May 2010 - galaxy-commits - lists.galaxyproject.org

[hg] galaxy 3730: lims:
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e12587356892 changeset: 3730:e12587356892 user: rc date: Mon May 03 09:34:13 2010 -0400 description: lims: request page now shows a msg if the request has library selected forms default value bug fixed diffstat: lib/galaxy/model/__init__.py | 6 ++++++ lib/galaxy/web/controllers/forms.py | 4 ++-- templates/admin/requests/show_request.mako | 6 ++++++ 3 files changed, 14 insertions(+), 2 deletions(-) diffs (53 lines): diff -r a367a7cd53bb -r e12587356892 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Sun May 02 15:34:41 2010 -0400 +++ b/lib/galaxy/model/__init__.py Mon May 03 09:34:13 2010 -0400 @@ -1448,6 +1448,12 @@ return self.state() == self.states.NEW def complete(self): return self.state() == self.states.COMPLETE + def sequence_run_ready(self): + samples = [] + for s in self.samples: + if not s.library: + samples.append(s.name) + return samples class RequestEvent( object ): diff -r a367a7cd53bb -r e12587356892 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Sun May 02 15:34:41 2010 -0400 +++ b/lib/galaxy/web/controllers/forms.py Mon May 03 09:34:13 2010 -0400 @@ -469,7 +469,7 @@ 'required': row[3], 'type': row[4], 'selectlist': options, - 'default': row[7]}) + 'default': row[6]}) except: return trans.response.send_redirect( web.url_for( controller='forms', action='new', @@ -565,7 +565,7 @@ # helptext self.helptext.value = field['helptext'] # default value - self.default.value = field['default'] + self.default.value = field.get('default', TextField('field_default_'+str(index), 40, '')) # type self.fieldtype = SelectField('field_type_'+str(self.index), refresh_on_change=True, diff -r a367a7cd53bb -r e12587356892 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Sun May 02 15:34:41 2010 -0400 +++ b/templates/admin/requests/show_request.mako Mon May 03 09:34:13 2010 -0400 @@ -108,6 +108,12 @@ document.onkeypress = stopRKey </script> +%if request.submitted(): + <% samples_not_ready = request.sequence_run_ready() %> + %if samples_not_ready: + ${render_msg( "Select a target library and folder for all the samples before starting the sequence run", "warning" )} + %endif +%endif %if request.rejected(): ${render_msg( "Reason for rejection: "+request.last_comment(), "warning" )}

1 0

[hg] galaxy 3729: Bug fixes for history import: (a) import can n...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/a367a7cd53bb changeset: 3729:a367a7cd53bb user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sun May 02 15:34:41 2010 -0400 description: Bug fixes for history import: (a) import can now be used by users who have access via sharing and (b) import changes the current history to the imported history. Functional tests updated to reflect new functionality and error messages. diffstat: lib/galaxy/web/controllers/history.py | 9 +++------ test/functional/test_history_functions.py | 9 +++++++-- 2 files changed, 10 insertions(+), 8 deletions(-) diffs (56 lines): diff -r 3ac0dfcdf44e -r a367a7cd53bb lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri Apr 30 18:26:49 2010 -0400 +++ b/lib/galaxy/web/controllers/history.py Sun May 02 15:34:41 2010 -0400 @@ -513,7 +513,6 @@ """Import another user's history via a shared URL""" msg = "" user = trans.get_user() - user_history = trans.get_history() # Set referer message if 'referer' in kwd: referer = kwd['referer'] @@ -527,11 +526,9 @@ # Do import. if not id: return trans.show_error_message( "You must specify a history you want to import.<br>You can %s." % referer_message, use_panels=True ) - import_history = self.get_history( trans, id, check_ownership=False ) + import_history = self.get_history( trans, id, check_ownership=False, check_accessible=True ) if not import_history: return trans.show_error_message( "The specified history does not exist.<br>You can %s." % referer_message, use_panels=True ) - if not import_history.importable: - return trans.show_error_message( "The owner of this history has disabled imports via this link.<br>You can %s." % referer_message, use_panels=True ) if user: if import_history.user_id == user.id: return trans.show_error_message( "You cannot import your own history.<br>You can %s." % referer_message, use_panels=True ) @@ -548,8 +545,8 @@ new_history.add_galaxy_session( galaxy_session, association=association ) trans.sa_session.add( new_history ) trans.sa_session.flush() - if not user_history.datasets: - trans.set_history( new_history ) + # Set imported history to be user's current history. + trans.set_history( new_history ) return trans.show_ok_message( message="""History "%s" has been imported. <br>You can <a href="%s">start using this history</a> or %s.""" % ( new_history.name, web.url_for( '/' ), referer_message ), use_panels=True ) diff -r 3ac0dfcdf44e -r a367a7cd53bb test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Fri Apr 30 18:26:49 2010 -0400 +++ b/test/functional/test_history_functions.py Sun May 02 15:34:41 2010 -0400 @@ -196,10 +196,15 @@ self.disable_access_via_link( self.security.encode_id( history3.id ), check_str='Anyone can view and import this history', check_str_after_submit='Make History Accessible via Link' ) - # Try importing history3 after disabling access via link. + # Try importing history3 after disabling access via link. To do this, need to login as regular user 2, who cannot access + # history via sharing or via link. + self.logout() + self.login( email=regular_user2.email ) self.import_history_via_url( self.security.encode_id( history3.id ), admin_user.email, - check_str_after_submit='The owner of this history has disabled imports via this link.' ) + check_str_after_submit='History is not accessible to current user' ) + self.logout() + self.login( email=admin_user.email ) # Test sharing history3 with an invalid user self.share_current_history( 'jack(a)jill.com', check_str_after_submit='jack(a)jill.com is not a valid Galaxy user.' )

