June 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Fix the ToolParamSanitizer unit test. Since mercurial imports locale.getpreferredencoding(), which is part of the Python stdlib, the behavior of python strings is re-sorted, so we have to sort them back...
by Bitbucket 01 Jun '11

01 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/cf7ef2464568/ changeset: cf7ef2464568 branches: user: greg date: 2011-06-01 22:21:12 summary: Fix the ToolParamSanitizer unit test. Since mercurial imports locale.getpreferredencoding(), which is part of the Python stdlib, the behavior of python strings is re-sorted, so we have to sort them back... affected #: 1 file (72 bytes) --- a/lib/galaxy/tools/parameters/sanitize.py Wed Jun 01 15:47:04 2011 -0400 +++ b/lib/galaxy/tools/parameters/sanitize.py Wed Jun 01 16:21:12 2011 -0400 @@ -19,7 +19,7 @@ ... <valid initial="string.letters"/> ... </sanitizer> ... ''' ) ) - >>> sanitizer.sanitize_param( string.printable ) == string.letters + >>> sanitizer.sanitize_param( ''.join( sorted( [ c for c in string.printable ] ) ) ) == ''.join( sorted( [ c for c in string.letters ] ) ) True >>> slash = chr( 92 ) >>> sanitizer = ToolParameterSanitizer.from_element( XML( Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes for editing role name, descriptionn, and renaming groups. Resolves issue #539.
by Bitbucket 01 Jun '11

01 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c1d5b67e2090/ changeset: c1d5b67e2090 branches: user: greg date: 2011-06-01 21:47:04 summary: Fixes for editing role name, descriptionn, and renaming groups. Resolves issue #539. affected #: 2 files (479 bytes) --- a/lib/galaxy/web/base/controller.py Wed Jun 01 15:20:43 2011 -0400 +++ b/lib/galaxy/web/base/controller.py Wed Jun 01 15:47:04 2011 -0400 @@ -1278,20 +1278,23 @@ if not new_name: message = 'Enter a valid name' status='error' - elif trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==new_name ).first(): - message = 'A role with that name already exists' - status = 'error' else: - role.name = new_name - role.description = new_description - trans.sa_session.add( role ) - trans.sa_session.flush() - message = "Role '%s' has been renamed to '%s'" % ( old_name, new_name ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='roles', - webapp=webapp, - message=util.sanitize_text( message ), - status='done' ) ) + existing_role = trans.sa_session.query( trans.app.model.Role ).filter( trans.app.model.Role.table.c.name==new_name ).first() + if existing_role and existing_role.id != role.id: + message = 'A role with that name already exists' + status = 'error' + else: + if not ( role.name == new_name and role.description == new_description ): + role.name = new_name + role.description = new_description + trans.sa_session.add( role ) + trans.sa_session.flush() + message = "Role '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='roles', + webapp=webapp, + message=util.sanitize_text( message ), + status='done' ) ) return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, webapp=webapp, @@ -1556,19 +1559,22 @@ if not new_name: message = 'Enter a valid name' status = 'error' - elif trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==new_name ).first(): - message = 'A group with that name already exists' - status = 'error' else: - group.name = new_name - trans.sa_session.add( group ) - trans.sa_session.flush() - message = "Group '%s' has been renamed to '%s'" % ( old_name, new_name ) - return trans.response.send_redirect( web.url_for( controller='admin', - action='groups', - webapp=webapp, - message=util.sanitize_text( message ), - status='done' ) ) + existing_group = trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==new_name ).first() + if existing_group and existing_group.id != group.id: + message = 'A group with that name already exists' + status = 'error' + else: + if group.name != new_name: + group.name = new_name + trans.sa_session.add( group ) + trans.sa_session.flush() + message = "Group '%s' has been renamed to '%s'" % ( old_name, new_name ) + return trans.response.send_redirect( web.url_for( controller='admin', + action='groups', + webapp=webapp, + message=util.sanitize_text( message ), + status='done' ) ) return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, webapp=webapp, --- a/lib/galaxy/web/controllers/admin.py Wed Jun 01 15:20:43 2011 -0400 +++ b/lib/galaxy/web/controllers/admin.py Wed Jun 01 15:47:04 2011 -0400 @@ -169,7 +169,7 @@ global_actions = [ grids.GridAction( "Add new role", dict( controller='admin', action='roles', operation='create' ) ) ] - operations = [ grids.GridOperation( "Rename", + operations = [ grids.GridOperation( "Edit", condition=( lambda item: not item.deleted ), allow_multiple=False, url_args=dict( webapp="galaxy", action="rename_role" ) ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Several data library bug fixes:
