role for %s' % regular_user2.email: @@ -849,9 +850,9 @@ permissions_in = [ k for k, v in galaxy.model.Dataset.permitted_actions.items() ] + \ [ k for k, v in galaxy.model.Library.permitted_actions.items() ] permissions_out = [] - role_ids = "%s,%s" % ( str( role_one.id ), str( admin_user_private_role.id ) ) + role_ids_str = '%s,%s' % ( str( role_one.id ), str( admin_user_private_role.id ) ) self.set_library_dataset_permissions( str( library_one.id ), str( folder_one.id ), str( ldda_four.id ), ldda_four.name, - role_ids, permissions_in, permissions_out ) + role_ids_str, permissions_in, permissions_out ) # admin_user should now be able to see 4.bed from the analysis view's access libraries self.home() self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_one.id ) ) ) @@ -1309,6 +1310,7 @@ def test_170_mark_group_deleted( self ): """Testing marking a group as deleted""" + # Logged in as admin_user self.home() self.visit_url( '%s/admin/groups' % self.url ) self.check_page_for_string( group_two.name ) @@ -1323,12 +1325,14 @@ raise AssertionError( '%s incorrectly lost all role associations when it was marked as deleted.' % group_two.name ) def test_175_undelete_group( self ): """Testing undeleting a deleted group""" + # Logged in as admin_user self.undelete_group( str( group_two.id ), group_two.name ) group_two.refresh() if group_two.deleted: raise AssertionError( '%s was not correctly marked as not deleted.' % group_two.name ) def test_180_mark_role_deleted( self ): """Testing marking a role as deleted""" + # Logged in as admin_user self.home() self.visit_url( '%s/admin/roles' % self.url ) self.check_page_for_string( role_two.name ) @@ -1343,9 +1347,11 @@ raise AssertionError( '%s incorrectly lost all group associations when it was marked as deleted.' % role_two.name ) def test_185_undelete_role( self ): """Testing undeleting a deleted role""" + # Logged in as admin_user self.undelete_role( str( role_two.id ), role_two.name ) def test_190_mark_dataset_deleted( self ): """Testing marking a library dataset as deleted""" + # Logged in as admin_user self.home() self.delete_library_item( str( library_one.id ), str( ldda_two.library_dataset.id ), ldda_two.name, library_item_type='library_dataset' ) self.home() @@ -1359,12 +1365,14 @@ self.home() def test_195_display_deleted_dataset( self ): """Testing displaying deleted dataset""" + # Logged in as admin_user self.home() self.visit_url( "%s/library_admin/browse_library?obj_id=%s&show_deleted=True" % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( ldda_two.name ) self.home() def test_200_hide_deleted_dataset( self ): """Testing hiding deleted dataset""" + # Logged in as admin_user self.home() self.visit_url( "%s/library_admin/browse_library?obj_id=%s&show_deleted=False" % ( self.url, str( library_one.id ) ) ) try: @@ -1375,6 +1383,7 @@ self.home() def test_205_mark_folder_deleted( self ): """Testing marking a library folder as deleted""" + # Logged in as admin_user self.home() self.delete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' ) self.home() @@ -1387,6 +1396,7 @@ self.home() def test_210_mark_folder_undeleted( self ): """Testing marking a library folder as undeleted""" + # Logged in as admin_user self.home() self.undelete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' ) self.home() @@ -1402,6 +1412,7 @@ self.home() def test_215_mark_library_deleted( self ): """Testing marking a library as deleted""" + # Logged in as admin_user self.home() # First mark folder_two as deleted to further test state saving when we undelete the library self.delete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' ) @@ -1412,6 +1423,7 @@ self.home() def test_220_mark_library_undeleted( self ): """Testing marking a library as undeleted""" + # Logged in as admin_user self.home() self.undelete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' ) self.home() @@ -1426,6 +1438,7 @@ self.home() def test_225_purge_user( self ): """Testing purging a user account""" + # Logged in as admin_user self.mark_user_deleted( user_id=self.security.encode_id( regular_user3.id ), email=regular_user3.email ) regular_user3.refresh() self.purge_user( self.security.encode_id( regular_user3.id ), regular_user3.email ) @@ -1458,6 +1471,7 @@ raise AssertionError( 'UserRoleAssociations for user %s are not related with the private role.' % regular_user3.email ) def test_230_manually_unpurge_user( self ): """Testing manually un-purging a user account""" + # Logged in as admin_user # Reset the user for later test runs. The user's private Role and DefaultUserPermissions for that role # should have been preserved, so all we need to do is reset purged and deleted. # TODO: If we decide to implement the GUI feature for un-purging a user, replace this with a method call @@ -1466,6 +1480,7 @@ regular_user3.flush() def test_235_purge_group( self ): """Testing purging a group""" + # Logged in as admin_user group_id = str( group_two.id ) self.mark_group_deleted( group_id, group_two.name ) self.purge_group( group_id, group_two.name ) @@ -1481,6 +1496,7 @@ self.undelete_group( group_id, group_two.name ) def test_240_purge_role( self ): """Testing purging a role""" + # Logged in as admin_user role_id = str( role_two.id ) self.mark_role_deleted( role_id, role_two.name ) self.purge_role( role_id, role_two.name ) @@ -1506,6 +1522,7 @@ raise AssertionError( "Purging the role did not delete the DatasetPermissionss for role_id '%s'" % role_id ) def test_245_manually_unpurge_role( self ): """Testing manually un-purging a role""" + # Logged in as admin_user # Manually unpurge, then undelete the role for later test runs # TODO: If we decide to implement the GUI feature for un-purging a role, replace this with a method call role_two.purged = False @@ -1513,6 +1530,7 @@ self.undelete_role( str( role_two.id ), role_two.name ) def test_250_purge_library( self ): """Testing purging a library""" + # Logged in as admin_user self.home() self.delete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' ) self.purge_library( str( library_one.id ), library_one.name ) @@ -1549,6 +1567,7 @@ check_folder( library_one.root_folder ) def test_255_no_library_template( self ): """Test library features when library has no template""" + # Logged in as admin_user name = "Library Two" description = "This is Library Two" # Create a library, adding no template @@ -1585,6 +1604,7 @@ self.home() def test_260_library_permissions( self ): """Test library permissions""" + # Logged in as admin_user name = "Library Three" description = "This is Library Three" # Create a library, adding no template @@ -1596,12 +1616,30 @@ galaxy.model.Library.table.c.description==description, galaxy.model.Library.table.c.deleted==False ) ).first() assert library_three is not None, 'Problem retrieving library named "%s" from the database' % name - # TODO: add tests here... - self.home() + # Set library permissions for regular_user1 and regular_user2. Each of these users will be permitted to + # LIBRARY_ADD, LIBRARY_MODIFY, LIBRARY_MANAGE for library items. + permissions_in = [ k for k, v in galaxy.model.Library.permitted_actions.items() ] + permissions_out = [] + role_ids_str = '%s,%s' % ( str( regular_user1_private_role.id ), str( regular_user2_private_role.id ) ) + self.set_library_permissions( str( library_three.id ), library_three.name, role_ids_str, permissions_in, permissions_out ) + self.logout() + # Login as regular_user1 and make sure they can see the library + self.login( email=regular_user1.email ) + self.visit_url( '%s/library/browse_libraries' % self.url ) + self.check_page_for_string( name ) + self.logout() + # Login as regular_user1 and make sure they can see the library + self.login( email=regular_user2.email ) + self.visit_url( '%s/library/browse_libraries' % self.url ) + self.check_page_for_string( name ) + # TODO: add more tests here to cover adding, modifying, managing permissions from the Librarys persoective as a regular user + self.logout() + self.login( email=admin_user.email ) self.delete_library_item( str( library_three.id ), str( library_three.id ), library_three.name, library_item_type='library' ) self.purge_library( str( library_three.id ), library_three.name ) def test_265_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" + # Logged in as admin_user ################## # Eliminate all non-private roles ##################