1 0

[hg] galaxy 3728: merge
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/3ac0dfcdf44e changeset: 3728:3ac0dfcdf44e user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Apr 30 18:26:49 2010 -0400 description: merge diffstat: lib/galaxy/web/framework/__init__.py | 4 +- lib/galaxy/webapps/community/controllers/admin.py | 385 +++++++-- lib/galaxy/webapps/community/controllers/common.py | 105 ++- lib/galaxy/webapps/community/controllers/tool.py | 293 +++++-- lib/galaxy/webapps/community/controllers/upload.py | 68 +- lib/galaxy/webapps/community/model/__init__.py | 7 +- lib/galaxy/webapps/community/model/mapping.py | 14 +- lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py | 3 +- lib/galaxy/webapps/community/security/__init__.py | 6 + templates/webapps/community/admin/index.mako | 43 +- templates/webapps/community/category/edit_category.mako | 44 + templates/webapps/community/category/rename_category.mako | 44 - templates/webapps/community/index.mako | 64 +- templates/webapps/community/tool/browse_tool.mako | 37 - templates/webapps/community/tool/edit_tool.mako | 3 +- templates/webapps/community/tool/view_tool.mako | 58 +- templates/webapps/community/upload/upload.mako | 3 + tools/samtools/sam_to_bam.py | 2 +- tools/sr_mapping/bowtie_wrapper.py | 4 +- tools/sr_mapping/bwa_wrapper_code.py | 9 +- 20 files changed, 883 insertions(+), 313 deletions(-) diffs (1884 lines): diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Apr 30 18:26:49 2010 -0400 @@ -66,7 +66,7 @@ decorator.exposed = True return decorator -def require_login( verb="perform this action", use_panels=False ): +def require_login( verb="perform this action", use_panels=False, webapp='galaxy' ): def argcatcher( func ): def decorator( self, trans, *args, **kwargs ): if trans.get_user(): @@ -74,7 +74,7 @@ else: return trans.show_error_message( 'You must be <a target="_top" href="%s">logged in</a> to %s</div>.' - % ( url_for( controller='user', action='login' ), verb ), use_panels=use_panels ) + % ( url_for( controller='user', action='login', webapp=webapp ), verb ), use_panels=use_panels ) return decorator return argcatcher diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 18:26:49 2010 -0400 @@ -2,7 +2,7 @@ from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids -from common import get_categories, get_category +from common import get_categories, get_category, get_tools, get_event, get_tool, get_versions import logging log = logging.getLogger( __name__ ) @@ -18,13 +18,6 @@ if user.username: return user.username return 'not set' - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.purged: - return "purged" - elif user.deleted: - return "deleted" - return "" class GroupsColumn( grids.GridColumn ): def get_value( self, trans, grid, user ): if user.groups: @@ -45,6 +38,16 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.purged: + return "purged" + elif user.deleted: + return "deleted" + return "" + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( user.id ), str( len( user.tools ) ) ) # Grid definition webapp = "community" @@ -69,6 +72,10 @@ ExternalColumn( "External", attach_popup=False ), LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), + ToolsColumn( "Uploaded Tools", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -200,7 +207,7 @@ return None def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): return query.filter( model.Role.type != model.Role.types.PRIVATE ) class GroupListGrid( grids.Grid ): @@ -280,34 +287,31 @@ def build_initial_query( self, session ): return session.query( self.model_class ) -class CategoryListGrid( grids.Grid ): +class ManageCategoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.name class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.description - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, category ): - if category.deleted: - return "deleted" - return "" # Grid definition webapp = "community" - title = "Categories" + title = "Manage Categories" model_class = model.Category template='/webapps/community/category/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="Edit category", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Edit", id=item.id, webapp="community" ) ), model_class=model.Category, - attach_popup=True, + attach_popup=False, filterable="advanced" ), - DescriptionColumn( "Description", attach_popup=False ), - StatusColumn( "Status", attach_popup=False ), + DescriptionColumn( "Description", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -318,13 +322,9 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Add new category", - dict( controller='admin', action='categories', operation='create', webapp="community" ) ) + dict( controller='admin', action='manage_categories', operation='create', webapp="community" ) ) ] - operations = [ grids.GridOperation( "Rename", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( webapp="community", action="rename_category" ) ), - grids.GridOperation( "Delete", + operations = [ grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True, url_args=dict( webapp="community", action="mark_category_deleted" ) ), @@ -349,16 +349,77 @@ def build_initial_query( self, session ): return session.query( self.model_class ) +class ToolsByCategoryListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + return category.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + return category.description + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + if category.tools: + return len( category.tools ) + return 0 + + # Grid definition + webapp = "community" + title = "Tools by Category" + model_class = model.Category + template='/webapps/community/category/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="Browse Category", id=item.id, webapp="community" ) ), + model_class=model.Category, + attach_popup=True, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + ToolsColumn( "Tools", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def get_current_item( self, trans ): + return None + def build_initial_query( self, session ): + return session.query( self.model_class ) + class ToolListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): if tool.categories: rval = '' for tca in tool.categories: - rval = '%s%s<br/>' % ( rval, tca.category.name ) + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' class StateColumn( grids.GridColumn ): @@ -389,7 +450,7 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return tool.user.email + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition title = "Tools" model_class = model.Tool @@ -402,36 +463,39 @@ link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='admin', webapp="community" ) ), attach_popup=True, filterable="advanced" ), + VersionColumn( "Version", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), CategoryColumn( "Category", - key="category", model_class=model.Category, attach_popup=False, filterable="advanced" ), - StateColumn( "State", - key="state", + StateColumn( "Status", model_class=model.Event, - attach_popup=False, - filterable="advanced" ), + attach_popup=False ), + UserColumn( "Uploaded By", + key="username", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", model_class=model.Tool, key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) ) - global_actions = [ - grids.GridAction( "Upload tool", dict( controller='upload', action='upload', type='tool' ) ) - ] operations = [ grids.GridOperation( "Edit information", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( controller="common", action="edit_tool", cntrller="admin", webapp="community" ) ), - grids.GridOperation( "Manage categories", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( controller="common", action="manage_categories", cntrller="admin", webapp="community" ) ) + url_args=dict( controller="common", action="edit_tool", cntrller="admin", webapp="community" ) ) ] standard_filters = [ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), @@ -443,57 +507,128 @@ use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): + tool_id = kwd.get( 'tool_id', False ) + if tool_id: + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) return query.filter( self.model_class.deleted==False ) -class AdminCommunity( BaseController, Admin ): +class AdminController( BaseController, Admin ): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() group_list_grid = GroupListGrid() - category_list_grid = CategoryListGrid() + manage_category_list_grid = ManageCategoryListGrid() + tools_by_category_list_grid = ToolsByCategoryListGrid() tool_list_grid = ToolListGrid() @web.expose @web.require_admin - def browse_tools( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def browse_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='admin', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='admin', + **kwd ) ) + # Render the list view + return self.tool_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_category( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse category": + return self.browse_category( trans, id=kwd['id'] ) + # Render the list view + return self.tools_by_category_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_user( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "browse": - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tools', + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_tools_by_user', cntrller='admin', - **kwargs ) ) + **kwd ) ) + elif operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='admin', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='admin', + **kwd ) ) elif operation == "edit tool": return trans.response.send_redirect( web.url_for( controller='common', action='edit_tool', cntrller='admin', - **kwargs ) ) - elif operation == "view tool": - return trans.response.send_redirect( web.url_for( controller='common', - action='view_tool', - cntrller='admin', - **kwargs ) ) + **kwd ) ) + elif operation == "download tool": + return trans.response.send_redirect( web.url_for( controller='tool', + action='download_tool', + **kwd ) ) # Render the list view - return self.tool_list_grid( trans, **kwargs ) + return self.tool_list_grid( trans, **kwd ) @web.expose @web.require_admin - def categories( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def manage_categories( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "create": - return self.create_category( trans, **kwargs ) + return self.create_category( trans, **kwd ) if operation == "delete": - return self.mark_category_deleted( trans, **kwargs ) + return self.mark_category_deleted( trans, **kwd ) if operation == "undelete": - return self.undelete_category( trans, **kwargs ) + return self.undelete_category( trans, **kwd ) if operation == "purge": - return self.purge_category( trans, **kwargs ) - if operation == "rename": - return self.rename_category( trans, **kwargs ) + return self.purge_category( trans, **kwd ) + if operation == "edit": + return self.edit_category( trans, **kwd ) # Render the list view - return self.category_list_grid( trans, **kwargs ) - + return self.manage_category_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_state( self, trans, state=None, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if state is None: + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message='Select a status', + status='error' ) ) + event = get_event( trans, id ) + state = event.state + tool_id = get_tools_by_state( trans, state ) + if not tool_id: + tool_id = 'None' + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools', + tool_id=tool_id ) ) + @web.expose + @web.require_admin + def browse_category( self, trans, **kwd ): + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='admin', + **kwd ) ) @web.expose @web.require_admin def create_category( self, trans, **kwd ): @@ -515,7 +650,7 @@ message = "Category '%s' has been created" % category.name trans.sa_session.flush() trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -530,42 +665,76 @@ status=status ) @web.expose @web.require_admin - def rename_category( self, trans, **kwd ): + def set_tool_state( self, trans, state, **kwd ): + params = util.Params( kwd ) + webapp = params.get( 'webapp', 'galaxy' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + redirect = params.get( 'no_redirect', True ) + id = params.get( 'id', None ) + if not id: + message = "No tool id received for setting status" + status = 'error' + else: + tool = get_tool( trans, id ) + if state == trans.app.model.Tool.states.APPROVED: + # If we're approving a tool, all previous versions must be set to archived + for version in get_versions( trans, tool ): + if version != tool and version.is_approved(): + self.set_tool_state( trans, trans.app.model.Tool.states.ARCHIVED, id=trans.app.security.encode_id( version.id ), redirect='False' ) + event = trans.model.Event( state ) + # Flush so we an get an id + trans.sa_session.add( event ) + trans.sa_session.flush() + tea = trans.model.ToolEventAssociation( tool, event ) + trans.sa_session.add( tea ) + trans.sa_session.flush() + message = "State of tool '%s' is now %s" % ( tool.name, state ) + if redirect: + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools', + webapp=webapp, + message=message, + status=status ) ) + @web.expose + @web.require_admin + def edit_category( self, trans, **kwd ): params = util.Params( kwd ) webapp = params.get( 'webapp', 'galaxy' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) id = params.get( 'id', None ) if not id: - message = "No category ids received for renaming" + message = "No category ids received for editing" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) category = get_category( trans, id ) - if params.get( 'rename_category_button', False ): + if params.get( 'edit_category_button', False ): old_name = category.name new_name = util.restore_text( params.name ) new_description = util.restore_text( params.description ) - if not new_name: - message = 'Enter a valid name' - status = 'error' - elif trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): - message = 'A category with that name already exists' - status = 'error' + if old_name != new_name: + if not new_name: + message = 'Enter a valid name' + status = 'error' + elif trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): + message = 'A category with that name already exists' + status = 'error' else: category.name = new_name category.description = new_description trans.sa_session.add( category ) trans.sa_session.flush() - message = "Category '%s' has been renamed to '%s'" % ( old_name, new_name ) + message = "The information has been saved for category '%s'" % ( new_name ) return trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) - return trans.fill_template( '/webapps/community/category/rename_category.mako', + return trans.fill_template( '/webapps/community/category/edit_category.mako', category=category, webapp=webapp, message=message, @@ -579,7 +748,7 @@ if not id: message = "No category ids received for deleting" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) @@ -592,7 +761,7 @@ trans.sa_session.flush() message += " %s " % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -605,7 +774,7 @@ if not id: message = "No category ids received for undeleting" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) @@ -617,7 +786,7 @@ if not category.deleted: message = "Category '%s' has not been deleted, so it cannot be undeleted." % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -628,7 +797,7 @@ undeleted_categories += " %s" % category.name message = "Undeleted %d categories: %s" % ( count, undeleted_categories ) trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -644,7 +813,7 @@ if not id: message = "No category ids received for purging" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -655,7 +824,7 @@ if not category.deleted: message = "Category '%s' has not been deleted, so it cannot be purged." % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -665,7 +834,41 @@ trans.sa_session.flush() message += " %s " % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) + +## ---- Utility methods ------------------------------------------------------- + +def get_tools_by_state( trans, state ): + tool_id = [] + if state == trans.model.Tool.states.NEW: + for tool in get_tools( trans ): + if tool.is_new(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.ERROR: + for tool in get_tools( trans ): + if tool.is_error(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.DELETED: + for tool in get_tools( trans ): + if tool.is_deleted(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.WAITING: + for tool in get_tools( trans ): + if tool.is_waiting(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.APPROVED: + for tool in get_tools( trans ): + if tool.is_approved(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.REJECTED: + for tool in get_tools( trans ): + if tool.is_rejected(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.ARCHIVED: + for tool in get_tools( trans ): + if tool.is_archived(): + tool_id.append( tool.id ) + return tool_id diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 18:26:49 2010 -0400 @@ -8,7 +8,7 @@ import logging log = logging.getLogger( __name__ ) -class CommunityCommon( BaseController ): +class CommonController( BaseController ): @web.expose def edit_tool( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -81,9 +81,11 @@ tool = get_tool( trans, id ) categories = [ tca.category for tca in tool.categories ] tool_file_contents = tarfile.open( tool.file_name, 'r' ).getnames() + versions = get_versions( trans, tool ) return trans.fill_template( '/webapps/community/tool/view_tool.mako', tool=tool, tool_file_contents=tool_file_contents, + versions=versions, categories=categories, cntrller=cntrller, message=message, @@ -100,22 +102,78 @@ message='Select a tool to to upload a new version', status='error' ) ) tool = get_tool( trans, id ) - if params.save_button and ( params.file_data != '' or params.url != '' ): - # TODO: call the upload method in the upload controller. - message = 'Uploading new version not implemented' - status = 'error' + return trans.response.send_redirect( web.url_for( controller='upload', + action='upload', + message=message, + status=status, + replace_id=id ) ) + @web.expose + def browse_category( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_categories', + message='Select a category', + status='error' ) ) + category = get_category( trans, id ) + # If request came from the tool controller, then we need to filter by the state of the + # tool in addition to the category. + if cntrller == 'tool': + tool_id = get_approved_tools( trans, category=category ) + else: + # If request came from the admin controller, we don't filter on tool state. + tool_id = [ tca.tool.id for tca in category.tools ] + if not tool_id: + tool_id = 'None' return trans.response.send_redirect( web.url_for( controller=cntrller, action='browse_tools', - message='Not yet implemented, sorry...', - status='error' ) ) + tool_id=tool_id ) ) + @web.expose + def browse_tools_by_user( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message='Select a user', + status='error' ) ) + user = get_user( trans, id ) + # If request came from the tool controller, then we need to filter by the state of the + # tool if the user is not viewing his own tools + if cntrller == 'tool': + tool_id = get_approved_tools( trans, user=user ) + else: + # If request came from the admin controller, we don't filter on tool state. + tool_id = [ tool.id for tool in user.tools ] + if not tool_id: + tool_id = 'None' + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools_by_user', + tool_id=tool_id ) ) ## ---- Utility methods ------------------------------------------------------- +def get_versions( trans, tool ): + versions = [tool] + this_tool = tool + while tool.newer_version: + versions.insert( 0, tool.newer_version ) + tool = tool.newer_version + tool = this_tool + while tool.older_version: + versions.append( tool.older_version[0] ) + tool = tool.older_version[0] + return versions def get_categories( trans ): """Get all categories from the database""" return trans.sa_session.query( trans.model.Category ) \ .filter( trans.model.Category.table.c.deleted==False ) \ - .order_by( trans.model.Category.table.c.name ) + .order_by( trans.model.Category.table.c.name ).all() def get_unassociated_categories( trans, obj ): """Get all categories from the database that are not associated with obj""" # TODO: we currently assume we are setting a tool category, so this method may need @@ -142,4 +200,33 @@ obj.categories.append( trans.model.ToolCategoryAssociation( obj, category ) ) def get_tool( trans, id ): return trans.sa_session.query( trans.model.Tool ).get( trans.app.security.decode_id( id ) ) - +def get_tools( trans ): + return trans.sa_session.query( trans.model.Tool ).order_by( trans.model.Tool.name ) +def get_approved_tools( trans, category=None, user=None ): + tool_id = [] + if category: + # Return only the approved tools in the category + for tca in category.tools: + tool = tca.tool + if tool.is_approved(): + tool_id.append( tool.id ) + elif user: + if trans.user == user: + # If the current user is browsing his own tools, then don't filter on state + tool_id = [ tool.id for tool in user.tools ] + else: + # The current user is viewing all tools uploaded by another user, so show only + # approved tools + for tool in user.active_tools: + if tool.is_approved(): + tool_id.append( tool.id ) + else: + # Return all approved tools + for tool in get_tools( trans ): + if tool.is_approved(): + tool_id.append( tool.id ) + return tool_id +def get_event( trans, id ): + return trans.sa_session.query( trans.model.Event ).get( trans.security.decode_id( id ) ) +def get_user( trans, id ): + return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/controllers/tool.py --- a/lib/galaxy/webapps/community/controllers/tool.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/tool.py Fri Apr 30 18:26:49 2010 -0400 @@ -15,38 +15,111 @@ class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): if tool.categories: rval = '' for tca in tool.categories: - rval += '%s<br/>\n' % tca.category.name + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' - def filter( self, trans, user, query, column_filter ): - # Category.name conflicts with Tool.name, so we have to make our own filter - def get_single_filter( filter ): - return func.lower( model.Category.name ).like( "%" + filter.lower() + "%" ) - if column_filter == 'All': - pass - elif isinstance( column_filter, list ): - clause_list = [] - for filter in column_filter: - clause_list.append( get_single_filter( filter ) ) - query = query.filter( or_( *clause_list ) ) - else: - query = query.filter( get_single_filter( column_filter ) ) - return query - def get_link( self, trans, grid, tool, filter_params ): + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) + # Grid definition + title = "Tools" + model_class = model.Tool + template='/webapps/community/tool/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + model_class=model.Tool, + link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), + attach_popup=True, + filterable="advanced" ), + VersionColumn( "Version", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + CategoryColumn( "Categories", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + UserColumn( "Uploaded By", + key="username", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ + grids.GridOperation( "Download tool", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( controller="tool", action="download_tool", cntrller="tool", webapp="community" ) ) + ] + standard_filters = [ + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + default_filter = dict( name="All", deleted="False", username="All" ) + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, session ): + return session.query( self.model_class ) + def apply_default_filter( self, trans, query, **kwd ): + def filter_query( query, tool_id ): + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) + return query.filter( self.model_class.deleted==False ) + tool_id = kwd.get( 'tool_id', False ) + if not tool_id: + # Display only approved tools + tool_id = get_approved_tools( trans ) + if not tool_id: + tool_id = 'None' + return filter_query( query, tool_id ) + +class ToolsByUserListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description + class CategoryColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): if tool.categories: - filter_params['f-category'] = [] + rval = '' for tca in tool.categories: - filter_params['f-category'].append( tca.category.name ) - if len( filter_params['f-category'] ) == 1: - filter_params['f-category'] = filter_params['f-category'][0] - filter_params['advanced-search'] = 'True' - return filter_params - return None + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) + return rval + return 'not set' class StateColumn( grids.GridColumn ): def get_value( self, trans, grid, tool ): state = tool.state() @@ -75,13 +148,9 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return tool.user.username - def get_link( self, trans, grid, tool, filter_params ): - filter_params['f-username'] = tool.user.username - filter_params['advanced-search'] = 'True' - return filter_params + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition - title = "Tools" + title = "Tools By User" model_class = model.Tool template='/webapps/community/tool/grid.mako' default_sort_key = "name" @@ -92,21 +161,26 @@ link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), attach_popup=True, filterable="advanced" ), - CategoryColumn( "Categories", - key="category", + VersionColumn( "Version", model_class=model.Tool, attach_popup=False, filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + CategoryColumn( "Categories", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + StateColumn( "Status", + model_class=model.Event, + attach_popup=False ), UserColumn( "Uploaded By", key="username", model_class=model.User, attach_popup=False, filterable="advanced" ), - StateColumn( "State", - key="state", - model_class=model.Event, - attach_popup=False, - filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -130,18 +204,44 @@ preserve_state = False use_paging = True def build_initial_query( self, session ): - return session.query( self.model_class ).outerjoin( model.ToolCategoryAssociation ).outerjoin( model.Category ) - def apply_default_filter( self, trans, query, **kwargs ): - return query.filter( self.model_class.deleted==False ) + return session.query( self.model_class ) + def apply_default_filter( self, trans, query, **kwd ): + def filter_query( query, tool_id ): + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) + return query.filter( self.model_class.deleted==False ) + tool_id = kwd.get( 'tool_id', False ) + if not tool_id: + # Display only approved tools + tool_id = get_approved_tools( trans ) + if not tool_id: + tool_id = 'None' + return filter_query( query, tool_id ) -class ToolCategoryListGrid( grids.Grid ): +class CategoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.name class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.description + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + if category.tools: + viewable_tools = 0 + for tca in category.tools: + tool = tca.tool + if tool.is_approved(): + viewable_tools += 1 + return viewable_tools + return 0 + # Grid definition + webapp = "community" title = "Tool Categories" model_class = model.Category