by Bitbucket 01 Jun '11

01 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3297ec86d657/ changeset: 3297ec86d657 branches: user: greg date: 2011-06-01 21:20:43 summary: Several data library bug fixes: - Determiining if an accessible dataset exists somewhere in the data library hierarchy now works all the time ( I believe ). It used to work most of the time, but under corner conditions, it would break. - When importing dataset from a history into a data library, the dataset permissions are now correctly applied to the library dataset. The DATASET_MANAGE_PERMISSIONS permission is a spoecial case in that if it exists on the dataset, the LIBRARY_MANAGE permission must be applied to the library dataset. - Fix for message display and db flushing when importing library dataset into a history. - Do not render the folder pop-up menu option for selecting library dataset to import into histories if the folder does not contain any accessible library datasets. affected #: 3 files (2.6 KB) --- a/lib/galaxy/security/__init__.py Wed Jun 01 15:12:12 2011 -0400 +++ b/lib/galaxy/security/__init__.py Wed Jun 01 15:20:43 2011 -0400 @@ -287,8 +287,12 @@ if self.can_access_library_item( roles, library_dataset, user ): return True if search_downward: - for folder in folder.active_folders: - return self.has_accessible_library_datasets( trans, folder, user, roles, search_downward=search_downward ) + return self.__active_folders_have_accessible_library_datasets( trans, folder, user, roles ) + return False + def __active_folders_have_accessible_library_datasets( self, trans, folder, user, roles ): + for active_folder in folder.active_folders: + if self.has_accessible_library_datasets( trans, active_folder, user, roles ): + return True return False def can_access_library_item( self, roles, item, user ): if type( item ) == self.model.Library: --- a/lib/galaxy/web/controllers/library_common.py Wed Jun 01 15:12:12 2011 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Wed Jun 01 15:20:43 2011 -0400 @@ -11,6 +11,7 @@ from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField, WorkflowField, WorkflowMappingField, HistoryField import logging, tempfile, zipfile, tarfile, os, sys, operator from galaxy.eggs import require +from galaxy.security import Action # Whoosh is compatible with Python 2.5+ Try to import Whoosh and set flag to indicate whether tool search is enabled. try: require( "Whoosh" ) @@ -829,7 +830,7 @@ **kwd ) if created_outputs_dict: if cntrller == 'api': - # created_outputs_dict can only ever be a string if cntrller == 'api' + # created_outputs_dict can be a string only if cntrller == 'api' if type( created_outputs_dict ) == str: return 400, created_outputs_dict return 200, created_outputs_dict @@ -1211,6 +1212,27 @@ # LDDA and LibraryDataset. trans.app.security_agent.copy_library_permissions( folder, ldda ) trans.app.security_agent.copy_library_permissions( folder, ldda.library_dataset ) + # Make sure to apply any defined dataset permissions, allowing the permissions inherited from the folder to + # over-ride the same permissions on the dataset, if they exist. + dataset_permissions_dict = trans.app.security_agent.get_permissions( hda.dataset ) + current_library_dataset_actions = [ permission.action for permission in ldda.library_dataset.actions ] + # The DATASET_MANAGE_PERMISSIONS permission on a dataset is a special case because if + # it exists, then we need to apply the LIBRARY_MANAGE permission to the library dataset. + dataset_manage_permissions_action = trans.app.security_agent.get_action( 'DATASET_MANAGE_PERMISSIONS' ).action + flush_needed = False + for action, roles in dataset_permissions_dict.items(): + if isinstance( action, Action ): + action = action.action + if action == dataset_manage_permissions_action: + # Apply the LIBRARY_MANAGE permission to the library dataset. + action = trans.app.security_agent.get_action( 'LIBRARY_MANAGE' ).action + # Allow the permissions inherited from the folder to over-ride the same permissions on the dataset. + if action not in current_library_dataset_actions: + for ldp in [ trans.model.LibraryDatasetPermissions( action, ldda.library_dataset, role ) for role in roles ]: + trans.sa_session.add( ldp ) + flush_needed = True + if flush_needed: + trans.sa_session.flush() # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset trans.app.security_agent.copy_library_permissions( ldda.library_dataset, ldda ) if created_ldda_ids: @@ -1605,7 +1627,7 @@ valid_lddas = [] invalid_lddas = [] for ldda in lddas: - if trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ): + if is_admin or trans.app.security_agent.can_manage_library_item( current_user_roles, ldda ): valid_lddas.append( ldda ) valid_ldda_ids.append( ldda.id ) else: @@ -1634,7 +1656,7 @@ valid_lddas = [] invalid_lddas = [] for ldda in lddas: - if trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ): + if is_admin or trans.app.security_agent.can_modify_library_item( current_user_roles, ldda ): valid_lddas.append( ldda ) else: invalid_lddas.append( ldda ) @@ -1859,6 +1881,7 @@ if len( target_histories ) != len( target_history_ids ): message += "You do not have permission to add datasets to %i requested histories. " % ( len( target_history_ids ) - len( target_histories ) ) status = 'error' + flush_needed = False for ldda in map( trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get, ldda_ids ): if ldda is None: message += "You tried to import a dataset that does not exist. " @@ -1875,15 +1898,18 @@ else: for target_history in target_histories: hda = ldda.to_history_dataset_association( target_history=target_history, add_to_history=True ) - trans.sa_session.flush() - hist_names_str = ", ".join( [ target_history.name for target_history in target_histories ] ) - num_source = len( ldda_ids ) - invalid_datasets - num_target = len( target_histories ) - message = "%i %s imported into %i %s: %s" % ( num_source, - inflector.cond_plural( num_source, "dataset" ), - num_target, - inflector.cond_plural( num_target, "history" ), - hist_names_str ) + if not flush_needed: + flush_needed = True + if flush_needed: + trans.sa_session.flush() + hist_names_str = ", ".join( [ target_history.name for target_history in target_histories ] ) + num_source = len( ldda_ids ) - invalid_datasets + num_target = len( target_histories ) + message += "%i %s imported into %i %s: %s" % ( num_source, + inflector.cond_plural( num_source, "dataset" ), + num_target, + inflector.cond_plural( num_target, "history" ), + hist_names_str ) trans.sa_session.refresh( current_history ) current_user_roles = trans.get_current_user_roles() source_lddas = [] --- a/templates/library/common/browse_library.mako Wed Jun 01 15:12:12 2011 -0400 +++ b/templates/library/common/browse_library.mako Wed Jun 01 15:20:43 2011 -0400 @@ -314,6 +314,7 @@ from galaxy.web.controllers.library_common import active_folders, active_folders_and_library_datasets, activatable_folders_and_library_datasets, branch_deleted is_admin = trans.user_is_admin() and cntrller == 'library_admin' + has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, folder, trans.user, current_user_roles, search_downward=False ) if root_folder: pad = folder_pad @@ -380,7 +381,7 @@ <a class="action-button" href="${h.url_for( controller='library_common', action='create_folder', cntrller=cntrller, parent_id=trans.security.encode_id( folder.id ), library_id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Add sub-folder</a> %endif %if not branch_deleted( folder ): - %if self.has_accessible_datasets: + %if has_accessible_library_datasets: <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a> %endif %if can_modify: @@ -488,6 +489,7 @@ form_type = trans.