1 0

[hg] galaxy 2816: A couple bug fixes, additional functional test...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5024f44ab7f7 changeset: 2816:5024f44ab7f7 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Oct 02 08:55:01 2009 -0400 description: A couple bug fixes, additional functional tests for the Data Libraries features. 4 file(s) affected in this change: lib/galaxy/web/controllers/library_common.py templates/base_panels.mako test/base/twilltestcase.py test/functional/test_security_and_libraries.py diffs (269 lines): diff -r 80d4b33c85ca -r 5024f44ab7f7 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Thu Oct 01 15:07:22 2009 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Fri Oct 02 08:55:01 2009 -0400 @@ -266,7 +266,7 @@ if cntrller == 'library_admin': tmplt = '/admin/library/select_info_template.mako' else: - tmplt = '/ibrary/select_info_template.mako' + tmplt = '/library/select_info_template.mako' return trans.fill_template( tmplt, library_item_name=library_item.name, library_item_desc=library_item_desc, diff -r 80d4b33c85ca -r 5024f44ab7f7 templates/base_panels.mako --- a/templates/base_panels.mako Thu Oct 01 15:07:22 2009 -0400 +++ b/templates/base_panels.mako Fri Oct 02 08:55:01 2009 -0400 @@ -113,7 +113,7 @@ $(this).ajaxSubmit( { iframe: true } ); if ( $(this).find("input[name='folder_id']").val() != undefined ) { var library_id = $(this).find("input[name='library_id']").val(); - if ( location.pathname.indexOf( 'library_admin' ) ) { + if ( location.pathname.indexOf( 'library_admin' ) != -1 ) { $("iframe#galaxy_main").attr("src","${h.url_for( controller='library_admin', action='browse_library' )}?obj_id=" + library_id + "&created_ldda_ids=" + async_datasets); } else { $("iframe#galaxy_main").attr("src","${h.url_for( controller='library', action='browse_library' )}?obj_id=" + library_id + "&created_ldda_ids=" + async_datasets); diff -r 80d4b33c85ca -r 5024f44ab7f7 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu Oct 01 15:07:22 2009 -0400 +++ b/test/base/twilltestcase.py Fri Oct 02 08:55:01 2009 -0400 @@ -1209,12 +1209,12 @@ check_str = "Information template '%s' has been updated" % name self.check_page_for_string( check_str ) self.home() - def add_folder_info_template( self, cntrller, library_id, library_name, folder_id, folder_name, num_fields='2', + def add_folder_info_template( self, controller, cntrller, library_id, library_name, folder_id, folder_name, num_fields='2', name='Folder Template 1', ele_name_0='Fu', ele_help_0='', ele_name_1='Bar', ele_help_1='' ): """Add a new info template to a folder""" self.home() - url = "%s/library_admin/info_template?cntrller=%s&library_id=%s&response_action='folder'&create_info_template_button=Go" % \ - ( self.url, cntrller, library_id, folder_id ) + url = "%s/%s/info_template?cntrller=%s&library_id=%s&response_action='folder'&create_info_template_button=Go" % \ + ( self.url, controller, cntrller, library_id, folder_id ) self.home() self.visit_url( url ) check_str = "Create a new information template for folder '%s'" % folder_name @@ -1229,14 +1229,27 @@ tc.fv( '1', 'new_element_description_1', ele_help_1.replace( '+', ' ' ) ) tc.submit( 'new_info_template_button' ) self.home() - def add_folder( self, library_id, folder_id, name='Folder One', description='This is Folder One' ): + def add_folder( self, controller, library_id, folder_id, name='Folder One', description='This is Folder One' ): """Create a new folder""" self.home() - self.visit_url( "%s/library_admin/folder?library_id=%s&obj_id=%s&new=True" % ( self.url, library_id, folder_id ) ) + self.visit_url( "%s/%s/folder?library_id=%s&obj_id=%s&new=True" % \ + ( self.url, controller, library_id, folder_id ) ) self.check_page_for_string( 'Create a new folder' ) tc.fv( "1", "name", name ) # form field 1 is the field named name... tc.fv( "1", "description", description ) # form field 2 is the field named description... tc.submit( "new_folder_button" ) + self.home() + def edit_folder_info( self, controller, folder_id, library_id, name, new_name, description ): + """Add information to a library using an existing template with 2 elements""" + self.home() + self.visit_url( "%s/%s/folder?obj_id=%s&library_id=%s&information=True" % \ + ( self.url, controller, folder_id, library_id) ) + self.check_page_for_string( "Edit folder name and description" ) + tc.fv( '1', "name", new_name ) + tc.fv( '1', "description", description ) + tc.submit( 'rename_folder_button' ) + check_str = "Folder '%s' has been renamed to '%s'" % ( name, new_name ) + self.check_page_for_string( check_str ) self.home() def rename_folder( self, library_id, folder_id, old_name, name='Folder One Renamed', description='This is Folder One Re-described' ): """Rename a Folder""" @@ -1251,13 +1264,14 @@ check_str = "Folder '%s' has been renamed to '%s'" % ( old_name, name ) self.check_page_for_string( check_str ) self.home() - def add_library_dataset( self, filename, library_id, folder_id, folder_name, file_type='auto', - dbkey='hg18', roles=[], message='', root=False, template_field_name1='', template_field_contents1='' ): + def add_library_dataset( self, controller, filename, library_id, folder_id, folder_name, + file_type='auto', dbkey='hg18', roles=[], message='', root=False, + template_field_name1='', template_field_contents1='' ): """Add a dataset to a folder""" filename = self.get_filename( filename ) self.home() - self.visit_url( "%s/library_admin/upload_library_dataset?upload_option=upload_file&library_id=%s&folder_id=%s&message=%s" % \ - ( self.url, library_id, folder_id, message ) ) + self.visit_url( "%s/%s/upload_library_dataset?upload_option=upload_file&library_id=%s&folder_id=%s&message=%s" % \ + ( self.url, controller, library_id, folder_id, message ) ) self.check_page_for_string( 'Upload files' ) tc.fv( "1", "folder_id", folder_id ) tc.formfile( "1", "files_0|file_data", filename ) @@ -1274,7 +1288,7 @@ check_str = "Added 1 datasets to the library '%s' ( each is selected )." % folder_name else: check_str = "Added 1 datasets to the folder '%s' ( each is selected )." % folder_name - self.check_page_for_string( check_str ) + data = self.last_page() self.library_wait( library_id ) self.home() def set_library_dataset_permissions( self, library_id, folder_id, ldda_id, ldda_name, role_ids_str, permissions_in, permissions_out ): diff -r 80d4b33c85ca -r 5024f44ab7f7 test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Thu Oct 01 15:07:22 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Fri Oct 02 08:55:01 2009 -0400 @@ -540,7 +540,8 @@ message = 'Testing adding a public dataset to the root folder' # The form_one template should be inherited to the library dataset upload form. template_contents = "%s contents for root folder 1.bed" % form_one_field_label - self.add_library_dataset( '1.bed', + self.add_library_dataset( 'library_admin', + '1.bed', str( library_one.id ), str( library_one.root_folder.id ), library_one.root_folder.name, @@ -594,7 +595,11 @@ root_folder = library_one.root_folder name = "Root Folder's Folder One" description = "This is the root folder's Folder One" - self.add_folder( str( library_one.id ), str( root_folder.id ), name=name, description=description ) + self.add_folder( 'library_admin', + str( library_one.id ), + str( root_folder.id ), + name=name, + description=description ) global folder_one folder_one = galaxy.model.LibraryFolder.filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==root_folder.id, galaxy.model.LibraryFolder.table.c.name==name, @@ -626,7 +631,7 @@ """Testing adding a folder to a library folder""" name = "Folder One's Subfolder" description = "This is the Folder One's subfolder" - self.add_folder( str( library_one.id ), str( folder_one.id ), name=name, description=description ) + self.add_folder( 'library_admin', str( library_one.id ), str( folder_one.id ), name=name, description=description ) global subfolder_one subfolder_one = galaxy.model.LibraryFolder.filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==folder_one.id, galaxy.model.LibraryFolder.table.c.name==name, @@ -659,7 +664,7 @@ root_folder = library_one.root_folder name = "Folder Two" description = "This is the root folder's Folder Two" - self.add_folder( str( library_one.id ), str( root_folder.id ), name=name, description=description ) + self.add_folder( 'library_admin', str( library_one.id ), str( root_folder.id ), name=name, description=description ) global folder_two folder_two = galaxy.model.LibraryFolder.filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==root_folder.id, galaxy.model.LibraryFolder.table.c.name==name, @@ -687,7 +692,8 @@ message = "Testing adding a public dataset to the folder named %s" % folder_two.name # The form_one template should be inherited to the library dataset upload form. template_contents = "%s contents for %s 2.bed" % ( form_one_field_label, folder_two.name ) - self.add_library_dataset( '2.bed', + self.add_library_dataset( 'library_admin', + '2.bed', str( library_one.id ), str( folder_two.id ), folder_two.name, @@ -718,7 +724,8 @@ message = "Testing adding a 2nd public dataset to the folder named %s" % folder_two.name # The form_one template should be inherited to the library dataset upload form. template_contents = "%s contents for %s 3.bed" % ( form_one_field_label, folder_two.name ) - self.add_library_dataset( '3.bed', + self.add_library_dataset( 'library_admin', + '3.bed', str( library_one.id ), str( folder_two.id ), folder_two.name, @@ -760,7 +767,8 @@ message ='This is a test of the fourth dataset uploaded' # The form_one template should be inherited to the library dataset upload form. template_contents = "%s contents for %s 4.bed" % ( form_one_field_label, folder_one.name ) - self.add_library_dataset( '4.bed', + self.add_library_dataset( 'library_admin', + '4.bed', str( library_one.id ), str( folder_one.id ), folder_one.name, @@ -867,7 +875,8 @@ message = 'Testing adding a dataset with a role that is associated with a group and users' # The form_one template should be inherited to the library dataset upload form. template_contents = "%s contents for %s 5.bed" % ( form_one_field_label, folder_one.name ) - self.add_library_dataset( '5.bed', + self.add_library_dataset( 'library_admin', + '5.bed', str( library_one.id ), str( folder_one.id ), folder_one.name, @@ -1580,7 +1589,8 @@ galaxy.model.Library.table.c.deleted==False ) ).first() assert library_two is not None, 'Problem retrieving library named "%s" from the database' % name # Add a dataset to the library - self.add_library_dataset( '7.bed', + self.add_library_dataset( 'library_admin', + '7.bed', str( library_two.id ), str( library_two.root_folder.id ), library_two.root_folder.name, @@ -1628,11 +1638,57 @@ self.visit_url( '%s/library/browse_libraries' % self.url ) self.check_page_for_string( name ) self.logout() - # Login as regular_user1 and make sure they can see the library + # Login as regular_user2 and make sure they can see the library self.login( email=regular_user2.email ) self.visit_url( '%s/library/browse_libraries' % self.url ) self.check_page_for_string( name ) - # TODO: add more tests here to cover adding, modifying, managing permissions from the Librarys persoective as a regular user + # Add a dataset to the library + message = 'Testing adding 1.bed to Library Three root folder' + self.add_library_dataset( 'library', + '1.bed', + str( library_three.id ), + str( library_three.root_folder.id ), + library_three.root_folder.name, + file_type='bed', + dbkey='hg18', + message=message.replace( ' ', '+' ), + root=True ) + # Add a folder to the library + name = "Root Folder's Folder X" + description = "This is the root folder's Folder X" + self.add_folder( 'library', + str( library_three.id ), + str( library_three.root_folder.id ), + name=name, + description=description ) + folder_x = galaxy.model.LibraryFolder.filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==library_three.root_folder.id, + galaxy.model.LibraryFolder.table.c.name==name, + galaxy.model.LibraryFolder.table.c.description==description ) ).first() + # Modify the folder's information + new_name = "Root Folder's Folder Y" + new_description = "This is the root folder's Folder Y" + self.edit_folder_info( 'library', str( folder_x.id ), str( library_three.id ), name, new_name, new_description ) + folder_x.refresh() + # Add a dataset to the folder + name2 = "Folder Y subfolder" + description2 = "Folder Y subfolder description" + self.add_library_dataset( 'library', + '2.bed', + str( library_three.id ), + str( folder_x.id ), + folder_x.name, + file_type='bed', + dbkey='hg18', + message=message.replace( ' ', '+' ), + root=False ) + ldda_x = galaxy.model.LibraryDatasetDatasetAssociation.query() \ + .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() + assert ldda_x is not None, 'Problem retrieving ldda_x from the database' + # Log in as regular_user1 + self.logout() + self.login( email=regular_user1.email ) + self.visit_url( '%s/library/browse_library?obj_id=%s' % ( self.url, str( library_three.id ) ) ) + self.check_page_for_string( ldda_x.name ) self.logout() self.login( email=admin_user.email ) self.delete_library_item( str( library_three.id ), str( library_three.id ), library_three.name, library_item_type='library' ) @@ -1671,11 +1727,11 @@ # Reset DefaultHistoryPermissions for regular_user1 ##################### self.logout() - self.login( email='test1(a)bx.psu.edu' ) + self.login( email=regular_user1.email ) # Change DefaultHistoryPermissions for regular_user1 back to the default permissions_in = [ 'DATASET_MANAGE_PERMISSIONS' ] permissions_out = [ 'DATASET_ACCESS' ] role_id = str( regular_user1_private_role.id ) self.user_set_default_permissions( permissions_in=permissions_in, permissions_out=permissions_out, role_id=role_id ) self.logout() - self.login( email='test(a)bx.psu.edu' ) + self.login( email=admin_user.email )

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[hg] galaxy 2817: Fix forms and request functional test - broke ...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4fb6326ced59 changeset: 2817:4fb6326ced59 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Oct 02 09:30:50 2009 -0400 description: Fix forms and request functional test - broke with my last commit. 1 file(s) affected in this change: test/functional/test_forms_and_requests.py diffs (12 lines): diff -r 5024f44ab7f7 -r 4fb6326ced59 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Fri Oct 02 08:55:01 2009 -0400 +++ b/test/functional/test_forms_and_requests.py Fri Oct 02 09:30:50 2009 -0400 @@ -156,7 +156,7 @@ # create a folder in the library root_folder = library_one.root_folder name = "Folder One" - self.add_folder( str( library_one.id ), str( root_folder.id ), name=name, description='' ) + self.add_folder( 'library_admin', str( library_one.id ), str( root_folder.id ), name=name, description='' ) global folder_one folder_one = galaxy.model.LibraryFolder.filter( and_( galaxy.model.LibraryFolder.table.c.parent_id==root_folder.id, galaxy.model.LibraryFolder.table.c.name==name ) ).first()