template='/webapps/community/category/grid.mako' @@ -157,7 +257,13 @@ key="description", model_class=model.Category, attach_popup=False, - filterable="advanced" ) + filterable="advanced" ), + ToolsColumn( "Tools", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -165,21 +271,23 @@ visible=False, filterable="standard" ) ) standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) ] - default_filter = dict( name="All", deleted="False" ) num_rows_per_page = 50 preserve_state = False use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): return query.filter( self.model_class.deleted==False ) -class ToolBrowserController( BaseController ): - - tool_category_list_grid = ToolCategoryListGrid() +class ToolController( BaseController ): + tool_list_grid = ToolListGrid() + tools_by_user_list_grid = ToolsByUserListGrid() + category_list_grid = CategoryListGrid() @web.expose def index( self, trans, **kwd ): @@ -188,53 +296,84 @@ status = params.get( 'status', 'done' ) return trans.fill_template( '/webapps/community/index.mako', message=message, status=status ) @web.expose - def browse_tool_categories( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def browse_categories( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "browse category": - category_id = int( trans.app.security.decode_id( kwargs['id'] ) ) - category = trans.sa_session.query( model.Category ).get( category_id ) - del kwargs['id'] - del kwargs['operation'] - kwargs['f-category'] = category.name - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tools', - **kwargs ) ) - return self.tool_category_list_grid( trans, **kwargs ) + return self.browse_category( trans, id=kwd['id'] ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_category', + cntrller='tool', + **kwd ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_category', + cntrller='tool', + **kwd ) ) + # Render the list view + return self.category_list_grid( trans, **kwd ) @web.expose - def browse_tools( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() - if operation == "browse": - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tool', + def browse_category( self, trans, **kwd ): + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='tool', + **kwd ) ) + @web.expose + def browse_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "view tool": return trans.response.send_redirect( web.url_for( controller='common', action='view_tool', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "edit tool": return trans.response.send_redirect( web.url_for( controller='common', action='edit_tool', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "download tool": return trans.response.send_redirect( web.url_for( controller='tool', action='download_tool', - **kwargs ) ) + **kwd ) ) # Render the list view - return self.tool_list_grid( trans, **kwargs ) + return self.tool_list_grid( trans, **kwd ) @web.expose - def browse_tool( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - return trans.fill_template( '/webapps/community/tool/browse_tool.mako', - tools=tools, - message=message, - status=status ) + def browse_tools_by_user( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_tools_by_user', + cntrller='tool', + **kwd ) ) + elif operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='tool', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='tool', + **kwd ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='tool', + **kwd ) ) + elif operation == "download tool": + return trans.response.send_redirect( web.url_for( controller='tool', + action='download_tool', + **kwd ) ) + # Render the list view + return self.tools_by_user_list_grid( trans, **kwd ) @web.expose def download_tool( self, trans, **kwd ): params = util.Params( kwd ) diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 30 18:26:49 2010 -0400 @@ -3,23 +3,36 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.model.orm import * from galaxy.webapps.community import datatypes -from common import get_categories, get_category +from common import get_categories, get_category, get_versions log = logging.getLogger( __name__ ) # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" +class UploadError( Exception ): + pass + class UploadController( BaseController ): @web.expose + @web.require_login( 'upload', use_panels=True, webapp='community' ) def upload( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) category_ids = util.listify( params.get( 'category_id', '' ) ) + replace_id = params.get( 'replace_id', None ) + replace_version = None uploaded_file = None - if params.file_data == '' and params.url.strip() == '': + categories = get_categories( trans ) + if not get_categories( trans ): + return trans.response.send_redirect( web.url_for( controller='tool', + action='browse_tools', + cntrller='tool', + message='No categories have been configured in this instance of the Galaxy Community. An administrator needs to create some via the Administrator control panel before anything can be uploaded', + status='error' ) ) + elif params.file_data == '' and params.url.strip() == '': message = 'No files were entered on the upload form.' status = 'error' elif params.file_data == '': @@ -47,6 +60,29 @@ obj = datatype.create_model_object( meta ) trans.sa_session.add( obj ) if isinstance( obj, trans.app.model.Tool ): + existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).all() + if existing and replace_id is None: + raise UploadError( 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' ) + elif existing: + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) + if replace_version.newer_version: + # If the user has picked an old version, switch to the newest version + replace_version = get_versions( trans, replace_version )[0] + if trans.user != replace_version.user: + raise UploadError( 'You are not the owner of this tool and may not upload new versions of it.' ) + if replace_version.tool_id != meta.id: + raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Please check the tool XML file' % ( meta.id, replace_version.tool_id ) ) + for old_version in get_versions( trans, replace_version ): + if old_version.version == meta.version: + raise UploadError( 'The new version (%s) matches an old version. Please check your version in the tool XML file' % meta.version ) + if old_version.is_new(): + raise UploadError( 'There is an existing version of this tool which is unsubmitted. Please either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.app.security.encode_id( old_version.id ) ) ) + if old_version.is_waiting(): + raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' ) + # Defer setting the id since the newer version id doesn't exist until the new Tool object is flushed if category_ids: for category_id in category_ids: category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) @@ -58,6 +94,9 @@ tea = trans.app.model.ToolEventAssociation( obj, event ) trans.sa_session.add_all( ( event, tea ) ) trans.sa_session.flush() + if replace_version and replace_id: + replace_version.newer_version_id = obj.id + trans.sa_session.flush() try: os.link( uploaded_file.name, obj.file_name ) except OSError: @@ -69,13 +108,29 @@ id=trans.app.security.encode_id( obj.id ), message='Uploaded %s' % meta.message, status='done' ) ) - except datatypes.DatatypeVerificationError, e: + except ( datatypes.DatatypeVerificationError, UploadError ), e: message = str( e ) status = 'error' - except sqlalchemy.exc.IntegrityError: - message = 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' - status = 'error' uploaded_file.close() + elif replace_id is not None: + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) + old_version = None + for old_version in get_versions( trans, replace_version ): + if old_version.is_new(): + message = 'There is an existing version of this tool which is unsubmitted. Please either submit or delete it before uploading a new version.' + break + if old_version.is_waiting(): + message = 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' + break + else: + old_version = None + if old_version is not None: + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.app.security.encode_id( old_version.id ), + message=message, + status='error' ) ) selected_upload_type = params.get( 'type', 'tool' ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/upload/upload.mako', @@ -83,5 +138,6 @@ status=status, selected_upload_type=selected_upload_type, upload_types=trans.app.datatypes_registry.get_datatypes_for_select_list(), + replace_id=replace_id, selected_categories=selected_categories, categories=get_categories( trans ) ) diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Fri Apr 30 18:26:49 2010 -0400 @@ -92,7 +92,8 @@ DELETED = 'deleted', WAITING = 'waiting for approval', APPROVED = 'approved', - REJECTED = 'rejected' ) + REJECTED = 'rejected', + ARCHIVED = 'archived' ) def __init__( self, guid=None, tool_id=None, name=None, description=None, user_description=None, category=None, version=None, user_id=None, external_filename=None ): self.guid = guid self.tool_id = tool_id @@ -153,10 +154,14 @@ return self.state() == self.states.ERROR def is_deleted( self ): return self.state() == self.states.DELETED + def is_waiting( self ): + return self.state() == self.states.WAITING def is_approved( self ): return self.state() == self.states.APPROVED def is_rejected( self ): return self.state() == self.states.REJECTED + def is_archived( self ): + return self.state() == self.states.ARCHIVED @property def extension( self ): # if instantiated via a query, this unmapped property won't exist diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 18:26:49 2010 -0400 @@ -103,9 +103,10 @@ Tool.table = Table( "tool", metadata, Column( "id", Integer, primary_key=True ), Column( "guid", TrimmedString( 255 ), index=True, unique=True ), - Column( "tool_id", TrimmedString( 255 ), index=True, unique=True ), + Column( "tool_id", TrimmedString( 255 ), index=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "newer_version_id", Integer, ForeignKey( "tool.id" ), nullable=True ), Column( "name", TrimmedString( 255 ), index=True ), Column( "description" , TEXT ), Column( "user_description" , TEXT ), @@ -164,8 +165,8 @@ # With the tables defined we can define the mappers and setup the # relationships between the model objects. assign_mapper( context, User, User.table, - properties=dict( tools=relation( Tool, order_by=desc( Tool.table.c.update_time ) ), - active_tools=relation( Tool, primaryjoin=( ( Tool.table.c.user_id == User.table.c.id ) & ( not_( Tool.table.c.deleted ) ) ), order_by=desc( Tool.table.c.update_time ) ), + properties=dict( tools=relation( Tool, primaryjoin=( Tool.table.c.user_id == User.table.c.id ), order_by=( Tool.table.c.name ) ), + active_tools=relation( Tool, primaryjoin=( ( Tool.table.c.user_id == User.table.c.id ) & ( not_( Tool.table.c.deleted ) ) ), order_by=( Tool.table.c.name ) ), galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ) ) ) assign_mapper( context, Group, Group.table, @@ -215,7 +216,11 @@ properties = dict( categories=relation( ToolCategoryAssociation ), events=relation( ToolEventAssociation ), - user=relation( User.mapper ) + user=relation( User.mapper ), + older_version=relation( + Tool, + primaryjoin=( Tool.table.c.newer_version_id == Tool.table.c.id ), + backref=backref( "newer_version", primaryjoin=( Tool.table.c.newer_version_id == Tool.table.c.id ), remote_side=[Tool.table.c.id] ) ) ) ) assign_mapper( context, Event, Event.table, @@ -238,7 +243,6 @@ ) ) - def guess_dialect_for_url( url ): return (url.split(':', 1))[0] diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py --- a/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Fri Apr 30 18:26:49 2010 -0400 @@ -80,9 +80,10 @@ Tool_table = Table( "tool", metadata, Column( "id", Integer, primary_key=True ), Column( "guid", TrimmedString( 255 ), index=True, unique=True ), - Column( "tool_id", TrimmedString( 255 ), index=True, unique=True ), + Column( "tool_id", TrimmedString( 255 ), index=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "newer_version_id", Integer, ForeignKey( "tool.id" ), nullable=True ), Column( "name", TrimmedString( 255 ), index=True ), Column( "description" , TEXT ), Column( "user_description" , TEXT ), diff -r 8e00344d941a -r 3ac0dfcdf44e lib/galaxy/webapps/community/security/__init__.py --- a/lib/galaxy/webapps/community/security/__init__.py Fri Apr 30 18:26:06 2010 -0400 +++ b/lib/galaxy/webapps/community/security/__init__.py Fri Apr 30 18:26:49 2010 -0400 @@ -167,6 +167,12 @@ # We currently assume the current user can edit the item if they are the owner (i.e., they # uploaded the item), and the item is in a NEW state. return user and user==item.user and item.is_new() + def can_upload_new_version( self, user, item, versions ): + state_ok = True + for version in versions: + if version.is_new() or version.is_approved(): + state_ok = False + return user and user==item.user and state_ok def get_permitted_actions( filter=None ): '''Utility method to return a subset of RBACAgent's permitted actions''' diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako Fri Apr 30 18:26:06 2010 -0400 +++ b/templates/webapps/community/admin/index.mako Fri Apr 30 18:26:49 2010 -0400 @@ -54,7 +54,6 @@ </style> </%def> - <%def name="init()"> <% self.has_left_panel=True @@ -71,32 +70,34 @@ <div class="toolMenu"> <div class="toolSectionList"> <div class="toolSectionTitle"> + <span>Tools</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools_by_state', state=trans.model.Tool.states.WAITING, webapp='community' )}">Tools awaiting approval</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools_by_category' )}">Browse by category</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools', webapp='community' )}">Browse all tools</a></div> + </div> + </div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + <span>Categories</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories', webapp='community' )}">Manage categories</a></div> + </div> + </div> + <div class="toolSectionTitle"> <span>Security</span> </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users', webapp='community' )}" target="galaxy_main">Manage users</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups', webapp='community' )}" target="galaxy_main">Manage groups</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles', webapp='community' )}" target="galaxy_main">Manage roles</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='users', webapp='community' )}">Manage users</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='groups', webapp='community' )}">Manage groups</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='roles', webapp='community' )}">Manage roles</a></div> </div> </div> - <div class="toolSectionTitle"> - <span>Tools</span> - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tools', webapp='community' )}" target="galaxy_main">Manage tools</a></div> - </div> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - <span>Community</span> - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='categories', webapp='community' )}" target="galaxy_main">Manage categories</a></div> - </div> - </div> </div> </div> </div> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/category/edit_category.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/category/edit_category.mako Fri Apr 30 18:26:49 2010 -0400 @@ -0,0 +1,44 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Change category name and description</div> + <div class="toolFormBody"> + <form name="library" action="${h.url_for( controller='admin', action='edit_category' )}" method="post" > + <div class="form-row"> + <input name="webapp" type="hidden" value="${webapp}" size=40"/> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="name" value="${category.name}" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input name="description" type="textfield" value="${category.description}" size=40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="rename" value="submitted"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="edit_category_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/category/rename_category.mako --- a/templates/webapps/community/category/rename_category.mako Fri Apr 30 18:26:06 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Change category name and description</div> - <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='rename_category' )}" method="post" > - <div class="form-row"> - <input name="webapp" type="hidden" value="${webapp}" size=40"/> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${category.name}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Description:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input name="description" type="textfield" value="${category.description}" size=40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="rename" value="submitted"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="rename_category_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako Fri Apr 30 18:26:06 2010 -0400 +++ b/templates/webapps/community/index.mako Fri Apr 30 18:26:49 2010 -0400 @@ -1,6 +1,57 @@ <%inherit file="/webapps/community/base_panels.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ## TODO: Clean up these styles and move into panel_layout.css (they are + ## used here and in the editor). + <style type="text/css"> + #left { + background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; + } + div.toolMenu { + margin: 5px; + margin-left: 10px; + margin-right: 10px; + } + div.toolSectionPad { + margin: 0; + padding: 0; + height: 5px; + font-size: 0px; + } + div.toolSectionDetailsInner { + margin-left: 5px; + margin-right: 5px; + } + div.toolSectionTitle { + padding-bottom: 0px; + font-weight: bold; + } + div.toolMenuGroupHeader { + font-weight: bold; + padding-top: 0.5em; + padding-bottom: 0.5em; + color: #333; + font-style: italic; + border-bottom: dotted #333 1px; + margin-bottom: 0.5em; + } + div.toolTitle { + padding-top: 5px; + padding-bottom: 5px; + margin-left: 16px; + margin-right: 10px; + display: list-item; + list-style: square outside; + } + a:link, a:visited, a:active + { + color: #303030; + } + </style> +</%def> + <%def name="init()"> <% self.has_left_panel=True @@ -29,17 +80,20 @@ </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='tool', action='browse_tool_categories' )}" target="galaxy_main">Browse tools by category</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='tool', action='browse_tools' )}" target="galaxy_main">Browse all tools</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_categories' )}">Browse by category</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools' )}">Browse all tools</a></div> + %if trans.user: + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools_by_user', operation='browse', id=trans.security.encode_id( trans.user.id ) )}">Browse your tools</a></div> + %endif </div> </div> <div class="toolSectionBody"> <div class="toolSectionBg"> <div class="toolTitle"> %if trans.user: - <a href="${h.url_for( controller='upload', action='upload', type='tool' )}" target="galaxy_main">Upload a tool</a> + <a target="galaxy_main" href="${h.url_for( controller='upload', action='upload', type='tool' )}">Upload a tool</a> %else: - Login to upload + <a target="galaxy_main" href="${h.url_for( controller='/user', action='login', webapp='community' )}">Login to upload</a> %endif </div> </div> @@ -54,7 +108,7 @@ if trans.app.config.require_login and not trans.user: center_url = h.url_for( controller='user', action='login', message=message, status=status ) else: - center_url = h.url_for( controller='tool', action='browse_tool_categories', message=message, status=status ) + center_url = h.url_for( controller='tool', action='browse_categories', message=message, status=status ) %> <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"> </iframe> </%def> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/tool/browse_tool.mako --- a/templates/webapps/community/tool/browse_tool.mako Fri Apr 30 18:26:06 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -<%namespace file="/message.mako" import="render_msg" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/community/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="title()">Browse Tool</%def> - -<h2>Galaxy Tool</h2> - -%if message: - ${render_msg( message, status )} -%endif - -%if not tools: - There are no tools -%else: - <table class="grid"> - <thead> - <tr> - <th>Name</th> - <th>Description</th> - </tr> - </thead> - <tbody> - <tr class="formRow id="toolRow"> - <td><a href="${h.url_for( controller='tool', action='browse', id=trans.security.encode_id( tool.id ) )}">${tool.name}</a></td> - <td>${tool.description}</td> - </tr> - </tbody> - </table> -%endif diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 18:26:06 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 18:26:49 2010 -0400 @@ -58,7 +58,6 @@ <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="tool-${tool.id}-popup"> <a class="action-button" href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">View information</a> - <a class="action-button" href="${h.url_for( controller='common', action='manage_categories', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Manage categories</a> <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> </div> @@ -123,7 +122,7 @@ <div class="toolParamHelp" style="clear: both;"> Tools must be approved before they are made available to others in the community. After you have submitted your tool to be published, you will no longer be able to modify it, so make sure the information above is - correct and has been saved before submitting for approval. + correct and and save any changes before submitting for approval. </div> </div> </form> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Fri Apr 30 18:26:06 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Fri Apr 30 18:26:49 2010 -0400 @@ -6,6 +6,12 @@ if cntrller in [ 'tool' ]: can_edit = trans.app.security_agent.can_edit_item( trans.user, tool ) + can_upload_new_version = trans.app.security_agent.can_upload_new_version( trans.user, tool, versions ) + + visible_versions = [] + for version in versions: + if version.is_approved() or version.is_archived() or version.user == trans.user: + visible_versions.append( version ) %> <%! @@ -49,6 +55,30 @@ <h2>View Tool: ${tool.name} <em>${tool.description}</em></h2> +%if tool.is_approved(): + <b><i>This is the latest approved version of this tool</i></b> +%elif tool.is_deleted(): + <font color="red"><b><i>This is a deleted version of this tool</i></b></font> +%elif tool.is_archived(): + <font color="red"><b><i>This is an archived version of this tool</i></b></font> +%elif tool.is_new(): + <font color="red"><b><i>This is an unsubmitted version of this tool</i></b></font> +%elif tool.is_waiting(): + <font color="red"><b><i>This version of this tool is awaiting administrative approval</i></b></font> +%elif tool.is_rejected(): + <font color="red"><b><i>This version of this tool has been rejected by an administrator</i></b></font> +%endif +<p/> + +%if cntrller=='admin' and tool.is_waiting(): + <p> + <ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='admin', action='set_tool_state', state=trans.model.Tool.states.APPROVED, id=trans.security.encode_id( tool.id ), cntrller=cntrller )}"><span>Approve</span></a></li> + <li><a class="action-button" href="${h.url_for( controller='admin', action='set_tool_state', state=trans.model.Tool.states.REJECTED, id=trans.security.encode_id( tool.id ), cntrller=cntrller )}"><span>Reject</span></a></li> + </ul> + </p> +%endif + %if message: ${render_msg( message, status )} %endif @@ -59,7 +89,8 @@ <div popupmenu="tool-${tool.id}-popup"> %if cntrller=='admin' or can_edit: <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a> - <a class="action-button" href="${h.url_for( controller='common', action='manage_categories', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Manage categories</a> + %endif + %if cntrller=='admin' or can_upload_new_version: <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> %endif <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> @@ -93,11 +124,30 @@ </div> <div class="form-row"> <label>Categories:</label> - %for category in categories: - ${category.name} - %endfor + %if categories: + %for category in categories: + ${category.name} + %endfor + %else: + none set + %endif <div style="clear: both"></div> </div> + %if len( visible_versions ) > 1: + <div class="form-row"> + <label>All Versions:</label> + <ul> + %for version in visible_versions: + %if version == tool: + <li><strong>${version.version} (this version)</strong></li> + %else: + <li><a href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( version.id ), cntrller=cntrller )}">${version.version}</a></li> + %endif + %endfor + </ul> + <div style="clear: both"></div> + </div> + %endif </div> </div> diff -r 8e00344d941a -r 3ac0dfcdf44e templates/webapps/community/upload/upload.mako --- a/templates/webapps/community/upload/upload.mako Fri Apr 30 18:26:06 2010 -0400 +++ b/templates/webapps/community/upload/upload.mako Fri Apr 30 18:26:49 2010 -0400 @@ -22,6 +22,9 @@ <div class="toolFormBody"> ## TODO: nginx <form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload' )}" enctype="multipart/form-data" method="post"> + %if replace_id is not None: + <input type='hidden' name="replace_id" value="${replace_id}"/> + %endif <div class="form-row"> <label>Upload Type</label> <div class="form-row-input"> diff -r 8e00344d941a -r 3ac0dfcdf44e tools/samtools/sam_to_bam.py --- a/tools/samtools/sam_to_bam.py Fri Apr 30 18:26:06 2010 -0400 +++ b/tools/samtools/sam_to_bam.py Fri Apr 30 18:26:49 2010 -0400 @@ -94,7 +94,7 @@ tmp_stderr.close() if returncode != 0: raise Exception, stderr - if len( open( fai_index_file_path ).read().strip() ) == 0: + if os.path.getsize( fai_index_file_path ) == 0: raise Exception, 'Index file empty, there may be an error with your reference file or settings.' except Exception, e: #clean up temp files diff -r 8e00344d941a -r 3ac0dfcdf44e tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Fri Apr 30 18:26:06 2010 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Fri Apr 30 18:26:49 2010 -0400 @@ -387,8 +387,8 @@ if returncode != 0: raise Exception, stderr # check that there are results in the output file - if len( open( options.output, 'rb' ).read().strip() ) == 0: - raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + if os.path.getsize( options.output ) == 0: + raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + '\nextra: ' + str(extra) except Exception, e: stop_err( 'Error aligning sequence. ' + str( e ) ) finally: diff -r 8e00344d941a -r 3ac0dfcdf44e tools/sr_mapping/bwa_wrapper_code.py --- a/tools/sr_mapping/bwa_wrapper_code.py Fri Apr 30 18:26:06 2010 -0400 +++ b/tools/sr_mapping/bwa_wrapper_code.py Fri Apr 30 18:26:49 2010 -0400 @@ -2,11 +2,10 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool): try: - refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['indices'].value + refFile = param_dict[ 'genomeSource' ][ 'indices' ].value except: try: - refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['ownFile'].dbkey + refFile = param_dict[ 'genomeSource' ][ 'ownFile' ].dbkey except: - out_data['output'].set_dbkey('?') - return - out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0]) + refFile = '?' + out_data[ 'output' ].set_dbkey( os.path.split( refFile )[1].split( '.' )[0] )