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE self.has_accessible_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles ) + root_folder_has_accessible_library_datasets = trans.app.security_agent.has_accessible_library_datasets( trans, library.root_folder, trans.user, current_user_roles, search_downward=False ) has_accessible_folders = is_admin or trans.app.security_agent.has_accessible_folders( trans, library.root_folder, trans.user, current_user_roles ) tracked_datasets = {} @@ -500,7 +502,7 @@ def __str__( self ): return str( self.count ) %> - + <h2>Data Library “${library.name}”</h2><ul class="manage-table-actions"> @@ -534,7 +536,7 @@ %endif <a class="action-button" href="${h.url_for( controller='library_common', action='library_permissions', cntrller=cntrller, id=trans.security.encode_id( library.id ), use_panels=use_panels, show_deleted=show_deleted )}">Edit permissions</a> %endif - %if self.has_accessible_datasets: + %if root_folder_has_accessible_library_datasets: <a class="action-button" href="${h.url_for( controller='library_common', action='import_datasets_to_histories', cntrller=cntrller, library_id=trans.security.encode_id( library.id ), folder_id=trans.security.encode_id( library.root_folder.id ), use_panels=use_panels, show_deleted=show_deleted )}">Select datasets for import into selected histories</a> %endif %elif can_modify and not library.purged: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Fix the user create/login links in the FTP upload form
by Bitbucket 01 Jun '11

01 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c1468d790495/ changeset: c1468d790495 branches: user: natefoo date: 2011-06-01 21:12:12 summary: Fix the user create/login links in the FTP upload form affected #: 1 file (34 bytes) --- a/lib/galaxy/web/form_builder.py Wed Jun 01 11:40:38 2011 -0400 +++ b/lib/galaxy/web/form_builder.py Wed Jun 01 15:12:12 2011 -0400 @@ -185,7 +185,7 @@ def get_html( self, prefix="" ): rval = FTPFileField.thead if self.dir is None: - rval += '<tr><td colspan="3"><em>Please <a href="%s">create</a> or <a href="%s">log in to</a> a Galaxy account to view files uploaded via FTP.</em></td></tr>' % ( url_for( controller='user', action='create', referer=url_for( controller='root' ) ), url_for( controller='user', action='login', referer=url_for( controller='root' ) ) ) + rval += '<tr><td colspan="3"><em>Please <a href="%s">create</a> or <a href="%s">log in to</a> a Galaxy account to view files uploaded via FTP.</em></td></tr>' % ( url_for( controller='user', action='create', cntrller='user', referer=url_for( controller='root' ) ), url_for( controller='user', action='login', cntrller='user', referer=url_for( controller='root' ) ) ) elif not os.path.exists( self.dir ): rval += '<tr><td colspan="3"><em>Your FTP upload directory contains no files.</em></td></tr>' else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Minor reformatting for 5609:f530dbdde1f5
by Bitbucket 01 Jun '11

01 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/0a186b0aa953/ changeset: 0a186b0aa953 branches: user: dan date: 2011-06-01 17:40:38 summary: Minor reformatting for 5609:f530dbdde1f5 affected #: 1 file (0 bytes) --- a/lib/galaxy_utils/sequence/vcf.py Wed Jun 01 11:29:07 2011 -0400 +++ b/lib/galaxy_utils/sequence/vcf.py Wed Jun 01 11:40:38 2011 -0400 @@ -2,7 +2,7 @@ #See: http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf3.3 #See: http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:variant_call_… -NOT_A_NUMBER = float( 'NaN ') +NOT_A_NUMBER = float( 'NaN' ) class VariantCall( object ): version = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Allow VCF parser to accept unknown values for QUAL field.
by Bitbucket 01 Jun '11

01 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f530dbdde1f5/ changeset: f530dbdde1f5 branches: user: dan date: 2011-06-01 17:29:07 summary: Allow VCF parser to accept unknown values for QUAL field. affected #: 1 file (139 bytes) --- a/lib/galaxy_utils/sequence/vcf.py Tue May 31 12:03:52 2011 -0400 +++ b/lib/galaxy_utils/sequence/vcf.py Wed Jun 01 11:29:07 2011 -0400 @@ -2,6 +2,8 @@ #See: http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf3.3 #See: http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:variant_call_… +NOT_A_NUMBER = float( 'NaN ') + class VariantCall( object ): version = None header_startswith = None @@ -40,7 +42,10 @@ self.chrom, self.pos, self.id, self.ref, self.alt, self.qual, self.filter, self.info = self.fields[ :self.required_header_length ] self.pos = int( self.pos ) self.alt = self.alt.split( ',' ) - self.qual = float( self.qual ) + try: + self.qual = float( self.qual ) + except: + self.qual = NOT_A_NUMBER #Missing data can be denoted as a '.' if len( self.fields ) > self.required_header_length: self.format = self.fields[ self.required_header_length ].split( ':' ) for sample_value in self.fields[ self.required_header_length + 1: ]: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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