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[hg] galaxy 2818: Memory debugging patch from James
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/72020a46127e changeset: 2818:72020a46127e user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Oct 02 09:36:07 2009 -0400 description: Memory debugging patch from James 4 file(s) affected in this change: eggs.ini lib/galaxy/web/buildapp.py lib/galaxy/web/framework/base.py lib/galaxy/web/framework/memdebug.py diffs (89 lines): diff -r 4fb6326ced59 -r 72020a46127e eggs.ini --- a/eggs.ini Fri Oct 02 09:30:50 2009 -0400 +++ b/eggs.ini Fri Oct 02 09:36:07 2009 -0400 @@ -23,6 +23,7 @@ python_lzo = 1.08 threadframe = 0.2 guppy = 0.1.8 +PSI = 0.3b1.1 [eggs:noplatform] amqplib = 0.6.1 @@ -86,6 +87,7 @@ Paste = http://cheeseshop.python.org/packages/source/P/Paste/Paste-1.5.1.tar.gz PasteDeploy = http://cheeseshop.python.org/packages/source/P/PasteDeploy/PasteDeploy-1.3.… PasteScript = http://cheeseshop.python.org/packages/source/P/PasteScript/PasteScript-1.3.… +PSI = http://pypi.python.org/packages/source/P/PSI/PSI-0.3b1.1.tar.gz Routes = http://pypi.python.org/packages/source/R/Routes/Routes-1.6.3.tar.gz simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.ta… SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.4.7p1.tar.… diff -r 4fb6326ced59 -r 72020a46127e lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py Fri Oct 02 09:30:50 2009 -0400 +++ b/lib/galaxy/web/buildapp.py Fri Oct 02 09:36:07 2009 -0400 @@ -64,7 +64,12 @@ sys.exit( 1 ) atexit.register( app.shutdown ) # Create the universe WSGI application - webapp = galaxy.web.framework.WebApplication( app, session_cookie='galaxysession' ) + if app.config.log_memory_usage: + from galaxy.web.framework.memdebug import MemoryLoggingWebApplication + webapp = MemoryLoggingWebApplication( app, session_cookie='galaxysession' ) + else: + webapp = galaxy.web.framework.WebApplication( app, session_cookie='galaxysession' ) + # Find controllers add_controllers( webapp, app ) # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) diff -r 4fb6326ced59 -r 72020a46127e lib/galaxy/web/framework/base.py --- a/lib/galaxy/web/framework/base.py Fri Oct 02 09:30:50 2009 -0400 +++ b/lib/galaxy/web/framework/base.py Fri Oct 02 09:36:07 2009 -0400 @@ -122,7 +122,7 @@ # Special key for AJAX debugging, remove to avoid confusing methods kwargs.pop( '_', None ) try: - body = method( trans, **kwargs ) + body = self.call_body_method( method, trans, kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs ) if not body: @@ -139,6 +139,9 @@ start_response( trans.response.wsgi_status(), trans.response.wsgi_headeritems() ) return self.make_body_iterable( trans, body ) + + def call_body_method( self, method, trans, kwargs ): + return method( trans, **kwargs ) def make_body_iterable( self, trans, body ): if isinstance( body, ( types.GeneratorType, list, tuple ) ): diff -r 4fb6326ced59 -r 72020a46127e lib/galaxy/web/framework/memdebug.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/web/framework/memdebug.py Fri Oct 02 09:36:07 2009 -0400 @@ -0,0 +1,26 @@ +""" +Implementation of WebApplication that logs memory usage before and after +calling each controller method. +""" + +import pkg_resources +pkg_resources.require( "PSI" ) +import psi.process + +import os +import logging + +from galaxy.web.framework import WebApplication + +log = logging.getLogger( __name__ ) +pid = os.getpid() + +class MemoryLoggingWebApplication( WebApplication ): + def call_body_method( self, method, trans, kwargs ): + cls = method.im_class + process = psi.process.Process( pid ) + log.debug( "before controller=%s.%s method=%s rss=%d vsz=%d", cls.__module__, cls.__name__, method.__name__, process.rss, process.vsz ) + rval = method( trans, **kwargs ) + process = psi.process.Process( pid ) + log.debug( "after controller=%s.%s method=%s rss=%d vsz=%d", cls.__module__, cls.__name__, method.__name__, process.rss, process.vsz ) + return rval \ No newline at end of file

1 0

[hg] galaxy 2813: Updated BWA and Bowtie wrapper tools so that t...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/695f28311b36 changeset: 2813:695f28311b36 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Thu Oct 01 13:16:43 2009 -0400 description: Updated BWA and Bowtie wrapper tools so that the dbkey of the output is correctly assigned 4 file(s) affected in this change: tools/sr_mapping/bowtie_wrapper.xml tools/sr_mapping/bowtie_wrapper_code.py tools/sr_mapping/bwa_wrapper.xml tools/sr_mapping/bwa_wrapper_code.py diffs (69 lines): diff -r d31ab50dc8e0 -r 695f28311b36 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Thu Oct 01 12:35:41 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Thu Oct 01 13:16:43 2009 -0400 @@ -152,7 +152,6 @@ <options from_file="bowtie_indices.loc"> <column name="value" index="1" /> <column name="name" index="0" /> - <filter type="sort_by" column="0" /> </options> </param> </when> @@ -540,4 +539,5 @@ --seed <int> Random seed. Use <int> as the seed for the pseudo-random number generator. [off] </help> + <code file="bowtie_wrapper_code.py" /> </tool> diff -r d31ab50dc8e0 -r 695f28311b36 tools/sr_mapping/bowtie_wrapper_code.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/sr_mapping/bowtie_wrapper_code.py Thu Oct 01 13:16:43 2009 -0400 @@ -0,0 +1,15 @@ +import os + +def exec_before_job(app, inp_data, out_data, param_dict, tool): + try: + refFile = param_dict['refGenomeSource']['indices'].value + dbkey = os.path.split(refFile)[1].split('.')[0] + # deal with the one odd case + if dbkey.find('chrM') >= 0: + dbkey = 'equCab2' + out_data['output'].set_dbkey(dbkey) + except: + try: + refFile = param_dict['refGenomeSource']['ownFile'].dbkey + except: + out_data['output'].set_dbkey('?') diff -r d31ab50dc8e0 -r 695f28311b36 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Thu Oct 01 12:35:41 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Thu Oct 01 13:16:43 2009 -0400 @@ -80,7 +80,6 @@ <options from_file="sequence_index_color.loc"> <column name="value" index="1" /> <column name="name" index="0" /> - <filter type="sort_by" column="0" /> </options> </param> </when> @@ -100,7 +99,6 @@ <options from_file="sequence_index_base.loc"> <column name="value" index="1" /> <column name="name" index="0" /> - <filter type="sort_by" column="0" /> </options> </param> </when> diff -r d31ab50dc8e0 -r 695f28311b36 tools/sr_mapping/bwa_wrapper_code.py --- a/tools/sr_mapping/bwa_wrapper_code.py Thu Oct 01 12:35:41 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper_code.py Thu Oct 01 13:16:43 2009 -0400 @@ -4,5 +4,8 @@ try: refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['indices'].value out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0]) - except Exception, eq: - out_data['output'].set_dbkey(param_dict['dbkey']) + except: + try: + refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['ownFile'].dbkey + except: + out_data['output'].set_dbkey('?')