1 0

[hg] galaxy 3727: Cuffcompare wrapper handles all outputs gracef...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/8e00344d941a changeset: 3727:8e00344d941a user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Apr 30 18:26:06 2010 -0400 description: Cuffcompare wrapper handles all outputs gracefully. Tests needed. diffstat: tools/ngs_rna/cuffcompare_wrapper.py | 30 +++++++++++++++++++-------- tools/ngs_rna/cuffcompare_wrapper.xml | 38 +++++++++++++++++++++++++++++++++- 2 files changed, 57 insertions(+), 11 deletions(-) diffs (130 lines): diff -r c642fbb301fc -r 8e00344d941a tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py Fri Apr 30 13:09:29 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Fri Apr 30 18:26:06 2010 -0400 @@ -18,6 +18,11 @@ parser.add_option( '-A', '--transcripts-accuracy-output', dest='transcripts_accuracy_output_file', help='' ) parser.add_option( '-B', '--transcripts-combined-output', dest='transcripts_combined_output_file', help='' ) parser.add_option( '-C', '--transcripts-tracking-output', dest='transcripts_tracking_output_file', help='' ) + parser.add_option( '', '--input1-tmap-output', dest='input1_tmap_output_file', help='' ) + parser.add_option( '', '--input1-refmap-output', dest='input1_refmap_output_file', help='' ) + parser.add_option( '', '--input2-tmap-output', dest='input2_tmap_output_file', help='' ) + parser.add_option( '', '--input2-refmap-output', dest='input2_refmap_output_file', help='' ) + (options, args) = parser.parse_args() @@ -35,17 +40,22 @@ if options.ignore_nonoverlap: cmd += " -R " - # Output/debugging. - print cmd + # Add input files. - # Add input files. - cmd += " %s" % options.input1 + # Need to symlink inputs so that output files are written to temp directory. + print options.input1 + input1_file_name = tmp_output_dir + "/input1" + os.symlink( options.input1, input1_file_name ) + cmd += " %s" % input1_file_name two_inputs = ( options.input2 != None) if two_inputs: - cmd += " %s" % options.input2 + input2_file_name = tmp_output_dir + "/input2" + os.symlink( options.input2, input2_file_name ) + cmd += " %s" % input2_file_name + print cmd # Run command. - try: + try: tmp_name = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name tmp_stderr = open( tmp_name, 'wb' ) proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_output_dir, stderr=tmp_stderr.fileno() ) @@ -79,16 +89,18 @@ try: try: shutil.copyfile( tmp_output_dir + "/cc_output", options.transcripts_accuracy_output_file ) + shutil.copyfile( tmp_output_dir + "/input1.tmap", options.input1_tmap_output_file ) + shutil.copyfile( tmp_output_dir + "/input1.refmap", options.input1_refmap_output_file ) if two_inputs: shutil.copyfile( tmp_output_dir + "/cc_output.combined.gtf", options.transcripts_combined_output_file ) shutil.copyfile( tmp_output_dir + "/cc_output.tracking", options.transcripts_tracking_output_file ) - - # TODO: also copy *.tmap, *.refmap to outputs? + shutil.copyfile( tmp_output_dir + "/input2.tmap", options.input2_tmap_output_file ) + shutil.copyfile( tmp_output_dir + "/input2.refmap", options.input2_refmap_output_file ) except Exception, e: stop_err( 'Error in cuffcompare:\n' + str( e ) ) finally: # Clean up temp dirs - if os.path.exists( tmp_output_dir ): + if not os.path.exists( tmp_output_dir ): shutil.rmtree( tmp_output_dir ) if __name__=="__main__": __main__() \ No newline at end of file diff -r c642fbb301fc -r 8e00344d941a tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml Fri Apr 30 13:09:29 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Fri Apr 30 18:26:06 2010 -0400 @@ -3,9 +3,13 @@ <command interpreter="python"> cuffcompare_wrapper.py --transcripts-accuracy-output=$transcripts_accuracy + --input1-tmap-output=$input1_tmap + --input1-refmap-output=$input1_refmap #if $second_gtf.use_second_gtf == "Yes": --transcripts-combined-output=$transcripts_combined --transcripts-tracking-output=$transcripts_tracking + --input2-tmap-output=$input2_tmap + --input2-refmap-output=$input2_refmap #end if #if $annotation.use_ref_annotation == "Yes": -r $annotation.reference_annotation @@ -46,13 +50,43 @@ </inputs> <outputs> - <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/> - <data format="tracking" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking"/> + <data format="tmap" name="input1_tmap" label="${tool.name} on ${on_string}: data ${input1.hid} tmap file"/> + <data format="refmap" name="input1_refmap" label="${tool.name} on ${on_string}: data ${input1.hid} refmap file"/> + <data format="tmap" name="input2_tmap" label="${tool.name} on ${on_string}: data ${second_gtf.input2.hid} tmap file"> + <filter>second_gtf['use_second_gtf'] == "Yes"</filter> + </data> + <data format="refmap" name="input2_refmap" label="${tool.name} on ${on_string}: data ${second_gtf.input2.hid} refmap file"> + <filter>second_gtf['use_second_gtf'] == "Yes"</filter> + </data> + <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"> + <filter>second_gtf['use_second_gtf'] == "Yes"</filter> + </data> + <data format="tracking" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking"> + <filter>second_gtf['use_second_gtf'] == "Yes"</filter> + </data> <data format="gtf" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy"/> </outputs> <tests> +  <test> + <param name="input1" value="cuffcompare_in1.gtf" ftype="gtf"/> + <param name="use_second_gtf" value="Yes"/> + <param name="input2" value="cuffcompare_in2.gtf" ftype="gtf"/> + <param name="use_ref_annotation" value="Yes"/> + <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> + <param name="ignore_nonoverlapping_reference" value="Yes"/> + <output name="transcripts_combined" file="cuffcompare_out5.gtf"/> +  </test> </tests>