1 0

[hg] galaxy 2814: trackster: feature tracks auto-resize to fit d...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b45a5a51c7d1 changeset: 2814:b45a5a51c7d1 user: Kanwei Li <kanwei(a)gmail.com> date: Thu Oct 01 14:01:53 2009 -0400 description: trackster: feature tracks auto-resize to fit data, prepare for LRU cache 5 file(s) affected in this change: static/scripts/lrucache.js static/scripts/packed/lrucache.js static/scripts/packed/trackster.js static/scripts/trackster.js static/trackster.css diffs (407 lines): diff -r 695f28311b36 -r b45a5a51c7d1 static/scripts/lrucache.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/lrucache.js Thu Oct 01 14:01:53 2009 -0400 @@ -0,0 +1,238 @@ +/* +MIT LICENSE +Copyright (c) 2007 Monsur Hossain (http://www.monsur.com) + +Permission is hereby granted, free of charge, to any person +obtaining a copy of this software and associated documentation +files (the "Software"), to deal in the Software without +restriction, including without limitation the rights to use, +copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the +Software is furnished to do so, subject to the following +conditions: + +The above copyright notice and this permission notice shall be +included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES +OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT +HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, +WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR +OTHER DEALINGS IN THE SOFTWARE. +*/ + +// **************************************************************************** +// CachePriority ENUM +// An easier way to refer to the priority of a cache item +var CachePriority = { + Low: 1, + Normal: 2, + High: 4 +} + +// **************************************************************************** +// Cache constructor +// Creates a new cache object +// INPUT: maxSize (optional) - indicates how many items the cache can hold. +// default is -1, which means no limit on the +// number of items. +function Cache(maxSize) { + this.items = {}; + this.count = 0; + if (maxSize == null) + maxSize = -1; + this.maxSize = maxSize; + this.fillFactor = .75; + this.purgeSize = Math.round(this.maxSize * this.fillFactor); + + this.stats = {} + this.stats.hits = 0; + this.stats.misses = 0; +} + +// **************************************************************************** +// Cache.getItem +// retrieves an item from the cache, returns null if the item doesn't exist +// or it is expired. +// INPUT: key - the key to load from the cache +Cache.prototype.getItem = function(key) { + + // retrieve the item from the cache + var item = this.items[key]; + + if (item != null) { + if (!this._isExpired(item)) { + // if the item is not expired + // update its last accessed date + item.lastAccessed = new Date().getTime(); + } else { + // if the item is expired, remove it from the cache + this._removeItem(key); + item = null; + } + } + + // return the item value (if it exists), or null + var returnVal = null; + if (item != null) { + returnVal = item.value; + this.stats.hits++; + } else { + this.stats.misses++; + } + return returnVal; +} + +// **************************************************************************** +// Cache.setItem +// sets an item in the cache +// parameters: key - the key to refer to the object +// value - the object to cache +// options - an optional parameter described below +// the last parameter accepts an object which controls various caching options: +// expirationAbsolute: the datetime when the item should expire +// expirationSliding: an integer representing the seconds since +// the last cache access after which the item +// should expire +// priority: How important it is to leave this item in the cache. +// You can use the values CachePriority.Low, .Normal, or +// .High, or you can just use an integer. Note that +// placing a priority on an item does not guarantee +// it will remain in cache. It can still be purged if +// an expiration is hit, or if the cache is full. +// callback: A function that gets called when the item is purged +// from cache. The key and value of the removed item +// are passed as parameters to the callback function. +Cache.prototype.setItem = function(key, value, options) { + + function CacheItem(k, v, o) { + if ((k == null) || (k == '')) + throw new Error("key cannot be null or empty"); + this.key = k; + this.value = v; + if (o == null) + o = {}; + if (o.expirationAbsolute != null) + o.expirationAbsolute = o.expirationAbsolute.getTime(); + if (o.priority == null) + o.priority = CachePriority.Normal; + this.options = o; + this.lastAccessed = new Date().getTime(); + } + + // add a new cache item to the cache + if (this.items[key] != null) + this._removeItem(key); + this._addItem(new CacheItem(key, value, options)); + + // if the cache is full, purge it + if ((this.maxSize > 0) && (this.count > this.maxSize)) { + this._purge(); + } +} + +// **************************************************************************** +// Cache.clear +// Remove all items from the cache +Cache.prototype.clear = function() { + + // loop through each item in the cache and remove it + for (var key in this.items) { + this._removeItem(key); + } +} + +// **************************************************************************** +// Cache._purge (PRIVATE FUNCTION) +// remove old elements from the cache +Cache.prototype._purge = function() { + + var tmparray = new Array(); + + // loop through the cache, expire items that should be expired + // otherwise, add the item to an array + for (var key in this.items) { + var item = this.items[key]; + if (this._isExpired(item)) { + this._removeItem(key); + } else { + tmparray.push(item); + } + } + + if (tmparray.length > this.purgeSize) { + + // sort this array based on cache priority and the last accessed date + tmparray = tmparray.sort(function(a, b) { + if (a.options.priority != b.options.priority) { + return b.options.priority - a.options.priority; + } else { + return b.lastAccessed - a.lastAccessed; + } + }); + + // remove items from the end of the array + while (tmparray.length > this.purgeSize) { + var ritem = tmparray.pop(); + this._removeItem(ritem.key); + } + } +} + +// **************************************************************************** +// Cache._addItem (PRIVATE FUNCTION) +// add an item to the cache +Cache.prototype._addItem = function(item) { + this.items[item.key] = item; + this.count++; +} + +// **************************************************************************** +// Cache._removeItem (PRIVATE FUNCTION) +// Remove an item from the cache, call the callback function (if necessary) +Cache.prototype._removeItem = function(key) { + var item = this.items[key]; + delete this.items[key]; + this.count--; + + // if there is a callback function, call it at the end of execution + if (item.options.callback != null) { + var callback = function() { + item.options.callback(item.key, item.value); + } + setTimeout(callback, 0); + } +} + +// **************************************************************************** +// Cache._isExpired (PRIVATE FUNCTION) +// Returns true if the item should be expired based on its expiration options +Cache.prototype._isExpired = function(item) { + var now = new Date().getTime(); + var expired = false; + if ((item.options.expirationAbsolute) && (item.options.expirationAbsolute < now)) { + // if the absolute expiration has passed, expire the item + expired = true; + } + if ((expired == false) && (item.options.expirationSliding)) { + // if the sliding expiration has passed, expire the item + var lastAccess = item.lastAccessed + (item.options.expirationSliding * 1000); + if (lastAccess < now) { + expired = true; + } + } + return expired; +} + +Cache.prototype.toHtmlString = function() { + var returnStr = this.count + " item(s) in cache<br /><ul>"; + for (var key in this.items) { + var item = this.items[key]; + returnStr = returnStr + "<li>" + item.key.toString() + " = " + item.value.toString() + "</li>"; + } + returnStr = returnStr + "</ul>"; + return returnStr; +} diff -r 695f28311b36 -r b45a5a51c7d1 static/scripts/packed/lrucache.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/packed/lrucache.js Thu Oct 01 14:01:53 2009 -0400 @@ -0,0 +1,1 @@ +var CachePriority={Low:1,Normal:2,High:4};function Cache(a){this.items={};this.count=0;if(a==null){a=-1}this.maxSize=a;this.fillFactor=0.75;this.purgeSize=Math.round(this.maxSize*this.fillFactor);this.stats={};this.stats.hits=0;this.stats.misses=0}Cache.prototype.getItem=function(a){var c=this.items[a];if(c!=null){if(!this._isExpired(c)){c.lastAccessed=new Date().getTime()}else{this._removeItem(a);c=null}}var b=null;if(c!=null){b=c.value;this.stats.hits++}else{this.stats.misses++}return b};Cache.prototype.setItem=function(c,d,b){function a(f,e,g){if((f==null)||(f=="")){throw new Error("key cannot be null or empty")}this.key=f;this.value=e;if(g==null){g={}}if(g.expirationAbsolute!=null){g.expirationAbsolute=g.expirationAbsolute.getTime()}if(g.priority==null){g.priority=CachePriority.Normal}this.options=g;this.lastAccessed=new Date().getTime()}if(this.items[c]!=null){this._removeItem(c)}this._addItem(new a(c,d,b));if((this.maxSize>0)&&(this.count>this.maxSize)){this._purge()}} ;Cache.prototype.clear=function(){for(var a in this.items){this._removeItem(a)}};Cache.prototype._purge=function(){var d=new Array();for(var a in this.items){var b=this.items[a];if(this._isExpired(b)){this._removeItem(a)}else{d.push(b)}}if(d.length>this.purgeSize){d=d.sort(function(f,e){if(f.options.priority!=e.options.priority){return e.options.priority-f.options.priority}else{return e.lastAccessed-f.lastAccessed}});while(d.length>this.purgeSize){var c=d.pop();this._removeItem(c.key)}}};Cache.prototype._addItem=function(a){this.items[a.key]=a;this.count++};Cache.prototype._removeItem=function(a){var b=this.items[a];delete this.items[a];this.count--;if(b.options.callback!=null){var c=function(){b.options.callback(b.key,b.value)};setTimeout(c,0)}};Cache.prototype._isExpired=function(c){var a=new Date().getTime();var b=false;if((c.options.expirationAbsolute)&&(c.options.expirationAbsolute<a)){b=true}if((b==false)&&(c.options.expirationSliding)){var d=c.lastAccessed+(c.options. expirationSliding*1000);if(d<a){b=true}}return b};Cache.prototype.toHtmlString=function(){var b=this.count+" item(s) in cache<br /><ul>";for(var a in this.items){var c=this.items[a];b=b+"<li>"+c.key.toString()+" = "+c.value.toString()+"</li>"}b=b+"</ul>";return b}; \ No newline at end of file diff -r 695f28311b36 -r b45a5a51c7d1 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js Thu Oct 01 13:16:43 2009 -0400 +++ b/static/scripts/packed/trackster.js Thu Oct 01 14:01:53 2009 -0400 @@ -1,1 +1,1 @@ -var DENSITY=1000;var DataCache=function(b,a){this.type=b;this.track=a;this.cache=Object()};$.extend(DataCache.prototype,{get:function(d,b){var c=this.cache;if(!(c[d]&&c[d][b])){if(!c[d]){c[d]=Object()}var a=b*DENSITY*d;var e=(b+1)*DENSITY*d;c[d][b]={state:"loading"};$.getJSON(data_url,{track_type:this.track.track_type,chrom:this.track.view.chrom,low:a,high:e,dataset_id:this.track.dataset_id},function(f){if(f=="pending"){setTimeout(fetcher,5000)}else{c[d][b]={state:"loaded",values:f}}$(document).trigger("redraw")})}return c[d][b]}});var View=function(a,b){this.chrom=a;this.tracks=[];this.max_low=0;this.max_high=b;this.low=this.max_low;this.high=this.max_high;this.length=this.max_high-this.max_low};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){$("#overview-box").css({left:(this.low/this.length)*$("#overview-viewport").width(),width:Math.max(4,((this.high-this.low)/this.length)*$("#overview-viewport").widt h())}).show();$("#low").text(this.low);$("#high").text(this.high);for(var a in this.tracks){this.tracks[a].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},move:function(b,a){this.low=Math.max(this.max_low,Math.floor(b));this.high=Math.min(this.length,Math.ceil(a))},zoom_in:function(d,b){if(this.max_high==0){return}var c=this.high-this.low;var e=c/d/2;if(b==undefined){var a=(this.low+this.high)/2}else{var a=this.low+c*b/$(document).width()}this.low=Math.floor(a-e);this.high=Math.ceil(a+e);if(this.low<this.max_low){this.low=this.max_low;this.high=c/d}else{if(this.high>this.max_high){this.high=this.max_high;this.low=this.max_high-c/d}}if(this.high-this.low<1){this.high=this.low+1}},zoom_out:function(c){if(this.max_high==0){return}var a=(this.low+this.high)/2;var b=this.high-this.low;var d=b*c/2;this.low=Math.floor(Math.max(0,a-d));this.high=Math.ceil(Math.min(this.length,a+d))},left:function(b){var a=this.high- this.low;var c=Math.floor(a/b);if(this.low-c<0){this.low=0;this.high=this.low+a}else{this.low-=c;this.high-=c}},right:function(b){var a=this.high-this.low;var c=Math.floor(a/b);if(this.high+c>this.length){this.high=this.length;this.low=this.high-a}else{this.low+=c;this.high+=c}}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.last_resolution=null;this.last_w_scale=null;this.tile_cache={}};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,c=this.view.high,e=c-i;var b=Math.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));b=Math.max(b,1);b=Math.min(b,100000);var n=$("< div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(n);var l=this.content_div.width(),d=this.content_div.height(),o=l/e,k={},m={};if(this.last_resolution==b&&this.last_w_scale==o){k=this.tile_cache}var g;var a=Math.floor(i/b/DENSITY);while((a*1000*b)<c){if(a in k){g=k[a];var f=a*DENSITY*b;g.css({left:(f-this.view.low)*o});n.append(g)}else{g=this.draw_tile(b,a,n,o,d)}if(g){m[a]=g}a+=1}this.last_resolution=b;this.last_w_scale=o;this.tile_cache=m}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.high){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+a+"</div>").css({position:"absolute",left:f-1 }));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.content_div.css("height",this.height_px+"px");this.dataset_id=b;this.cache=new DataCache("",this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(b){if(b){if(b=="error"){a.content_div.addClass("error").text("There was an error in indexing this dataset.")}else{if(b=="no data"){a.content_div.addClass("nodata").text("No data for this chrom/contig.")}else{a.min_value=b.min;a.max_value=b.max;a.vertical_range=a.max_value-a.min_value;a.view.redraw()}}}})},draw_tile:function(d,a,o,s,p){if(!this.vertical_range){return}var k=a*DENSITY*d,r=(a+1)*DENSITY*d,c=DENSITY*d;var n=this.cache.get(d,a) ;var h;if(n.state=="loading"){h=$("<div class='loading tile'></div>")}else{h=$("<canvas class='tile'></canvas>")}h.css({position:"absolute",top:0,left:(k-this.view.low)*s,});o.append(h);if(n.state=="loading"){e=false;return null}var b=h;b.get(0).width=Math.ceil(c*s);b.get(0).height=this.height_px;var q=b.get(0).getContext("2d");var e=false;q.beginPath();var g=n.values;if(!g){return}for(var f=0;f<g.length-1;f++){var m=g[f][0]-k;var l=g[f][1];if(isNaN(l)){e=false}else{m=m*s;y_above_min=l-this.min_value;l=y_above_min/this.vertical_range*this.height_px;if(e){q.lineTo(m,l)}else{q.moveTo(m,l);e=true}}}q.stroke();return h}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.content_div.css("height",this.height_px+"px");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.01;this.showing_labels=false};$.extend(FeatureTrack.prototype,TiledTrack.prototype,{calc_ slots:function(e){var a=new Array();var d=this.container_div.width()/(this.view.high-this.view.low);if(e){this.zi_slots=new Object()}var c=$("<canvas></canvas>").get(0).getContext("2d");for(var b in this.values){feature=this.values[b];f_start=Math.floor(Math.max(this.view.max_low,(feature.start-this.view.max_low)*d));if(e){f_start-=c.measureText(feature.name).width}f_end=Math.ceil(Math.min(this.view.max_high,(feature.end-this.view.max_low)*d));j=0;while(true){if(a[j]==undefined||a[j]<f_start){a[j]=f_end;if(e){this.zi_slots[feature.name]=j}else{this.zo_slots[feature.name]=j}break}j++}}},init:function(){var a=this;$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()})},draw_tile:function(q,t,e,g,f){if(!this.values){return null}if(g>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(tr ue)}this.slots=this.zi_slots}else{if(g<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var u=t*DENSITY*q,c=(t+1)*DENSITY*q,b=DENSITY*q;var k=this.view,m=k.high-k.low,o=Math.ceil(b*g),h=new Array(),n=200,l=$("<canvas class='tile'></canvas>");l.css({position:"absolute",top:0,left:(u-this.view.low)*g,});l.get(0).width=o;l.get(0).height=n;var p=l.get(0).getContext("2d");var r=0;for(var s in this.values){feature=this.values[s];if(feature.start<=c&&feature.end>=u){f_start=Math.floor(Math.max(0,(feature.start-u)*g));f_end=Math.ceil(Math.min(o,(feature.end-u)*g));p.fillStyle="#000";p.fillRect(f_start,this.slots[feature.name]*10+5,f_end-f_start,1);if(this.showing_labels&&p.fillText){p.font="10px monospace";p.textAlign="right";p.fillText(feature.name,f_start,this.slots[feature.name]*10+8)}if(feature.exon_start&&feature.exon_end){var d=Math.floor(Math.max(0,(feature.exon_start-u)*g));var w=Math.ceil(Math.min(o,(feature.exon_end-u)*g))}f or(var s in feature.blocks){block=feature.blocks[s];block_start=Math.floor(Math.max(0,(block[0]-u)*g));block_end=Math.ceil(Math.min(o,(block[1]-u)*g));var a=3,v=4;if(d&&block_start>=d&&block_end<=w){a=5,v=3}p.fillRect(d,this.slots[feature.name]*10+v,block_end-block_start,a)}r++}}e.append(l);return l},}); \ No newline at end of file +var DENSITY=1000,DATA_ERROR="There was an error in indexing this dataset.",DATA_NONE="No data for this chrom/contig.";var DataCache=function(b,a){this.type=b;this.track=a;this.cache=Object()};$.extend(DataCache.prototype,{get:function(d,b){var c=this.cache;if(!(c[d]&&c[d][b])){if(!c[d]){c[d]=Object()}var a=b*DENSITY*d;var e=(b+1)*DENSITY*d;c[d][b]={state:"loading"};$.getJSON(data_url,{track_type:this.track.track_type,chrom:this.track.view.chrom,low:a,high:e,dataset_id:this.track.dataset_id},function(f){if(f=="pending"){setTimeout(fetcher,5000)}else{c[d][b]={state:"loaded",values:f}}$(document).trigger("redraw")})}return c[d][b]}});var View=function(a,b){this.chrom=a;this.tracks=[];this.max_low=0;this.max_high=b;this.low=this.max_low;this.high=this.max_high;this.length=this.max_high-this.max_low};$.extend(View.prototype,{add_track:function(a){a.view=this;this.tracks.push(a);if(a.init){a.init()}},redraw:function(){$("#overview-box").css({left:(this.low/this.length)*$("#overvie w-viewport").width(),width:Math.max(4,((this.high-this.low)/this.length)*$("#overview-viewport").width())}).show();$("#low").text(this.low);$("#high").text(this.high);for(var a in this.tracks){this.tracks[a].draw()}$("#bottom-spacer").remove();$("#viewport").append('<div id="bottom-spacer" style="height: 200px;"></div>')},move:function(b,a){this.low=Math.max(this.max_low,Math.floor(b));this.high=Math.min(this.length,Math.ceil(a))},zoom_in:function(d,b){if(this.max_high==0){return}var c=this.high-this.low;var e=c/d/2;if(b==undefined){var a=(this.low+this.high)/2}else{var a=this.low+c*b/$(document).width()}this.low=Math.floor(a-e);this.high=Math.ceil(a+e);if(this.low<this.max_low){this.low=this.max_low;this.high=c/d}else{if(this.high>this.max_high){this.high=this.max_high;this.low=this.max_high-c/d}}if(this.high-this.low<1){this.high=this.low+1}},zoom_out:function(c){if(this.max_high==0){return}var a=(this.low+this.high)/2;var b=this.high-this.low;var d=b*c/2;this.low=Math.flo or(Math.max(0,a-d));this.high=Math.ceil(Math.min(this.length,a+d))},left:function(b){var a=this.high-this.low;var c=Math.floor(a/b);if(this.low-c<0){this.low=0;this.high=this.low+a}else{this.low-=c;this.high-=c}},right:function(b){var a=this.high-this.low;var c=Math.floor(a/b);if(this.high+c>this.length){this.high=this.length;this.low=this.high-a}else{this.low+=c;this.high+=c}}});var Track=function(a,b){this.name=a;this.parent_element=b;this.make_container()};$.extend(Track.prototype,{make_container:function(){this.header_div=$("<div class='track-header'>").text(this.name);this.content_div=$("<div class='track-content'>");this.container_div=$("<div class='track'></div>").append(this.header_div).append(this.content_div);this.parent_element.append(this.container_div)}});var TiledTrack=function(){this.last_resolution=null;this.last_w_scale=null;this.tile_cache={}};$.extend(TiledTrack.prototype,Track.prototype,{draw:function(){var i=this.view.low,c=this.view.high,e=c-i;var b=Mat h.pow(10,Math.ceil(Math.log(e/DENSITY)/Math.log(10)));b=Math.max(b,1);b=Math.min(b,100000);var m=$("<div style='position: relative;'></div>");this.content_div.children(":first").remove();this.content_div.append(m);var k=this.content_div.width(),d=this.content_div.height(),n=k/e,j={},l={};if(this.last_resolution==b&&this.last_w_scale==n){j=this.tile_cache}var g;var a=Math.floor(i/b/DENSITY);while((a*1000*b)<c){if(a in j){g=j[a];var f=a*DENSITY*b;g.css({left:(f-this.view.low)*n});m.append(g)}else{g=this.draw_tile(b,a,m,n,d)}if(g){l[a]=g}a+=1}this.last_resolution=b;this.last_w_scale=n;this.tile_cache=l}});var LabelTrack=function(a){Track.call(this,null,a);this.container_div.addClass("label-track")};$.extend(LabelTrack.prototype,Track.prototype,{draw:function(){var c=this.view,d=c.high-c.low,g=Math.floor(Math.pow(10,Math.floor(Math.log(d)/Math.log(10)))),a=Math.floor(c.low/g)*g,e=this.content_div.width(),b=$("<div style='position: relative; height: 1.3em;'></div>");while(a<c.hig h){var f=(a-c.low)/d*e;b.append($("<div class='label'>"+a+"</div>").css({position:"absolute",left:f-1}));a+=g}this.content_div.children(":first").remove();this.content_div.append(b)}});var LineTrack=function(c,b,a){Track.call(this,c,$("#viewport"));this.track_type="line";this.height_px=(a?a:100);this.container_div.addClass("line-track");this.content_div.css("height",this.height_px+"px");this.dataset_id=b;this.cache=new DataCache("",this)};$.extend(LineTrack.prototype,TiledTrack.prototype,{init:function(){var a=this;$.getJSON(data_url,{stats:true,track_type:a.track_type,chrom:a.view.chrom,low:null,high:null,dataset_id:a.dataset_id},function(b){if(!b||b=="error"){a.content_div.addClass("error").text(DATA_ERROR)}else{if(b=="no data"){a.content_div.addClass("nodata").text(DATA_NONE)}else{a.min_value=b.min;a.max_value=b.max;a.vertical_range=a.max_value-a.min_value;a.view.redraw()}}})},draw_tile:function(d,a,n,r,o){if(!this.vertical_range){return}var j=a*DENSITY*d,q=(a+1)*DENSITY* d,c=DENSITY*d;var m=this.cache.get(d,a);var h;if(m.state=="loading"){h=$("<div class='loading tile'></div>")}else{h=$("<canvas class='tile'></canvas>")}h.css({position:"absolute",top:0,left:(j-this.view.low)*r,});n.append(h);if(m.state=="loading"){e=false;return null}var b=h;b.get(0).width=Math.ceil(c*r);b.get(0).height=this.height_px;var p=b.get(0).getContext("2d");var e=false;p.beginPath();var g=m.values;if(!g){return}for(var f=0;f<g.length-1;f++){var l=g[f][0]-j;var k=g[f][1];if(isNaN(k)){e=false}else{l=l*r;y_above_min=k-this.min_value;k=y_above_min/this.vertical_range*this.height_px;if(e){p.lineTo(l,k)}else{p.moveTo(l,k);e=true}}}p.stroke();return h}});var FeatureTrack=function(c,b,a){Track.call(this,c,$("#viewport"));this.track_type="feature";this.height_px=(a?a:100);this.container_div.addClass("feature-track");this.content_div.css("height",this.height_px+"px");this.dataset_id=b;this.zo_slots={};this.show_labels_scale=0.01;this.showing_labels=false;this.vertical_gap=10} ;$.extend(FeatureTrack.prototype,TiledTrack.prototype,{calc_slots:function(h){var b=[];var a=this.container_div.width()/(this.view.high-this.view.low);if(h){this.zi_slots={}}var g=$("<canvas></canvas>").get(0).getContext("2d");for(var d in this.values){var k=this.values[d];var e=Math.floor(Math.max(this.view.max_low,(k.start-this.view.max_low)*a));if(h){e-=g.measureText(k.name).width;e-=10}var f=Math.ceil(Math.min(this.view.max_high,(k.end-this.view.max_low)*a));var c=0;while(true){if(b[c]==undefined||b[c]<e){b[c]=f;if(h){this.zi_slots[k.name]=c}else{this.zo_slots[k.name]=c}break}c++}}this.height_px=b.length*this.vertical_gap+15;this.content_div.css("height",this.height_px+"px")},init:function(){var a=this;$.getJSON(data_url,{track_type:a.track_type,low:a.view.max_low,high:a.view.max_high,dataset_id:a.dataset_id,chrom:a.view.chrom},function(b){if(b=="error"){a.content_div.addClass("error").text(DATA_ERROR)}else{if(b.length==0||b=="no data"){a.content_div.addClass("nodata").t ext(DATA_NONE)}else{a.values=b;a.calc_slots();a.slots=a.zo_slots;a.draw()}}})},draw_tile:function(q,t,e,g,f){if(!this.values){return null}if(g>this.show_labels_scale&&!this.showing_labels){this.showing_labels=true;if(!this.zi_slots){this.calc_slots(true)}this.slots=this.zi_slots}else{if(g<=this.show_labels_scale&&this.showing_labels){this.showing_labels=false;this.slots=this.zo_slots}}var u=t*DENSITY*q,c=(t+1)*DENSITY*q,b=DENSITY*q;var k=this.view,m=k.high-k.low,o=Math.ceil(b*g),h=new Array(),n=this.height_px,l=$("<canvas class='tile'></canvas>");l.css({position:"absolute",top:0,left:(u-this.view.low)*g,});l.get(0).width=o;l.get(0).height=n;var p=l.get(0).getContext("2d");var r=0;for(var s in this.values){feature=this.values[s];if(feature.start<=c&&feature.end>=u){f_start=Math.floor(Math.max(0,(feature.start-u)*g));f_end=Math.ceil(Math.min(o,(feature.end-u)*g));p.fillStyle="#000";p.fillRect(f_start,this.slots[feature.name]*this.vertical_gap+5,f_end-f_start,1);if(this.showing _labels&&p.fillText){p.font="10px monospace";p.textAlign="right";p.fillText(feature.name,f_start,this.slots[feature.name]*10+8)}if(feature.exon_start&&feature.exon_end){var d=Math.floor(Math.max(0,(feature.exon_start-u)*g));var w=Math.ceil(Math.min(o,(feature.exon_end-u)*g))}for(var s in feature.blocks){block=feature.blocks[s];block_start=Math.floor(Math.max(0,(block[0]-u)*g));block_end=Math.ceil(Math.min(o,(block[1]-u)*g));var a=3,v=4;if(d&&block_start>=d&&block_end<=w){a=5,v=3}p.fillRect(d,this.slots[feature.name]*this.vertical_gap+v,block_end-block_start,a)}r++}}e.append(l);return l},}); \ No newline at end of file diff -r 695f28311b36 -r b45a5a51c7d1 static/scripts/trackster.js --- a/static/scripts/trackster.js Thu Oct 01 13:16:43 2009 -0400 +++ b/static/scripts/trackster.js Thu Oct 01 14:01:53 2009 -0400 @@ -2,7 +2,9 @@ 2009, James Taylor, Kanwei Li */ -var DENSITY = 1000; +var DENSITY = 1000, + DATA_ERROR = "There was an error in indexing this dataset.", + DATA_NONE = "No data for this chrom/contig."; var DataCache = function( type, track ) { this.type = type; @@ -239,18 +241,16 @@ var track = this; $.getJSON( data_url, { stats: true, track_type: track.track_type, chrom: track.view.chrom, low: null, high: null, dataset_id: track.dataset_id }, function ( data ) { - if (data) { - if (data == "error") { - track.content_div.addClass("error").text("There was an error in indexing this dataset."); - } else if (data == "no data") { - // console.log(track.content_div); - track.content_div.addClass("nodata").text("No data for this chrom/contig."); - } else { - track.min_value = data['min']; - track.max_value = data['max']; - track.vertical_range = track.max_value - track.min_value; - track.view.redraw(); - } + if (!data || data == "error") { + track.content_div.addClass("error").text(DATA_ERROR); + } else if (data == "no data") { + // console.log(track.content_div); + track.content_div.addClass("nodata").text(DATA_NONE); + } else { + track.min_value = data['min']; + track.max_value = data['max']; + track.vertical_range = track.max_value - track.min_value; + track.view.redraw(); } }); }, @@ -321,27 +321,28 @@ this.zo_slots = {}; this.show_labels_scale = 0.01; this.showing_labels = false; + this.vertical_gap = 10; }; $.extend( FeatureTrack.prototype, TiledTrack.prototype, { - calc_slots: function( include_labels ) { // console.log("num vals: " + this.values.length); - var end_ary = new Array(); + var end_ary = []; var scale = this.container_div.width() / (this.view.high - this.view.low); - // console.log(scale); - if (include_labels) this.zi_slots = new Object(); + // console.log(scale, this.view.high, this.view.low); + if (include_labels) this.zi_slots = {}; var dummy_canvas = $("<canvas></canvas>").get(0).getContext("2d"); for (var i in this.values) { - feature = this.values[i]; - f_start = Math.floor( Math.max(this.view.max_low, (feature.start - this.view.max_low) * scale) ); + var feature = this.values[i]; + var f_start = Math.floor( Math.max(this.view.max_low, (feature.start - this.view.max_low) * scale) ); if (include_labels) { f_start -= dummy_canvas.measureText(feature.name).width; + f_start -= 10; // Spacing between text and line } - f_end = Math.ceil( Math.min(this.view.max_high, (feature.end - this.view.max_low) * scale) ); + var f_end = Math.ceil( Math.min(this.view.max_high, (feature.end - this.view.max_low) * scale) ); // if (include_labels) { console.log(f_start, f_end); } - j = 0; + var j = 0; while (true) { if (end_ary[j] == undefined || end_ary[j] < f_start) { end_ary[j] = f_end; @@ -355,17 +356,26 @@ j++; } } + this.height_px = end_ary.length * this.vertical_gap + 15; + this.content_div.css( "height", this.height_px + "px" ); }, init: function() { var track = this; $.getJSON( data_url, { track_type: track.track_type, low: track.view.max_low, high: track.view.max_high, dataset_id: track.dataset_id, chrom: track.view.chrom }, function ( data ) { - track.values = data; - track.calc_slots(); - track.slots = track.zo_slots; - // console.log(track.zo_slots); - track.draw(); + if (data == "error") { + track.content_div.addClass("error").text(DATA_ERROR); + } else if (data.length == 0 || data == "no data") { + // console.log(track.content_div); + track.content_div.addClass("nodata").text(DATA_NONE); + } else { + track.values = data; + track.calc_slots(); + track.slots = track.zo_slots; + // console.log(track.zo_slots); + track.draw(); + } }); }, @@ -391,7 +401,7 @@ range = view.high - view.low, width = Math.ceil( tile_length * w_scale ), slots = new Array(), - height = 200, + height = this.height_px, new_canvas = $("<canvas class='tile'></canvas>"); new_canvas.css({ @@ -412,7 +422,7 @@ f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ); // console.log(feature.start, feature.end, f_start, f_end, j); ctx.fillStyle = "#000"; - ctx.fillRect(f_start, this.slots[feature.name] * 10 + 5, f_end - f_start, 1); + ctx.fillRect(f_start, this.slots[feature.name] * this.vertical_gap + 5, f_end - f_start, 1); if (this.showing_labels && ctx.fillText) { ctx.font = "10px monospace"; @@ -435,7 +445,7 @@ if (exon_start && block_start >= exon_start && block_end <= exon_end) { thickness = 5, y_start = 3; } - ctx.fillRect(exon_start, this.slots[feature.name] * 10 + y_start, block_end - block_start, thickness); + ctx.fillRect(exon_start, this.slots[feature.name] * this.vertical_gap + y_start, block_end - block_start, thickness); // console.log(block_start, block_end); } diff -r 695f28311b36 -r b45a5a51c7d1 static/trackster.css --- a/static/trackster.css Thu Oct 01 13:16:43 2009 -0400 +++ b/static/trackster.css Thu Oct 01 14:01:53 2009 -0400 @@ -86,7 +86,7 @@ .track-content.error { text-align: center; padding-top: 30px; - background-color: #600; + background-color: #ECB4AF; } .track-content.nodata { text-align: center;