1 0

[hg] galaxy 3725: Fix dbkey setting for BWA.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/e71a3d03a529 changeset: 3725:e71a3d03a529 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Apr 30 15:45:32 2010 -0400 description: Fix dbkey setting for BWA. diffstat: tools/sr_mapping/bwa_wrapper_code.py | 9 ++++----- 1 files changed, 4 insertions(+), 5 deletions(-) diffs (19 lines): diff -r 007f175c8b88 -r e71a3d03a529 tools/sr_mapping/bwa_wrapper_code.py --- a/tools/sr_mapping/bwa_wrapper_code.py Fri Apr 30 15:27:41 2010 -0400 +++ b/tools/sr_mapping/bwa_wrapper_code.py Fri Apr 30 15:45:32 2010 -0400 @@ -2,11 +2,10 @@ def exec_before_job(app, inp_data, out_data, param_dict, tool): try: - refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['indices'].value + refFile = param_dict[ 'genomeSource' ][ 'indices' ].value except: try: - refFile = param_dict['solidOrSolexa']['solidRefGenomeSource']['ownFile'].dbkey + refFile = param_dict[ 'genomeSource' ][ 'ownFile' ].dbkey except: - out_data['output'].set_dbkey('?') - return - out_data['output'].set_dbkey(os.path.split(refFile)[1].split('.')[0]) + refFile = '?' + out_data[ 'output' ].set_dbkey( os.path.split( refFile )[1].split( '.' )[0] )

1 0

[hg] galaxy 3726: Community: Add tool versioning and tighten up ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/42f3f5d78f9a changeset: 3726:42f3f5d78f9a user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Apr 30 16:11:17 2010 -0400 description: Community: Add tool versioning and tighten up the requirements in the upload/approval process diffstat: lib/galaxy/web/framework/__init__.py | 4 +- lib/galaxy/webapps/community/controllers/admin.py | 19 +- lib/galaxy/webapps/community/controllers/common.py | 28 ++- lib/galaxy/webapps/community/controllers/upload.py | 68 +++++++++- lib/galaxy/webapps/community/model/mapping.py | 9 +- lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py | 3 +- lib/galaxy/webapps/community/security/__init__.py | 6 + templates/webapps/community/tool/view_tool.mako | 49 ++++++- templates/webapps/community/upload/upload.mako | 3 + 9 files changed, 160 insertions(+), 29 deletions(-) diffs (410 lines): diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Apr 30 16:11:17 2010 -0400 @@ -66,7 +66,7 @@ decorator.exposed = True return decorator -def require_login( verb="perform this action", use_panels=False ): +def require_login( verb="perform this action", use_panels=False, webapp='galaxy' ): def argcatcher( func ): def decorator( self, trans, *args, **kwargs ): if trans.get_user(): @@ -74,7 +74,7 @@ else: return trans.show_error_message( 'You must be <a target="_top" href="%s">logged in</a> to %s</div>.' - % ( url_for( controller='user', action='login' ), verb ), use_panels=use_panels ) + % ( url_for( controller='user', action='login', webapp=webapp ), verb ), use_panels=use_panels ) return decorator return argcatcher diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 16:11:17 2010 -0400 @@ -2,7 +2,7 @@ from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids -from common import get_categories, get_category, get_tools, get_event, get_tool +from common import get_categories, get_category, get_tools, get_event, get_tool, get_versions import logging log = logging.getLogger( __name__ ) @@ -670,12 +670,18 @@ webapp = params.get( 'webapp', 'galaxy' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + redirect = params.get( 'no_redirect', True ) id = params.get( 'id', None ) if not id: message = "No tool id received for setting status" status = 'error' else: tool = get_tool( trans, id ) + if state == trans.app.model.Tool.states.APPROVED: + # If we're approving a tool, all previous versions must be set to archived + for version in get_versions( trans, tool ): + if version != tool and version.is_approved(): + self.set_tool_state( trans, trans.app.model.Tool.states.ARCHIVED, id=trans.app.security.encode_id( version.id ), redirect='False' ) event = trans.model.Event( state ) # Flush so we an get an id trans.sa_session.add( event ) @@ -684,11 +690,12 @@ trans.sa_session.add( tea ) trans.sa_session.flush() message = "State of tool '%s' is now %s" % ( tool.name, state ) - trans.response.send_redirect( web.url_for( controller='admin', - action='browse_tools', - webapp=webapp, - message=message, - status=status ) ) + if redirect: + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools', + webapp=webapp, + message=message, + status=status ) ) @web.expose @web.require_admin def edit_category( self, trans, **kwd ): diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 16:11:17 2010 -0400 @@ -81,9 +81,11 @@ tool = get_tool( trans, id ) categories = [ tca.category for tca in tool.categories ] tool_file_contents = tarfile.open( tool.file_name, 'r' ).getnames() + versions = get_versions( trans, tool ) return trans.fill_template( '/webapps/community/tool/view_tool.mako', tool=tool, tool_file_contents=tool_file_contents, + versions=versions, categories=categories, cntrller=cntrller, message=message, @@ -100,14 +102,11 @@ message='Select a tool to to upload a new version', status='error' ) ) tool = get_tool( trans, id ) - if params.save_button and ( params.file_data != '' or params.url != '' ): - # TODO: call the upload method in the upload controller. - message = 'Uploading new version not implemented' - status = 'error' - return trans.response.send_redirect( web.url_for( controller=cntrller, - action='browse_tools', - message='Not yet implemented, sorry...', - status='error' ) ) + return trans.response.send_redirect( web.url_for( controller='upload', + action='upload', + message=message, + status=status, + replace_id=id ) ) @web.expose def browse_category( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -159,11 +158,22 @@ ## ---- Utility methods ------------------------------------------------------- +def get_versions( trans, tool ): + versions = [tool] + this_tool = tool + while tool.newer_version: + versions.insert( 0, tool.newer_version ) + tool = tool.newer_version + tool = this_tool + while tool.older_version: + versions.append( tool.older_version[0] ) + tool = tool.older_version[0] + return versions def get_categories( trans ): """Get all categories from the database""" return trans.sa_session.query( trans.model.Category ) \ .filter( trans.model.Category.table.c.deleted==False ) \ - .order_by( trans.model.Category.table.c.name ) + .order_by( trans.model.Category.table.c.name ).all() def get_unassociated_categories( trans, obj ): """Get all categories from the database that are not associated with obj""" # TODO: we currently assume we are setting a tool category, so this method may need diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Fri Apr 30 16:11:17 2010 -0400 @@ -3,23 +3,36 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.model.orm import * from galaxy.webapps.community import datatypes -from common import get_categories, get_category +from common import get_categories, get_category, get_versions log = logging.getLogger( __name__ ) # States for passing messages SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" +class UploadError( Exception ): + pass + class UploadController( BaseController ): @web.expose + @web.require_login( 'upload', use_panels=True, webapp='community' ) def upload( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) category_ids = util.listify( params.get( 'category_id', '' ) ) + replace_id = params.get( 'replace_id', None ) + replace_version = None uploaded_file = None - if params.file_data == '' and params.url.strip() == '': + categories = get_categories( trans ) + if not get_categories( trans ): + return trans.response.send_redirect( web.url_for( controller='tool', + action='browse_tools', + cntrller='tool', + message='No categories have been configured in this instance of the Galaxy Community. An administrator needs to create some via the Administrator control panel before anything can be uploaded', + status='error' ) ) + elif params.file_data == '' and params.url.strip() == '': message = 'No files were entered on the upload form.' status = 'error' elif params.file_data == '': @@ -47,6 +60,29 @@ obj = datatype.create_model_object( meta ) trans.sa_session.add( obj ) if isinstance( obj, trans.app.model.Tool ): + existing = trans.sa_session.query( trans.app.model.Tool ).filter_by( tool_id = meta.id ).all() + if existing and replace_id is None: + raise UploadError( 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' ) + elif existing: + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) + if replace_version.newer_version: + # If the user has picked an old version, switch to the newest version + replace_version = get_versions( trans, replace_version )[0] + if trans.user != replace_version.user: + raise UploadError( 'You are not the owner of this tool and may not upload new versions of it.' ) + if replace_version.tool_id != meta.id: + raise UploadError( 'The new tool id (%s) does not match the old tool id (%s). Please check the tool XML file' % ( meta.id, replace_version.tool_id ) ) + for old_version in get_versions( trans, replace_version ): + if old_version.version == meta.version: + raise UploadError( 'The new version (%s) matches an old version. Please check your version in the tool XML file' % meta.version ) + if old_version.is_new(): + raise UploadError( 'There is an existing version of this tool which is unsubmitted. Please either <a href="%s">submit or delete it</a> before uploading a new version.' % url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.app.security.encode_id( old_version.id ) ) ) + if old_version.is_waiting(): + raise UploadError( 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' ) + # Defer setting the id since the newer version id doesn't exist until the new Tool object is flushed if category_ids: for category_id in category_ids: category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) @@ -58,6 +94,9 @@ tea = trans.app.model.ToolEventAssociation( obj, event ) trans.sa_session.add_all( ( event, tea ) ) trans.sa_session.flush() + if replace_version and replace_id: + replace_version.newer_version_id = obj.id + trans.sa_session.flush() try: os.link( uploaded_file.name, obj.file_name ) except OSError: @@ -69,13 +108,29 @@ id=trans.app.security.encode_id( obj.id ), message='Uploaded %s' % meta.message, status='done' ) ) - except datatypes.DatatypeVerificationError, e: + except ( datatypes.DatatypeVerificationError, UploadError ), e: message = str( e ) status = 'error' - except sqlalchemy.exc.IntegrityError: - message = 'A tool with the same ID already exists. If you are trying to update this tool to a new version, please use the upload form on the "Edit Tool" page. Otherwise, please choose a new ID.' - status = 'error' uploaded_file.close() + elif replace_id is not None: + replace_version = trans.sa_session.query( trans.app.model.Tool ).get( int( trans.app.security.decode_id( replace_id ) ) ) + old_version = None + for old_version in get_versions( trans, replace_version ): + if old_version.is_new(): + message = 'There is an existing version of this tool which is unsubmitted. Please either submit or delete it before uploading a new version.' + break + if old_version.is_waiting(): + message = 'There is an existing version of this tool which is waiting for administrative approval. Please contact an administrator for help.' + break + else: + old_version = None + if old_version is not None: + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='tool', + id=trans.app.security.encode_id( old_version.id ), + message=message, + status='error' ) ) selected_upload_type = params.get( 'type', 'tool' ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/upload/upload.mako', @@ -83,5 +138,6 @@ status=status, selected_upload_type=selected_upload_type, upload_types=trans.app.datatypes_registry.get_datatypes_for_select_list(), + replace_id=replace_id, selected_categories=selected_categories, categories=get_categories( trans ) ) diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 16:11:17 2010 -0400 @@ -103,9 +103,10 @@ Tool.table = Table( "tool", metadata, Column( "id", Integer, primary_key=True ), Column( "guid", TrimmedString( 255 ), index=True, unique=True ), - Column( "tool_id", TrimmedString( 255 ), index=True, unique=True ), + Column( "tool_id", TrimmedString( 255 ), index=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "newer_version_id", Integer, ForeignKey( "tool.id" ), nullable=True ), Column( "name", TrimmedString( 255 ), index=True ), Column( "description" , TEXT ), Column( "user_description" , TEXT ), @@ -215,7 +216,11 @@ properties = dict( categories=relation( ToolCategoryAssociation ), events=relation( ToolEventAssociation ), - user=relation( User.mapper ) + user=relation( User.mapper ), + older_version=relation( + Tool, + primaryjoin=( Tool.table.c.newer_version_id == Tool.table.c.id ), + backref=backref( "newer_version", primaryjoin=( Tool.table.c.newer_version_id == Tool.table.c.id ), remote_side=[Tool.table.c.id] ) ) ) ) assign_mapper( context, Event, Event.table, diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py --- a/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Fri Apr 30 16:11:17 2010 -0400 @@ -80,9 +80,10 @@ Tool_table = Table( "tool", metadata, Column( "id", Integer, primary_key=True ), Column( "guid", TrimmedString( 255 ), index=True, unique=True ), - Column( "tool_id", TrimmedString( 255 ), index=True, unique=True ), + Column( "tool_id", TrimmedString( 255 ), index=True ), Column( "create_time", DateTime, default=now ), Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "newer_version_id", Integer, ForeignKey( "tool.id" ), nullable=True ), Column( "name", TrimmedString( 255 ), index=True ), Column( "description" , TEXT ), Column( "user_description" , TEXT ), diff -r e71a3d03a529 -r 42f3f5d78f9a lib/galaxy/webapps/community/security/__init__.py --- a/lib/galaxy/webapps/community/security/__init__.py Fri Apr 30 15:45:32 2010 -0400 +++ b/lib/galaxy/webapps/community/security/__init__.py Fri Apr 30 16:11:17 2010 -0400 @@ -167,6 +167,12 @@ # We currently assume the current user can edit the item if they are the owner (i.e., they # uploaded the item), and the item is in a NEW state. return user and user==item.user and item.is_new() + def can_upload_new_version( self, user, item, versions ): + state_ok = True + for version in versions: + if version.is_new() or version.is_approved(): + state_ok = False + return user and user==item.user and state_ok def get_permitted_actions( filter=None ): '''Utility method to return a subset of RBACAgent's permitted actions''' diff -r e71a3d03a529 -r 42f3f5d78f9a templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Fri Apr 30 15:45:32 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Fri Apr 30 16:11:17 2010 -0400 @@ -6,6 +6,12 @@ if cntrller in [ 'tool' ]: can_edit = trans.app.security_agent.can_edit_item( trans.user, tool ) + can_upload_new_version = trans.app.security_agent.can_upload_new_version( trans.user, tool, versions ) + + visible_versions = [] + for version in versions: + if version.is_approved() or version.is_archived() or version.user == trans.user: + visible_versions.append( version ) %> <%! @@ -49,10 +55,26 @@ <h2>View Tool: ${tool.name} <em>${tool.description}</em></h2> +%if tool.is_approved(): + <b><i>This is the latest approved version of this tool</i></b> +%elif tool.is_deleted(): + <font color="red"><b><i>This is a deleted version of this tool</i></b></font> +%elif tool.is_archived(): + <font color="red"><b><i>This is an archived version of this tool</i></b></font> +%elif tool.is_new(): + <font color="red"><b><i>This is an unsubmitted version of this tool</i></b></font> +%elif tool.is_waiting(): + <font color="red"><b><i>This version of this tool is awaiting administrative approval</i></b></font> +%elif tool.is_rejected(): + <font color="red"><b><i>This version of this tool has been rejected by an administrator</i></b></font> +%endif +<p/> + %if cntrller=='admin' and tool.is_waiting(): <p> <ul class="manage-table-actions"> <li><a class="action-button" href="${h.url_for( controller='admin', action='set_tool_state', state=trans.model.Tool.states.APPROVED, id=trans.security.encode_id( tool.id ), cntrller=cntrller )}"><span>Approve</span></a></li> + <li><a class="action-button" href="${h.url_for( controller='admin', action='set_tool_state', state=trans.model.Tool.states.REJECTED, id=trans.security.encode_id( tool.id ), cntrller=cntrller )}"><span>Reject</span></a></li> </ul> </p> %endif @@ -67,6 +89,8 @@ <div popupmenu="tool-${tool.id}-popup"> %if cntrller=='admin' or can_edit: <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a> + %endif + %if cntrller=='admin' or can_upload_new_version: <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> %endif <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> @@ -100,11 +124,30 @@ </div> <div class="form-row"> <label>Categories:</label> - %for category in categories: - ${category.name} - %endfor + %if categories: + %for category in categories: + ${category.name} + %endfor + %else: + none set + %endif <div style="clear: both"></div> </div> + %if len( visible_versions ) > 1: + <div class="form-row"> + <label>All Versions:</label> + <ul> + %for version in visible_versions: + %if version == tool: + <li><strong>${version.version} (this version)</strong></li> + %else: + <li><a href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( version.id ), cntrller=cntrller )}">${version.version}</a></li> + %endif + %endfor + </ul> + <div style="clear: both"></div> + </div> + %endif </div> </div> diff -r e71a3d03a529 -r 42f3f5d78f9a templates/webapps/community/upload/upload.mako --- a/templates/webapps/community/upload/upload.mako Fri Apr 30 15:45:32 2010 -0400 +++ b/templates/webapps/community/upload/upload.mako Fri Apr 30 16:11:17 2010 -0400 @@ -22,6 +22,9 @@ <div class="toolFormBody"> ## TODO: nginx <form id="upload_form" name="upload_form" action="${h.url_for( controller='upload', action='upload' )}" enctype="multipart/form-data" method="post"> + %if replace_id is not None: + <input type='hidden' name="replace_id" value="${replace_id}"/> + %endif <div class="form-row"> <label>Upload Type</label> <div class="form-row-input">