1 0

[hg] galaxy 2810: Fixed trimmer test
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6eb4f3017fbe changeset: 2810:6eb4f3017fbe user: Anton Nekrutenko <anton(a)bx.psu.edu> date: Thu Oct 01 09:09:40 2009 -0400 description: Fixed trimmer test 1 file(s) affected in this change: tools/filters/trimmer.xml diffs (12 lines): diff -r 3bd7acfe34cc -r 6eb4f3017fbe tools/filters/trimmer.xml --- a/tools/filters/trimmer.xml Wed Sep 30 15:35:05 2009 -0400 +++ b/tools/filters/trimmer.xml Thu Oct 01 09:09:40 2009 -0400 @@ -1,7 +1,7 @@ <tool id="trimmer" name="Trim" version="0.0.1"> <description>leading or trailing characters</description> <command interpreter="python"> - chopper.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 + trimmer.py -a -f $input1 -c $col -s $start -e $end -i $ignore $fastq > $out_file1 </command> <inputs> <param format="tabular,text" name="input1" type="data" label="this dataset"/>

1 0

[hg] galaxy 2811: Fix spelling of Successfully when running a wo...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2364764e3604 changeset: 2811:2364764e3604 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Thu Oct 01 11:39:55 2009 -0400 description: Fix spelling of Successfully when running a workflow. 1 file(s) affected in this change: templates/workflow/run_complete.mako diffs (19 lines): diff -r 6eb4f3017fbe -r 2364764e3604 templates/workflow/run_complete.mako --- a/templates/workflow/run_complete.mako Thu Oct 01 09:09:40 2009 -0400 +++ b/templates/workflow/run_complete.mako Thu Oct 01 11:39:55 2009 -0400 @@ -14,7 +14,7 @@ <body> <div class="donemessage"> <p> - Sucesfully ran workflow "${workflow.name}", the following datasets have + Successfully ran workflow "${workflow.name}", the following datasets have been added to the queue. </p> @@ -28,4 +28,4 @@ </div> </body> -</html> \ No newline at end of file +</html>

1 0

[hg] galaxy 2812: Add a new option, 'allow_library_path_paste' t...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d31ab50dc8e0 changeset: 2812:d31ab50dc8e0 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Oct 01 12:35:41 2009 -0400 description: Add a new option, 'allow_library_path_paste' that adds a new upload page ("Upload files from filesystem paths") to the admin-side library upload pages. This form contains a textarea that allows Galaxy admins to paste any number of filesystem paths (files or directories) from which Galaxy will import library datasets, saving the directory structure (if desired). Since such ability allows admins access to any file on the Galaxy server which is readable by Galaxy's system user, this option is disabled by default, and system administrators should take care in assigning Galaxy administrators when this feature is enabled. Controls on what files are accessible to this tool based on ownership or other properties can be added at a later date if there is sufficient interest for such features. This commit also includes a checkbox on the "Upload directory of files" page (as well as the new "Upload files from filesystem paths" page above) that will prevent Galaxy from copying data to its files directory (by default, 'database/files/'). This is useful for large library datasets that live in their own managed locations on the filesystem, this will prevent the existence of duplicate copies of datasets (but means administrators must take care to manage data - moving or removing the data from its Galaxy-external location will render these datasets invalid within Galaxy). One unique feature to be aware of: when using the "Copy data into Galaxy?" checkbox on the "Upload directory of files" page, any symbolic links encountered in the chosen import directory will be made absolute and dereferenced ONCE. This allows administrators to link large datasets to the import directory, rather than having to make full copies, while being able to delete such links after importing. Only the first symlink (the one in the import directory itself) is dereferenced; all others remain. See the following for an example: library_import_dir = /galaxy/import % ls -lR /galaxy/import /galaxy/import: total 6 drwxr-xr-x 2 nate nate 512 Oct 1 11:31 link/ /galaxy/import/link: total 10 lrwxrwxrwx 1 nate nate 71 Oct 1 10:38 1.bed -> ../../../home/nate/galaxy/test-data/1.bed lrwxrwxrwx 1 nate nate 60 Oct 1 10:38 2.bed -> /home/nate/galaxy/test-data/2.bed lrwxrwxrwx 1 nate nate 11 Oct 1 10:38 3.bed -> ../../3.bed lrwxrwxrwx 1 nate nate 35 Oct 1 11:30 4.bed -> ../../galaxy_symlink/test-data/4.bed lrwxrwxrwx 1 nate nate 41 Oct 1 11:31 5.bed -> /galaxy/galaxy_symlink/test-data/5.bed % ls -l /galaxy/3.bed lrwxrwxrwx 1 nate nate 60 Oct 1 10:39 /galaxy/3.bed -> /home/nate/galaxy/test-data/3.bed % ls -l /galaxy/galaxy_symlink lrwxrwxrwx 1 nate nate 44 Oct 1 11:30 /galaxy/galaxy_symlink -> /home/nate/galaxy/ In this example, 1.bed is a relative symbolic link to the real 1.bed. 2.bed is an absolute symlink to the real 2.bed. 3.bed is a relative symlink to ../../3.bed, aka /galaxy/3.bed, which itself is a symlink to the real 3.bed. 4.bed is a relative symlink which follows another symlink (/galaxy/galaxy_symlink) to the real 4.bed. 5.bed is an absolute symlink in the same fashion as 4.bed If the 'link' server directory is chosen on the "Upload directory of files" page, and "Copy data into Galaxy?" is checked "No", the following files will be referenced by Galaxy: /home/nate/galaxy/test-data/1.bed /home/nate/galaxy/test-data/2.bed /galaxy/3.bed /galaxy/galaxy_symlink/test-data/4.bed /galaxy/galaxy_symlink/test-data/5.bed The Galaxy administrator may now safely delete /galaxy/import/link, but should take care not to remove the referenced symbolic links (/galaxy/3.bed, /galaxy/galaxy_symlink). Not all symbolic links are dereferenced because it is assumed that if an administrator links to a path in the import directory which itself is (or contains) links, that is the preferred path for accessing the data. 10 file(s) affected in this change: lib/galaxy/config.py lib/galaxy/tools/actions/upload_common.py lib/galaxy/util/__init__.py lib/galaxy/web/controllers/library_common.py templates/admin/library/browse_library.mako templates/admin/library/upload.mako templates/library/browse_library.mako templates/library/library_dataset_common.mako tools/data_source/upload.py universe_wsgi.ini.sample diffs (377 lines): diff -r 2364764e3604 -r d31ab50dc8e0 lib/galaxy/config.py --- a/lib/galaxy/config.py Thu Oct 01 11:39:55 2009 -0400 +++ b/lib/galaxy/config.py Thu Oct 01 12:35:41 2009 -0400 @@ -87,6 +87,7 @@ self.user_library_import_dir = kwargs.get( 'user_library_import_dir', None ) if self.user_library_import_dir is not None and not os.path.exists( self.user_library_import_dir ): raise ConfigurationError( "user_library_import_dir specified in config (%s) does not exist" % self.user_library_import_dir ) + self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False ) # Configuration options for taking advantage of nginx features self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) self.nginx_upload_store = kwargs.get( 'nginx_upload_store', False ) diff -r 2364764e3604 -r d31ab50dc8e0 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Thu Oct 01 11:39:55 2009 -0400 +++ b/lib/galaxy/tools/actions/upload_common.py Thu Oct 01 12:35:41 2009 -0400 @@ -3,6 +3,7 @@ from galaxy import datatypes, util from galaxy.datatypes import sniff from galaxy.util.json import to_json_string +from galaxy.model.orm import eagerload_all import logging log = logging.getLogger( __name__ ) @@ -127,12 +128,29 @@ or trans.user.email in trans.app.config.get( "admin_users", "" ).split( "," ) ): # This doesn't have to be pretty - the only time this should happen is if someone's being malicious. raise Exception( "User is not authorized to add datasets to this library." ) + folder = library_bunch.folder + if uploaded_dataset.get( 'in_folder', False ): + # Create subfolders if desired + for name in uploaded_dataset.in_folder.split( os.path.sep ): + folder.refresh() + matches = filter( lambda x: x.name == name, active_folders( trans, folder ) ) + if matches: + log.debug( 'DEBUGDEBUG: In %s, found a folder name match: %s:%s' % ( folder.name, matches[0].id, matches[0].name ) ) + folder = matches[0] + else: + new_folder = trans.app.model.LibraryFolder( name=name, description='Automatically created by upload tool' ) + new_folder.genome_build = util.dbnames.default_value + folder.add_folder( new_folder ) + new_folder.flush() + trans.app.security_agent.copy_library_permissions( folder, new_folder ) + log.debug( 'DEBUGDEBUG: In %s, created a new folder: %s:%s' % ( folder.name, new_folder.id, new_folder.name ) ) + folder = new_folder if library_bunch.replace_dataset: ld = library_bunch.replace_dataset else: - ld = trans.app.model.LibraryDataset( folder=library_bunch.folder, name=uploaded_dataset.name ) + ld = trans.app.model.LibraryDataset( folder=folder, name=uploaded_dataset.name ) ld.flush() - trans.app.security_agent.copy_library_permissions( library_bunch.folder, ld ) + trans.app.security_agent.copy_library_permissions( folder, ld ) ldda = trans.app.model.LibraryDatasetDatasetAssociation( name = uploaded_dataset.name, extension = uploaded_dataset.file_type, dbkey = uploaded_dataset.dbkey, @@ -153,8 +171,8 @@ else: # Copy the current user's DefaultUserPermissions to the new LibraryDatasetDatasetAssociation.dataset trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, trans.app.security_agent.user_get_default_permissions( trans.user ) ) - library_bunch.folder.add_library_dataset( ld, genome_build=uploaded_dataset.dbkey ) - library_bunch.folder.flush() + folder.add_library_dataset( ld, genome_build=uploaded_dataset.dbkey ) + folder.flush() ld.library_dataset_dataset_association_id = ldda.id ld.flush() # Handle template included in the upload form, if any @@ -230,6 +248,10 @@ is_binary = uploaded_dataset.datatype.is_binary except: is_binary = None + try: + link_data_only = uploaded_dataset.link_data_only + except: + link_data_only = False json = dict( file_type = uploaded_dataset.file_type, ext = uploaded_dataset.ext, name = uploaded_dataset.name, @@ -237,6 +259,7 @@ dbkey = uploaded_dataset.dbkey, type = uploaded_dataset.type, is_binary = is_binary, + link_data_only = link_data_only, space_to_tab = uploaded_dataset.space_to_tab, path = uploaded_dataset.path ) json_file.write( to_json_string( json ) + '\n' ) @@ -276,3 +299,13 @@ trans.app.job_queue.put( job.id, tool ) trans.log_event( "Added job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) return dict( [ ( 'output%i' % i, v ) for i, v in enumerate( data_list ) ] ) + +def active_folders( trans, folder ): + # Stolen from galaxy.web.controllers.library_common (importing from which causes a circular issues). + # Much faster way of retrieving all active sub-folders within a given folder than the + # performance of the mapper. This query also eagerloads the permissions on each folder. + return trans.sa_session.query( trans.app.model.LibraryFolder ) \ + .filter_by( parent=folder, deleted=False ) \ + .options( eagerload_all( "actions" ) ) \ + .order_by( trans.app.model.LibraryFolder.table.c.name ) \ + .all() diff -r 2364764e3604 -r d31ab50dc8e0 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Thu Oct 01 11:39:55 2009 -0400 +++ b/lib/galaxy/util/__init__.py Thu Oct 01 12:35:41 2009 -0400 @@ -178,7 +178,7 @@ # better solution I think is to more responsibility for # sanitizing into the tool parameters themselves so that # different parameters can be sanitized in different ways. - NEVER_SANITIZE = ['file_data', 'url_paste', 'URL'] + NEVER_SANITIZE = ['file_data', 'url_paste', 'URL', 'filesystem_paths'] def __init__( self, params, safe=True, sanitize=True, tool=None ): if safe: diff -r 2364764e3604 -r d31ab50dc8e0 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Thu Oct 01 11:39:55 2009 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Thu Oct 01 12:35:41 2009 -0400 @@ -81,7 +81,9 @@ tool_params = upload_common.persist_uploads( tool_params ) uploaded_datasets = upload_common.get_uploaded_datasets( trans, tool_params, precreated_datasets, dataset_upload_inputs, library_bunch=library_bunch ) elif upload_option == 'upload_directory': - uploaded_datasets = self.get_server_dir_uploaded_datasets( trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ) + uploaded_datasets, err_redirect, msg = self.get_server_dir_uploaded_datasets( trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ) + elif upload_option == 'upload_paths': + uploaded_datasets, err_redirect, msg = self.get_path_paste_uploaded_datasets( trans, params, library_bunch, err_redirect, msg ) upload_common.cleanup_unused_precreated_datasets( precreated_datasets ) if upload_option == 'upload_file' and not uploaded_datasets: msg = 'Select a file, enter a URL or enter text' @@ -98,37 +100,86 @@ json_file_path = upload_common.create_paramfile( uploaded_datasets ) data_list = [ ud.data for ud in uploaded_datasets ] return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder ) + def make_library_uploaded_dataset( self, trans, params, name, path, type, library_bunch, in_folder=None ): + library_bunch.replace_dataset = None # not valid for these types of upload + uploaded_dataset = util.bunch.Bunch() + uploaded_dataset.name = name + uploaded_dataset.path = path + uploaded_dataset.type = type + uploaded_dataset.ext = None + uploaded_dataset.file_type = params.file_type + uploaded_dataset.dbkey = params.dbkey + uploaded_dataset.space_to_tab = params.space_to_tab + if in_folder: + uploaded_dataset.in_folder = in_folder + uploaded_dataset.data = upload_common.new_upload( trans, uploaded_dataset, library_bunch ) + if params.get( 'link_data_only', False ): + uploaded_dataset.link_data_only = True + uploaded_dataset.data.file_name = os.path.abspath( path ) + uploaded_dataset.data.flush() + return uploaded_dataset def get_server_dir_uploaded_datasets( self, trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ): files = [] try: for entry in os.listdir( full_dir ): # Only import regular files - if os.path.isfile( os.path.join( full_dir, entry ) ): - files.append( entry ) + path = os.path.join( full_dir, entry ) + if os.path.islink( path ) and os.path.isfile( path ) and params.get( 'link_data_only', False ): + # If we're linking instead of copying, link the file the link points to, not the link itself. + link_path = os.readlink( path ) + if os.path.isabs( link_path ): + path = link_path + else: + path = os.path.abspath( os.path.join( os.path.dirname( path ), link_path ) ) + if os.path.isfile( path ): + files.append( path ) except Exception, e: msg = "Unable to get file list for configured %s, error: %s" % ( import_dir_desc, str( e ) ) err_redirect = True - return None + return None, err_redirect, msg if not files: msg = "The directory '%s' contains no valid files" % full_dir err_redirect = True - return None + return None, err_redirect, msg uploaded_datasets = [] for file in files: - library_bunch.replace_dataset = None - uploaded_dataset = util.bunch.Bunch() - uploaded_dataset.path = os.path.join( full_dir, file ) - if not os.path.isfile( uploaded_dataset.path ): + name = os.path.basename( file ) + uploaded_datasets.append( self.make_library_uploaded_dataset( trans, params, name, file, 'server_dir', library_bunch ) ) + return uploaded_datasets, None, None + def get_path_paste_uploaded_datasets( self, trans, params, library_bunch, err_redirect, msg ): + if params.get( 'filesystem_paths', '' ) == '': + msg = "No paths entered in the upload form" + err_redirect = True + return None, err_redirect, msg + preserve_dirs = True + if params.get( 'dont_preserve_dirs', False ): + preserve_dirs = False + # locate files + bad_paths = [] + uploaded_datasets = [] + for line in [ l.strip() for l in params.filesystem_paths.splitlines() if l.strip() ]: + path = os.path.abspath( line ) + if not os.path.exists( path ): + bad_paths.append( path ) continue - uploaded_dataset.type = 'server_dir' - uploaded_dataset.name = file - uploaded_dataset.ext = None - uploaded_dataset.file_type = params.file_type - uploaded_dataset.dbkey = params.dbkey - uploaded_dataset.space_to_tab = params.space_to_tab - uploaded_dataset.data = upload_common.new_upload( trans, uploaded_dataset, library_bunch ) - uploaded_datasets.append( uploaded_dataset ) - return uploaded_datasets + # don't bother processing if we're just going to return an error + if not bad_paths: + if os.path.isfile( path ): + name = os.path.basename( path ) + uploaded_datasets.append( self.make_library_uploaded_dataset( trans, params, name, path, 'path_paste', library_bunch ) ) + for basedir, dirs, files in os.walk( line ): + for file in files: + file_path = os.path.abspath( os.path.join( basedir, file ) ) + if preserve_dirs: + in_folder = os.path.dirname( file_path.replace( path, '', 1 ).lstrip( '/' ) ) + else: + in_folder = None + uploaded_datasets.append( self.make_library_uploaded_dataset( trans, params, file, file_path, 'path_paste', library_bunch, in_folder ) ) + if bad_paths: + msg = "Invalid paths:<br><ul><li>%s</li></ul>" % "</li><li>".join( bad_paths ) + err_redirect = True + return None, err_redirect, msg + return uploaded_datasets, None, None @web.expose def info_template( self, trans, cntrller, library_id, response_action='library', obj_id=None, folder_id=None, ldda_id=None, **kwd ): # Only adding a new templAte to a library or folder is currently allowed. Editing an existing template is diff -r 2364764e3604 -r d31ab50dc8e0 templates/admin/library/browse_library.mako --- a/templates/admin/library/browse_library.mako Thu Oct 01 11:39:55 2009 -0400 +++ b/templates/admin/library/browse_library.mako Thu Oct 01 12:35:41 2009 -0400 @@ -73,7 +73,7 @@ // Make ajax call $.ajax( { type: "POST", - url: "${h.url_for( controller='library_dataset', action='library_item_updates' )}", + url: "${h.url_for( controller='library_common', action='library_item_updates' )}", dataType: "json", data: { ids: ids.join( "," ), states: states.join( "," ) }, success : function ( data ) { diff -r 2364764e3604 -r d31ab50dc8e0 templates/admin/library/upload.mako --- a/templates/admin/library/upload.mako Thu Oct 01 11:39:55 2009 -0400 +++ b/templates/admin/library/upload.mako Thu Oct 01 12:35:41 2009 -0400 @@ -18,6 +18,9 @@ %if trans.app.config.library_import_dir and os.path.exists( trans.app.config.library_import_dir ): <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_directory' )}">Upload directory of files</a> %endif + %if trans.app.config.allow_library_path_paste: + <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='upload_paths' )}">Upload files from filesystem paths</a> + %endif <a class="action-button" href="${h.url_for( controller='library_admin', action='upload_library_dataset', library_id=library_id, folder_id=folder_id, replace_id=replace_id, upload_option='import_from_history' )}">Import datasets from your current history</a> </div> <br/><br/> diff -r 2364764e3604 -r d31ab50dc8e0 templates/library/browse_library.mako --- a/templates/library/browse_library.mako Thu Oct 01 11:39:55 2009 -0400 +++ b/templates/library/browse_library.mako Thu Oct 01 12:35:41 2009 -0400 @@ -105,7 +105,7 @@ // Make ajax call $.ajax( { type: "POST", - url: "${h.url_for( controller='library_dataset', action='library_item_updates' )}", + url: "${h.url_for( controller='library_common', action='library_item_updates' )}", dataType: "json", data: { ids: ids.join( "," ), states: states.join( "," ) }, success : function ( data ) { diff -r 2364764e3604 -r d31ab50dc8e0 templates/library/library_dataset_common.mako --- a/templates/library/library_dataset_common.mako Thu Oct 01 11:39:55 2009 -0400 +++ b/templates/library/library_dataset_common.mako Thu Oct 01 12:35:41 2009 -0400 @@ -1,11 +1,13 @@ <%def name="render_upload_form( controller, upload_option, action, library_id, folder_id, replace_dataset, file_formats, dbkeys, roles, history )"> <% import os, os.path %> - %if upload_option in [ 'upload_file', 'upload_directory' ]: + %if upload_option in [ 'upload_file', 'upload_directory', 'upload_paths' ]: <div class="toolForm" id="upload_library_dataset"> - %if upload_option == 'upload_file': + %if upload_option == 'upload_directory': + <div class="toolFormTitle">Upload a directory of files</div> + %elif upload_option == 'upload_paths': + <div class="toolFormTitle">Upload files from filesystem paths</div> + %else: <div class="toolFormTitle">Upload files</div> - %else: - <div class="toolFormTitle">Upload a directory of files</div> %endif <div class="toolFormBody"> <form name="upload_library_dataset" action="${action}" enctype="multipart/form-data" method="post"> @@ -103,6 +105,44 @@ %endif </div> <div style="clear: both"></div> + </div> + %elif upload_option == 'upload_paths': + <div class="form-row"> + <label>Paths to upload</label> + <div class="form-row-input"> + <textarea name="filesystem_paths" rows="10" cols="35"></textarea> + </div> + <div class="toolParamHelp" style="clear: both;"> + Upload all files pasted in the box. The (recursive) contents of any pasted directories will be added as well. + </div> + </div> + <div class="form-row"> + <label>Preserve directory structure?</label> + <div class="form-row-input"> + <input type="checkbox" name="dont_preserve_dirs" value="No"/>No + </div> + <div class="toolParamHelp" style="clear: both;"> + If checked, all files in subdirectories on the filesystem will be placed at the top level of the folder, instead of into subfolders. + </div> + </div> + %endif + %if upload_option in ( 'upload_directory', 'upload_paths' ): + <div class="form-row"> + <label>Copy data into Galaxy?</label> + <div class="form-row-input"> + <input type="checkbox" name="link_data_only" value="No"/>No + </div> + <div class="toolParamHelp" style="clear: both;"> + Normally data uploaded with this tool is copied into Galaxy's "files" directory + so any later changes to the data will not affect Galaxy. However, this may not + be desired (especially for large NGS datasets), so use of this option will + force Galaxy to always read the data from its original path. + %if upload_option == 'upload_directory': + Any symlinks encountered in the upload directory will be dereferenced once - + that is, Galaxy will point directly to the file that is linked, but no other + symlinks further down the line will be dereferenced. + %endif + </div> </div> %endif <div class="form-row"> diff -r 2364764e3604 -r d31ab50dc8e0 tools/data_source/upload.py --- a/tools/data_source/upload.py Thu Oct 01 11:39:55 2009 -0400 +++ b/tools/data_source/upload.py Thu Oct 01 12:35:41 2009 -0400 @@ -238,7 +238,9 @@ if ext == 'auto': ext = 'data' # Move the dataset to its "real" path - if dataset.type == 'server_dir': + if dataset.get( 'link_data_only', False ): + pass # data will remain in place + elif dataset.type in ( 'server_dir', 'path_paste' ): shutil.copy( dataset.path, output_path ) else: shutil.move( dataset.path, output_path ) diff -r 2364764e3604 -r d31ab50dc8e0 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Thu Oct 01 11:39:55 2009 -0400 +++ b/universe_wsgi.ini.sample Thu Oct 01 12:35:41 2009 -0400 @@ -60,13 +60,22 @@ # Galaxy session security id_secret = changethisinproductiontoo -# Directories of files contained in the following directory can be uploaded to a library from the Admin view +# Directories of files contained in the following directory can be uploaded to +# a library from the Admin view #library_import_dir = /var/opt/galaxy/import -# The following can be configured to allow non-admin users to upload a directory of files. The -# configured directory must contain sub-directories named the same as the non-admin user's Galaxy -# login ( email ). The non-admin user is restricted to uploading files or sub-directories of files -# contained in their directory. -# user_library_import_dir = /var/opt/galaxy/import/users + +# The following can be configured to allow non-admin users to upload a +# directory of files. The configured directory must contain sub-directories +# named the same as the non-admin user's Galaxy login ( email ). The non-admin +# user is restricted to uploading files or sub-directories of files contained +# in their directory. +#user_library_import_dir = /var/opt/galaxy/import/users + +# The admin library upload tool may contain a box allowing admins to paste +# filesystem paths to files and directories to add to a library. Set to True +# to enable. Please note the security implication that this will give Galaxy +# Admins access to anything your Galaxy user has access to. +#allow_library_path_paste = False # path to sendmail sendmail_path = /usr/sbin/sendmail