1 0

[hg] galaxy 3724: Change the way size of output file determined ...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/007f175c8b88 changeset: 3724:007f175c8b88 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Apr 30 15:27:41 2010 -0400 description: Change the way size of output file determined in Bowtie and SAM-to_BAM to deal with memory limitation. diffstat: tools/samtools/sam_to_bam.py | 2 +- tools/sr_mapping/bowtie_wrapper.py | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diffs (26 lines): diff -r 85e05920bada -r 007f175c8b88 tools/samtools/sam_to_bam.py --- a/tools/samtools/sam_to_bam.py Fri Apr 30 15:20:04 2010 -0400 +++ b/tools/samtools/sam_to_bam.py Fri Apr 30 15:27:41 2010 -0400 @@ -94,7 +94,7 @@ tmp_stderr.close() if returncode != 0: raise Exception, stderr - if len( open( fai_index_file_path ).read().strip() ) == 0: + if os.path.getsize( fai_index_file_path ) == 0: raise Exception, 'Index file empty, there may be an error with your reference file or settings.' except Exception, e: #clean up temp files diff -r 85e05920bada -r 007f175c8b88 tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Fri Apr 30 15:20:04 2010 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Fri Apr 30 15:27:41 2010 -0400 @@ -387,8 +387,8 @@ if returncode != 0: raise Exception, stderr # check that there are results in the output file - if len( open( options.output, 'rb' ).read().strip() ) == 0: - raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + if os.path.getsize( options.output ) == 0: + raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + '\nextra: ' + str(extra) except Exception, e: stop_err( 'Error aligning sequence. ' + str( e ) ) finally:

1 0

[hg] galaxy 3723: Add a link to the user's uploaded tools from t...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/85e05920bada changeset: 3723:85e05920bada user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Apr 30 15:20:04 2010 -0400 description: Add a link to the user's uploaded tools from the Manage users grid, and fix some more bugs in the community app. diffstat: lib/galaxy/webapps/community/controllers/admin.py | 60 ++++++---------------- templates/webapps/community/index.mako | 4 +- templates/webapps/community/tool/edit_tool.mako | 1 - templates/webapps/community/tool/view_tool.mako | 1 - 4 files changed, 20 insertions(+), 46 deletions(-) diffs (148 lines): diff -r db4f8befcd89 -r 85e05920bada lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 14:08:23 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 15:20:04 2010 -0400 @@ -18,13 +18,6 @@ if user.username: return user.username return 'not set' - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.purged: - return "purged" - elif user.deleted: - return "deleted" - return "" class GroupsColumn( grids.GridColumn ): def get_value( self, trans, grid, user ): if user.groups: @@ -45,6 +38,16 @@ if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.purged: + return "purged" + elif user.deleted: + return "deleted" + return "" + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( user.id ), str( len( user.tools ) ) ) # Grid definition webapp = "community" @@ -69,6 +72,10 @@ ExternalColumn( "External", attach_popup=False ), LastLoginColumn( "Last Login", format=time_ago ), StatusColumn( "Status", attach_popup=False ), + ToolsColumn( "Uploaded Tools", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -488,11 +495,7 @@ grids.GridOperation( "Edit information", condition=( lambda item: not item.deleted ), allow_multiple=False, - url_args=dict( controller="common", action="edit_tool", cntrller="admin", webapp="community" ) ), - grids.GridOperation( "Manage categories", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( controller="common", action="manage_categories", cntrller="admin", webapp="community" ) ) + url_args=dict( controller="common", action="edit_tool", cntrller="admin", webapp="community" ) ) ] standard_filters = [ grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), @@ -553,7 +556,6 @@ @web.expose @web.require_admin def browse_tools_by_user( self, trans, **kwd ): - # TODO: move this to the common controller as it is in the tool controller as well... if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "browse": @@ -580,35 +582,8 @@ return trans.response.send_redirect( web.url_for( controller='tool', action='download_tool', **kwd ) ) - @web.expose - @web.require_admin - def browse_tools_by_user( self, trans, **kwd ): - # TODO: move this to the common controller as it is in the tool controller as well... - if 'operation' in kwd: - operation = kwd['operation'].lower() - if operation == "browse": - return trans.response.send_redirect( web.url_for( controller='admin', - action='browse_tools_by_user', - **kwd ) ) - elif operation == "browse category": - return trans.response.send_redirect( web.url_for( controller='common', - action='browse_category', - cntrller='admin', - **kwd ) ) - elif operation == "view tool": - return trans.response.send_redirect( web.url_for( controller='common', - action='view_tool', - cntrller='admin', - **kwd ) ) - elif operation == "edit tool": - return trans.response.send_redirect( web.url_for( controller='common', - action='edit_tool', - cntrller='admin', - **kwd ) ) - elif operation == "download tool": - return trans.response.send_redirect( web.url_for( controller='tool', - action='download_tool', - **kwd ) ) + # Render the list view + return self.tool_list_grid( trans, **kwd ) @web.expose @web.require_admin def manage_categories( self, trans, **kwd ): @@ -860,7 +835,6 @@ ## ---- Utility methods ------------------------------------------------------- def get_tools_by_state( trans, state ): - # TODO: this can be written so that it is much cleaner and faster tool_id = [] if state == trans.model.Tool.states.NEW: for tool in get_tools( trans ): diff -r db4f8befcd89 -r 85e05920bada templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako Fri Apr 30 14:08:23 2010 -0400 +++ b/templates/webapps/community/index.mako Fri Apr 30 15:20:04 2010 -0400 @@ -82,7 +82,9 @@ <div class="toolSectionBg"> <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_categories' )}">Browse by category</a></div> <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools' )}">Browse all tools</a></div> - <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools_by_user', operation='browse', id=trans.security.encode_id( trans.user.id ) )}">Browse your tools</a></div> + %if trans.user: + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools_by_user', operation='browse', id=trans.security.encode_id( trans.user.id ) )}">Browse your tools</a></div> + %endif </div> </div> <div class="toolSectionBody"> diff -r db4f8befcd89 -r 85e05920bada templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 14:08:23 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 15:20:04 2010 -0400 @@ -58,7 +58,6 @@ <a id="tool-${tool.id}-popup" class="popup-arrow" style="display: none;">▼</a> <div popupmenu="tool-${tool.id}-popup"> <a class="action-button" href="${h.url_for( controller='common', action='view_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">View information</a> - <a class="action-button" href="${h.url_for( controller='common', action='manage_categories', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Manage categories</a> <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a> </div> diff -r db4f8befcd89 -r 85e05920bada templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Fri Apr 30 14:08:23 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Fri Apr 30 15:20:04 2010 -0400 @@ -67,7 +67,6 @@ <div popupmenu="tool-${tool.id}-popup"> %if cntrller=='admin' or can_edit: <a class="action-button" href="${h.url_for( controller='common', action='edit_tool', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Edit information</a> - <a class="action-button" href="${h.url_for( controller='common', action='manage_categories', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Manage categories</a> <a class="action-button" href="${h.url_for( controller='common', action='upload_new_tool_version', id=trans.app.security.encode_id( tool.id ), cntrller=cntrller )}">Upload a new version</a> %endif <a class="action-button" href="${h.url_for( controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ) )}">Download tool</a>