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[hg] galaxy 2808: If you populate a history before logging in, t...
by Nate Coraor 02 Oct '09

02 Oct '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9cc7a17e0ac7 changeset: 2808:9cc7a17e0ac7 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Sep 30 14:47:17 2009 -0400 description: If you populate a history before logging in, then login, your current history will be the one you populated before logging in - fixes ticket number 163. Also added additional functional tests to cover scenario. 2 file(s) affected in this change: lib/galaxy/web/framework/__init__.py test/functional/test_history_functions.py diffs (65 lines): diff -r aafecc059ba6 -r 9cc7a17e0ac7 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Wed Sep 30 14:11:01 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Wed Sep 30 14:47:17 2009 -0400 @@ -404,18 +404,17 @@ except: users_last_session = None last_accessed = False - if users_last_session and users_last_session.current_history: + if prev_galaxy_session.current_history and prev_galaxy_session.current_history.datasets: + if prev_galaxy_session.current_history.user is None or prev_galaxy_session.current_history.user == user: + # If the previous galaxy session had a history, associate it with the new + # session, but only if it didn't belong to a different user. + history = prev_galaxy_session.current_history + elif self.galaxy_session.current_history: + history = self.galaxy_session.current_history + if not history and users_last_session and users_last_session.current_history: history = users_last_session.current_history - if not history: - if prev_galaxy_session.current_history: - if prev_galaxy_session.current_history.user is None or prev_galaxy_session.current_history.user == user: - # If the previous galaxy session had a history, associate it with the new - # session, but only if it didn't belong to a different user. - history = prev_galaxy_session.current_history - elif self.galaxy_session.current_history: - history = self.galaxy_session.current_history - else: - history = self.get_history( create=True ) + elif not history: + history = self.get_history( create=True ) if history not in self.galaxy_session.histories: self.galaxy_session.add_history( history ) if history.user is None: diff -r aafecc059ba6 -r 9cc7a17e0ac7 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Wed Sep 30 14:11:01 2009 -0400 +++ b/test/functional/test_history_functions.py Wed Sep 30 14:47:17 2009 -0400 @@ -9,11 +9,28 @@ """Testing history behavior between logout and login""" self.logout() self.history_options() - # Make sure we have created the following 4 accounts + # Create a new, empty history named anonymous + name = 'anonymous' + self.new_history( name=name ) + global anonymous_history + anonymous_history = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.deleted==False, + galaxy.model.History.table.c.name==name ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + assert anonymous_history is not None, "Problem retrieving anonymous_history from database" + # Upload a dataset to anonymous_history so it will be set as the current history after login + self.upload_file( '1.bed', dbkey='hg18' ) self.login( email='test1(a)bx.psu.edu' ) global regular_user1 regular_user1 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() assert regular_user1 is not None, 'Problem retrieving user with email "test1(a)bx.psu.edu" from the database' + # Current history should be anonymous_history + self.check_history_for_string( name ) + self.logout() + # Login as the same user again to ensure anonymous_history is still the current history + self.login( email=regular_user1.email ) + self.check_history_for_string( name ) self.logout() self.login( email='test2(a)bx.psu.edu' ) global regular_user2

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galaxy-dev October 2009