1 0

[hg] galaxy 3722: Many fixes and additional features added to th...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/db4f8befcd89 changeset: 3722:db4f8befcd89 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Apr 30 14:08:23 2010 -0400 description: Many fixes and additional features added to the community. diffstat: lib/galaxy/webapps/community/controllers/admin.py | 374 +++++++++++-- lib/galaxy/webapps/community/controllers/common.py | 81 ++- lib/galaxy/webapps/community/controllers/tool.py | 293 ++++++++-- lib/galaxy/webapps/community/model/__init__.py | 7 +- lib/galaxy/webapps/community/model/mapping.py | 5 +- templates/webapps/community/admin/index.mako | 43 +- templates/webapps/community/category/edit_category.mako | 44 + templates/webapps/community/category/rename_category.mako | 44 - templates/webapps/community/index.mako | 62 ++- templates/webapps/community/tool/browse_tool.mako | 37 - templates/webapps/community/tool/edit_tool.mako | 2 +- templates/webapps/community/tool/view_tool.mako | 8 + 12 files changed, 733 insertions(+), 267 deletions(-) diffs (1467 lines): diff -r c642fbb301fc -r db4f8befcd89 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 13:09:29 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Fri Apr 30 14:08:23 2010 -0400 @@ -2,7 +2,7 @@ from galaxy.webapps.community import model from galaxy.model.orm import * from galaxy.web.framework.helpers import time_ago, iff, grids -from common import get_categories, get_category +from common import get_categories, get_category, get_tools, get_event, get_tool import logging log = logging.getLogger( __name__ ) @@ -200,7 +200,7 @@ return None def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): return query.filter( model.Role.type != model.Role.types.PRIVATE ) class GroupListGrid( grids.Grid ): @@ -280,34 +280,31 @@ def build_initial_query( self, session ): return session.query( self.model_class ) -class CategoryListGrid( grids.Grid ): +class ManageCategoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.name class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.description - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, category ): - if category.deleted: - return "deleted" - return "" # Grid definition webapp = "community" - title = "Categories" + title = "Manage Categories" model_class = model.Category template='/webapps/community/category/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", key="name", - link=( lambda item: dict( operation="Edit category", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="Edit", id=item.id, webapp="community" ) ), model_class=model.Category, - attach_popup=True, + attach_popup=False, filterable="advanced" ), - DescriptionColumn( "Description", attach_popup=False ), - StatusColumn( "Status", attach_popup=False ), + DescriptionColumn( "Description", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -318,13 +315,9 @@ filterable="standard" ) ) global_actions = [ grids.GridAction( "Add new category", - dict( controller='admin', action='categories', operation='create', webapp="community" ) ) + dict( controller='admin', action='manage_categories', operation='create', webapp="community" ) ) ] - operations = [ grids.GridOperation( "Rename", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( webapp="community", action="rename_category" ) ), - grids.GridOperation( "Delete", + operations = [ grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True, url_args=dict( webapp="community", action="mark_category_deleted" ) ), @@ -349,16 +342,77 @@ def build_initial_query( self, session ): return session.query( self.model_class ) +class ToolsByCategoryListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + return category.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + return category.description + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + if category.tools: + return len( category.tools ) + return 0 + + # Grid definition + webapp = "community" + title = "Tools by Category" + model_class = model.Category + template='/webapps/community/category/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="Browse Category", id=item.id, webapp="community" ) ), + model_class=model.Category, + attach_popup=True, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + ToolsColumn( "Tools", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def get_current_item( self, trans ): + return None + def build_initial_query( self, session ): + return session.query( self.model_class ) + class ToolListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): if tool.categories: rval = '' for tca in tool.categories: - rval = '%s%s<br/>' % ( rval, tca.category.name ) + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' class StateColumn( grids.GridColumn ): @@ -389,7 +443,7 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return tool.user.email + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition title = "Tools" model_class = model.Tool @@ -402,27 +456,34 @@ link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='admin', webapp="community" ) ), attach_popup=True, filterable="advanced" ), + VersionColumn( "Version", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), CategoryColumn( "Category", - key="category", model_class=model.Category, attach_popup=False, filterable="advanced" ), - StateColumn( "State", - key="state", + StateColumn( "Status", model_class=model.Event, - attach_popup=False, - filterable="advanced" ), + attach_popup=False ), + UserColumn( "Uploaded By", + key="username", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + grids.DeletedColumn( "Deleted", model_class=model.Tool, key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, filterable="standard" ) ) - global_actions = [ - grids.GridAction( "Upload tool", dict( controller='upload', action='upload', type='tool' ) ) - ] operations = [ grids.GridOperation( "Edit information", condition=( lambda item: not item.deleted ), @@ -443,57 +504,156 @@ use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): + tool_id = kwd.get( 'tool_id', False ) + if tool_id: + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) return query.filter( self.model_class.deleted==False ) -class AdminCommunity( BaseController, Admin ): +class AdminController( BaseController, Admin ): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() group_list_grid = GroupListGrid() - category_list_grid = CategoryListGrid() + manage_category_list_grid = ManageCategoryListGrid() + tools_by_category_list_grid = ToolsByCategoryListGrid() tool_list_grid = ToolListGrid() @web.expose @web.require_admin - def browse_tools( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def browse_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='admin', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='admin', + **kwd ) ) + # Render the list view + return self.tool_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_category( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse category": + return self.browse_category( trans, id=kwd['id'] ) + # Render the list view + return self.tools_by_category_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_user( self, trans, **kwd ): + # TODO: move this to the common controller as it is in the tool controller as well... + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "browse": - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tools', + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_tools_by_user', cntrller='admin', - **kwargs ) ) + **kwd ) ) + elif operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='admin', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='admin', + **kwd ) ) elif operation == "edit tool": return trans.response.send_redirect( web.url_for( controller='common', action='edit_tool', cntrller='admin', - **kwargs ) ) + **kwd ) ) + elif operation == "download tool": + return trans.response.send_redirect( web.url_for( controller='tool', + action='download_tool', + **kwd ) ) + @web.expose + @web.require_admin + def browse_tools_by_user( self, trans, **kwd ): + # TODO: move this to the common controller as it is in the tool controller as well... + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse": + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools_by_user', + **kwd ) ) + elif operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='admin', + **kwd ) ) elif operation == "view tool": return trans.response.send_redirect( web.url_for( controller='common', action='view_tool', cntrller='admin', - **kwargs ) ) - # Render the list view - return self.tool_list_grid( trans, **kwargs ) + **kwd ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='admin', + **kwd ) ) + elif operation == "download tool": + return trans.response.send_redirect( web.url_for( controller='tool', + action='download_tool', + **kwd ) ) @web.expose @web.require_admin - def categories( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def manage_categories( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "create": - return self.create_category( trans, **kwargs ) + return self.create_category( trans, **kwd ) if operation == "delete": - return self.mark_category_deleted( trans, **kwargs ) + return self.mark_category_deleted( trans, **kwd ) if operation == "undelete": - return self.undelete_category( trans, **kwargs ) + return self.undelete_category( trans, **kwd ) if operation == "purge": - return self.purge_category( trans, **kwargs ) - if operation == "rename": - return self.rename_category( trans, **kwargs ) + return self.purge_category( trans, **kwd ) + if operation == "edit": + return self.edit_category( trans, **kwd ) # Render the list view - return self.category_list_grid( trans, **kwargs ) - + return self.manage_category_list_grid( trans, **kwd ) + @web.expose + @web.require_admin + def browse_tools_by_state( self, trans, state=None, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if state is None: + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message='Select a status', + status='error' ) ) + event = get_event( trans, id ) + state = event.state + tool_id = get_tools_by_state( trans, state ) + if not tool_id: + tool_id = 'None' + return trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools', + tool_id=tool_id ) ) + @web.expose + @web.require_admin + def browse_category( self, trans, **kwd ): + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='admin', + **kwd ) ) @web.expose @web.require_admin def create_category( self, trans, **kwd ): @@ -515,7 +675,7 @@ message = "Category '%s' has been created" % category.name trans.sa_session.flush() trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -530,42 +690,69 @@ status=status ) @web.expose @web.require_admin - def rename_category( self, trans, **kwd ): + def set_tool_state( self, trans, state, **kwd ): params = util.Params( kwd ) webapp = params.get( 'webapp', 'galaxy' ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) id = params.get( 'id', None ) if not id: - message = "No category ids received for renaming" + message = "No tool id received for setting status" + status = 'error' + else: + tool = get_tool( trans, id ) + event = trans.model.Event( state ) + # Flush so we an get an id + trans.sa_session.add( event ) + trans.sa_session.flush() + tea = trans.model.ToolEventAssociation( tool, event ) + trans.sa_session.add( tea ) + trans.sa_session.flush() + message = "State of tool '%s' is now %s" % ( tool.name, state ) + trans.response.send_redirect( web.url_for( controller='admin', + action='browse_tools', + webapp=webapp, + message=message, + status=status ) ) + @web.expose + @web.require_admin + def edit_category( self, trans, **kwd ): + params = util.Params( kwd ) + webapp = params.get( 'webapp', 'galaxy' ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + message = "No category ids received for editing" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) category = get_category( trans, id ) - if params.get( 'rename_category_button', False ): + if params.get( 'edit_category_button', False ): old_name = category.name new_name = util.restore_text( params.name ) new_description = util.restore_text( params.description ) - if not new_name: - message = 'Enter a valid name' - status = 'error' - elif trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): - message = 'A category with that name already exists' - status = 'error' + if old_name != new_name: + if not new_name: + message = 'Enter a valid name' + status = 'error' + elif trans.sa_session.query( trans.app.model.Category ).filter( trans.app.model.Category.table.c.name==new_name ).first(): + message = 'A category with that name already exists' + status = 'error' else: category.name = new_name category.description = new_description trans.sa_session.add( category ) trans.sa_session.flush() - message = "Category '%s' has been renamed to '%s'" % ( old_name, new_name ) + message = "The information has been saved for category '%s'" % ( new_name ) return trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) - return trans.fill_template( '/webapps/community/category/rename_category.mako', + return trans.fill_template( '/webapps/community/category/edit_category.mako', category=category, webapp=webapp, message=message, @@ -579,7 +766,7 @@ if not id: message = "No category ids received for deleting" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) @@ -592,7 +779,7 @@ trans.sa_session.flush() message += " %s " % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -605,7 +792,7 @@ if not id: message = "No category ids received for undeleting" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=message, status='error' ) ) @@ -617,7 +804,7 @@ if not category.deleted: message = "Category '%s' has not been deleted, so it cannot be undeleted." % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -628,7 +815,7 @@ undeleted_categories += " %s" % category.name message = "Undeleted %d categories: %s" % ( count, undeleted_categories ) trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) @@ -644,7 +831,7 @@ if not id: message = "No category ids received for purging" trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -655,7 +842,7 @@ if not category.deleted: message = "Category '%s' has not been deleted, so it cannot be purged." % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) @@ -665,7 +852,42 @@ trans.sa_session.flush() message += " %s " % category.name trans.response.send_redirect( web.url_for( controller='admin', - action='categories', + action='manage_categories', webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) + +## ---- Utility methods ------------------------------------------------------- + +def get_tools_by_state( trans, state ): + # TODO: this can be written so that it is much cleaner and faster + tool_id = [] + if state == trans.model.Tool.states.NEW: + for tool in get_tools( trans ): + if tool.is_new(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.ERROR: + for tool in get_tools( trans ): + if tool.is_error(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.DELETED: + for tool in get_tools( trans ): + if tool.is_deleted(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.WAITING: + for tool in get_tools( trans ): + if tool.is_waiting(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.APPROVED: + for tool in get_tools( trans ): + if tool.is_approved(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.REJECTED: + for tool in get_tools( trans ): + if tool.is_rejected(): + tool_id.append( tool.id ) + elif state == trans.model.Tool.states.ARCHIVED: + for tool in get_tools( trans ): + if tool.is_archived(): + tool_id.append( tool.id ) + return tool_id diff -r c642fbb301fc -r db4f8befcd89 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 13:09:29 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/common.py Fri Apr 30 14:08:23 2010 -0400 @@ -8,7 +8,7 @@ import logging log = logging.getLogger( __name__ ) -class CommunityCommon( BaseController ): +class CommonController( BaseController ): @web.expose def edit_tool( self, trans, cntrller, **kwd ): params = util.Params( kwd ) @@ -108,6 +108,54 @@ action='browse_tools', message='Not yet implemented, sorry...', status='error' ) ) + @web.expose + def browse_category( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_categories', + message='Select a category', + status='error' ) ) + category = get_category( trans, id ) + # If request came from the tool controller, then we need to filter by the state of the + # tool in addition to the category. + if cntrller == 'tool': + tool_id = get_approved_tools( trans, category=category ) + else: + # If request came from the admin controller, we don't filter on tool state. + tool_id = [ tca.tool.id for tca in category.tools ] + if not tool_id: + tool_id = 'None' + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + tool_id=tool_id ) ) + @web.expose + def browse_tools_by_user( self, trans, cntrller, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + id = params.get( 'id', None ) + if not id: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message='Select a user', + status='error' ) ) + user = get_user( trans, id ) + # If request came from the tool controller, then we need to filter by the state of the + # tool if the user is not viewing his own tools + if cntrller == 'tool': + tool_id = get_approved_tools( trans, user=user ) + else: + # If request came from the admin controller, we don't filter on tool state. + tool_id = [ tool.id for tool in user.tools ] + if not tool_id: + tool_id = 'None' + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools_by_user', + tool_id=tool_id ) ) ## ---- Utility methods ------------------------------------------------------- @@ -142,4 +190,33 @@ obj.categories.append( trans.model.ToolCategoryAssociation( obj, category ) ) def get_tool( trans, id ): return trans.sa_session.query( trans.model.Tool ).get( trans.app.security.decode_id( id ) ) - +def get_tools( trans ): + return trans.sa_session.query( trans.model.Tool ).order_by( trans.model.Tool.name ) +def get_approved_tools( trans, category=None, user=None ): + tool_id = [] + if category: + # Return only the approved tools in the category + for tca in category.tools: + tool = tca.tool + if tool.is_approved(): + tool_id.append( tool.id ) + elif user: + if trans.user == user: + # If the current user is browsing his own tools, then don't filter on state + tool_id = [ tool.id for tool in user.tools ] + else: + # The current user is viewing all tools uploaded by another user, so show only + # approved tools + for tool in user.active_tools: + if tool.is_approved(): + tool_id.append( tool.id ) + else: + # Return all approved tools + for tool in get_tools( trans ): + if tool.is_approved(): + tool_id.append( tool.id ) + return tool_id +def get_event( trans, id ): + return trans.sa_session.query( trans.model.Event ).get( trans.security.decode_id( id ) ) +def get_user( trans, id ): + return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) diff -r c642fbb301fc -r db4f8befcd89 lib/galaxy/webapps/community/controllers/tool.py --- a/lib/galaxy/webapps/community/controllers/tool.py Fri Apr 30 13:09:29 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/tool.py Fri Apr 30 14:08:23 2010 -0400 @@ -15,38 +15,111 @@ class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): if tool.categories: rval = '' for tca in tool.categories: - rval += '%s<br/>\n' % tca.category.name + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) return rval return 'not set' - def filter( self, trans, user, query, column_filter ): - # Category.name conflicts with Tool.name, so we have to make our own filter - def get_single_filter( filter ): - return func.lower( model.Category.name ).like( "%" + filter.lower() + "%" ) - if column_filter == 'All': - pass - elif isinstance( column_filter, list ): - clause_list = [] - for filter in column_filter: - clause_list.append( get_single_filter( filter ) ) - query = query.filter( or_( *clause_list ) ) - else: - query = query.filter( get_single_filter( column_filter ) ) - return query - def get_link( self, trans, grid, tool, filter_params ): + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) + # Grid definition + title = "Tools" + model_class = model.Tool + template='/webapps/community/tool/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + model_class=model.Tool, + link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), + attach_popup=True, + filterable="advanced" ), + VersionColumn( "Version", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + CategoryColumn( "Categories", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + UserColumn( "Uploaded By", + key="username", + model_class=model.User, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ + grids.GridOperation( "Download tool", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( controller="tool", action="download_tool", cntrller="tool", webapp="community" ) ) + ] + standard_filters = [ + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + default_filter = dict( name="All", deleted="False", username="All" ) + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, session ): + return session.query( self.model_class ) + def apply_default_filter( self, trans, query, **kwd ): + def filter_query( query, tool_id ): + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) + return query.filter( self.model_class.deleted==False ) + tool_id = kwd.get( 'tool_id', False ) + if not tool_id: + # Display only approved tools + tool_id = get_approved_tools( trans ) + if not tool_id: + tool_id = 'None' + return filter_query( query, tool_id ) + +class ToolsByUserListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.name + class VersionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.version + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.description + class CategoryColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): if tool.categories: - filter_params['f-category'] = [] + rval = '' for tca in tool.categories: - filter_params['f-category'].append( tca.category.name ) - if len( filter_params['f-category'] ) == 1: - filter_params['f-category'] = filter_params['f-category'][0] - filter_params['advanced-search'] = 'True' - return filter_params - return None + rval += '<a href="browse_category?id=%s">%s</a><br/>\n' % ( trans.security.encode_id( tca.category.id ), tca.category.name ) + return rval + return 'not set' class StateColumn( grids.GridColumn ): def get_value( self, trans, grid, tool ): state = tool.state() @@ -75,13 +148,9 @@ return accepted_filters class UserColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - return tool.user.username - def get_link( self, trans, grid, tool, filter_params ): - filter_params['f-username'] = tool.user.username - filter_params['advanced-search'] = 'True' - return filter_params + return '<a href="browse_tools_by_user?operation=browse&id=%s">%s</a>' % ( trans.security.encode_id( tool.user.id ), tool.user.username ) # Grid definition - title = "Tools" + title = "Tools By User" model_class = model.Tool template='/webapps/community/tool/grid.mako' default_sort_key = "name" @@ -92,21 +161,26 @@ link=( lambda item: dict( operation="View Tool", id=item.id, cntrller='tool', webapp="community" ) ), attach_popup=True, filterable="advanced" ), - CategoryColumn( "Categories", - key="category", + VersionColumn( "Version", model_class=model.Tool, attach_popup=False, filterable="advanced" ), + DescriptionColumn( "Description", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + CategoryColumn( "Categories", + model_class=model.Category, + attach_popup=False, + filterable="advanced" ), + StateColumn( "Status", + model_class=model.Event, + attach_popup=False ), UserColumn( "Uploaded By", key="username", model_class=model.User, attach_popup=False, filterable="advanced" ), - StateColumn( "State", - key="state", - model_class=model.Event, - attach_popup=False, - filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -130,18 +204,44 @@ preserve_state = False use_paging = True def build_initial_query( self, session ): - return session.query( self.model_class ).outerjoin( model.ToolCategoryAssociation ).outerjoin( model.Category ) - def apply_default_filter( self, trans, query, **kwargs ): - return query.filter( self.model_class.deleted==False ) + return session.query( self.model_class ) + def apply_default_filter( self, trans, query, **kwd ): + def filter_query( query, tool_id ): + if str( tool_id ).lower() in [ '', 'none' ]: + # Return an empty query since the current user cannot view any + # tools (possibly due to state not being approved, etc). + return query.filter( model.Tool.id == None ) + tool_id = util.listify( tool_id ) + query = query.filter( or_( *map( lambda id: self.model_class.id == id, tool_id ) ) ) + return query.filter( self.model_class.deleted==False ) + tool_id = kwd.get( 'tool_id', False ) + if not tool_id: + # Display only approved tools + tool_id = get_approved_tools( trans ) + if not tool_id: + tool_id = 'None' + return filter_query( query, tool_id ) -class ToolCategoryListGrid( grids.Grid ): +class CategoryListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.name class DescriptionColumn( grids.TextColumn ): def get_value( self, trans, grid, category ): return category.description + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, category ): + if category.tools: + viewable_tools = 0 + for tca in category.tools: + tool = tca.tool + if tool.is_approved(): + viewable_tools += 1 + return viewable_tools + return 0 + # Grid definition + webapp = "community" title = "Tool Categories" model_class = model.Category template='/webapps/community/category/grid.mako' @@ -157,7 +257,13 @@ key="description", model_class=model.Category, attach_popup=False, - filterable="advanced" ) + filterable="advanced" ), + ToolsColumn( "Tools", + model_class=model.Tool, + attach_popup=False, + filterable="advanced" ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] columns.append( grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[1] ], @@ -165,21 +271,23 @@ visible=False, filterable="standard" ) ) standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) ] - default_filter = dict( name="All", deleted="False" ) num_rows_per_page = 50 preserve_state = False use_paging = True def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query, **kwargs ): + def apply_default_filter( self, trans, query, **kwd ): return query.filter( self.model_class.deleted==False ) -class ToolBrowserController( BaseController ): - - tool_category_list_grid = ToolCategoryListGrid() +class ToolController( BaseController ): + tool_list_grid = ToolListGrid() + tools_by_user_list_grid = ToolsByUserListGrid() + category_list_grid = CategoryListGrid() @web.expose def index( self, trans, **kwd ): @@ -188,53 +296,84 @@ status = params.get( 'status', 'done' ) return trans.fill_template( '/webapps/community/index.mako', message=message, status=status ) @web.expose - def browse_tool_categories( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() + def browse_categories( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() if operation == "browse category": - category_id = int( trans.app.security.decode_id( kwargs['id'] ) ) - category = trans.sa_session.query( model.Category ).get( category_id ) - del kwargs['id'] - del kwargs['operation'] - kwargs['f-category'] = category.name - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tools', - **kwargs ) ) - return self.tool_category_list_grid( trans, **kwargs ) + return self.browse_category( trans, id=kwd['id'] ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_category', + cntrller='tool', + **kwd ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_category', + cntrller='tool', + **kwd ) ) + # Render the list view + return self.category_list_grid( trans, **kwd ) @web.expose - def browse_tools( self, trans, **kwargs ): - if 'operation' in kwargs: - operation = kwargs['operation'].lower() - if operation == "browse": - return trans.response.send_redirect( web.url_for( controller='tool', - action='browse_tool', + def browse_category( self, trans, **kwd ): + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='tool', + **kwd ) ) + @web.expose + def browse_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "view tool": return trans.response.send_redirect( web.url_for( controller='common', action='view_tool', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "edit tool": return trans.response.send_redirect( web.url_for( controller='common', action='edit_tool', cntrller='tool', - **kwargs ) ) + **kwd ) ) elif operation == "download tool": return trans.response.send_redirect( web.url_for( controller='tool', action='download_tool', - **kwargs ) ) + **kwd ) ) # Render the list view - return self.tool_list_grid( trans, **kwargs ) + return self.tool_list_grid( trans, **kwd ) @web.expose - def browse_tool( self, trans, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - return trans.fill_template( '/webapps/community/tool/browse_tool.mako', - tools=tools, - message=message, - status=status ) + def browse_tools_by_user( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "browse": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_tools_by_user', + cntrller='tool', + **kwd ) ) + elif operation == "browse category": + return trans.response.send_redirect( web.url_for( controller='common', + action='browse_category', + cntrller='tool', + **kwd ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='view_tool', + cntrller='tool', + **kwd ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='tool', + **kwd ) ) + elif operation == "download tool": + return trans.response.send_redirect( web.url_for( controller='tool', + action='download_tool', + **kwd ) ) + # Render the list view + return self.tools_by_user_list_grid( trans, **kwd ) @web.expose def download_tool( self, trans, **kwd ): params = util.Params( kwd ) diff -r c642fbb301fc -r db4f8befcd89 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py Fri Apr 30 13:09:29 2010 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Fri Apr 30 14:08:23 2010 -0400 @@ -92,7 +92,8 @@ DELETED = 'deleted', WAITING = 'waiting for approval', APPROVED = 'approved', - REJECTED = 'rejected' ) + REJECTED = 'rejected', + ARCHIVED = 'archived' ) def __init__( self, guid=None, tool_id=None, name=None, description=None, user_description=None, category=None, version=None, user_id=None, external_filename=None ): self.guid = guid self.tool_id = tool_id @@ -153,10 +154,14 @@ return self.state() == self.states.ERROR def is_deleted( self ): return self.state() == self.states.DELETED + def is_waiting( self ): + return self.state() == self.states.WAITING def is_approved( self ): return self.state() == self.states.APPROVED def is_rejected( self ): return self.state() == self.states.REJECTED + def is_archived( self ): + return self.state() == self.states.ARCHIVED @property def extension( self ): # if instantiated via a query, this unmapped property won't exist diff -r c642fbb301fc -r db4f8befcd89 lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 13:09:29 2010 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Fri Apr 30 14:08:23 2010 -0400 @@ -164,8 +164,8 @@ # With the tables defined we can define the mappers and setup the # relationships between the model objects. assign_mapper( context, User, User.table, - properties=dict( tools=relation( Tool, order_by=desc( Tool.table.c.update_time ) ), - active_tools=relation( Tool, primaryjoin=( ( Tool.table.c.user_id == User.table.c.id ) & ( not_( Tool.table.c.deleted ) ) ), order_by=desc( Tool.table.c.update_time ) ), + properties=dict( tools=relation( Tool, primaryjoin=( Tool.table.c.user_id == User.table.c.id ), order_by=( Tool.table.c.name ) ), + active_tools=relation( Tool, primaryjoin=( ( Tool.table.c.user_id == User.table.c.id ) & ( not_( Tool.table.c.deleted ) ) ), order_by=( Tool.table.c.name ) ), galaxy_sessions=relation( GalaxySession, order_by=desc( GalaxySession.table.c.update_time ) ) ) ) assign_mapper( context, Group, Group.table, @@ -238,7 +238,6 @@ ) ) - def guess_dialect_for_url( url ): return (url.split(':', 1))[0] diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako Fri Apr 30 13:09:29 2010 -0400 +++ b/templates/webapps/community/admin/index.mako Fri Apr 30 14:08:23 2010 -0400 @@ -54,7 +54,6 @@ </style> </%def> - <%def name="init()"> <% self.has_left_panel=True @@ -71,32 +70,34 @@ <div class="toolMenu"> <div class="toolSectionList"> <div class="toolSectionTitle"> + <span>Tools</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools_by_state', state=trans.model.Tool.states.WAITING, webapp='community' )}">Tools awaiting approval</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools_by_category' )}">Browse by category</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='browse_tools', webapp='community' )}">Browse all tools</a></div> + </div> + </div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + <span>Categories</span> + </div> + <div class="toolSectionBody"> + <div class="toolSectionBg"> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='manage_categories', webapp='community' )}">Manage categories</a></div> + </div> + </div> + <div class="toolSectionTitle"> <span>Security</span> </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='users', webapp='community' )}" target="galaxy_main">Manage users</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='groups', webapp='community' )}" target="galaxy_main">Manage groups</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='roles', webapp='community' )}" target="galaxy_main">Manage roles</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='users', webapp='community' )}">Manage users</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='groups', webapp='community' )}">Manage groups</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='admin', action='roles', webapp='community' )}">Manage roles</a></div> </div> </div> - <div class="toolSectionTitle"> - <span>Tools</span> - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tools', webapp='community' )}" target="galaxy_main">Manage tools</a></div> - </div> - </div> - <div class="toolSectionPad"></div> - <div class="toolSectionTitle"> - <span>Community</span> - </div> - <div class="toolSectionBody"> - <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='admin', action='categories', webapp='community' )}" target="galaxy_main">Manage categories</a></div> - </div> - </div> </div> </div> </div> diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/category/edit_category.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/category/edit_category.mako Fri Apr 30 14:08:23 2010 -0400 @@ -0,0 +1,44 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Change category name and description</div> + <div class="toolFormBody"> + <form name="library" action="${h.url_for( controller='admin', action='edit_category' )}" method="post" > + <div class="form-row"> + <input name="webapp" type="hidden" value="${webapp}" size=40"/> + <label>Name:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="name" value="${category.name}" size="40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input name="description" type="textfield" value="${category.description}" size=40"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="rename" value="submitted"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" name="edit_category_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/category/rename_category.mako --- a/templates/webapps/community/category/rename_category.mako Fri Apr 30 13:09:29 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Change category name and description</div> - <div class="toolFormBody"> - <form name="library" action="${h.url_for( controller='admin', action='rename_category' )}" method="post" > - <div class="form-row"> - <input name="webapp" type="hidden" value="${webapp}" size=40"/> - <label>Name:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="text" name="name" value="${category.name}" size="40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Description:</label> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input name="description" type="textfield" value="${category.description}" size=40"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="rename" value="submitted"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="hidden" name="id" value="${trans.security.encode_id( category.id )}"/> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" name="rename_category_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako Fri Apr 30 13:09:29 2010 -0400 +++ b/templates/webapps/community/index.mako Fri Apr 30 14:08:23 2010 -0400 @@ -1,6 +1,57 @@ <%inherit file="/webapps/community/base_panels.mako"/> <%namespace file="/message.mako" import="render_msg" /> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ## TODO: Clean up these styles and move into panel_layout.css (they are + ## used here and in the editor). + <style type="text/css"> + #left { + background: #C1C9E5 url(${h.url_for('/static/style/menu_bg.png')}) top repeat-x; + } + div.toolMenu { + margin: 5px; + margin-left: 10px; + margin-right: 10px; + } + div.toolSectionPad { + margin: 0; + padding: 0; + height: 5px; + font-size: 0px; + } + div.toolSectionDetailsInner { + margin-left: 5px; + margin-right: 5px; + } + div.toolSectionTitle { + padding-bottom: 0px; + font-weight: bold; + } + div.toolMenuGroupHeader { + font-weight: bold; + padding-top: 0.5em; + padding-bottom: 0.5em; + color: #333; + font-style: italic; + border-bottom: dotted #333 1px; + margin-bottom: 0.5em; + } + div.toolTitle { + padding-top: 5px; + padding-bottom: 5px; + margin-left: 16px; + margin-right: 10px; + display: list-item; + list-style: square outside; + } + a:link, a:visited, a:active + { + color: #303030; + } + </style> +</%def> + <%def name="init()"> <% self.has_left_panel=True @@ -29,17 +80,18 @@ </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='tool', action='browse_tool_categories' )}" target="galaxy_main">Browse tools by category</a></div> - <div class="toolTitle"><a href="${h.url_for( controller='tool', action='browse_tools' )}" target="galaxy_main">Browse all tools</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_categories' )}">Browse by category</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools' )}">Browse all tools</a></div> + <div class="toolTitle"><a target="galaxy_main" href="${h.url_for( controller='tool', action='browse_tools_by_user', operation='browse', id=trans.security.encode_id( trans.user.id ) )}">Browse your tools</a></div> </div> </div> <div class="toolSectionBody"> <div class="toolSectionBg"> <div class="toolTitle"> %if trans.user: - <a href="${h.url_for( controller='upload', action='upload', type='tool' )}" target="galaxy_main">Upload a tool</a> + <a target="galaxy_main" href="${h.url_for( controller='upload', action='upload', type='tool' )}">Upload a tool</a> %else: - Login to upload + <a target="galaxy_main" href="${h.url_for( controller='/user', action='login', webapp='community' )}">Login to upload</a> %endif </div> </div> @@ -54,7 +106,7 @@ if trans.app.config.require_login and not trans.user: center_url = h.url_for( controller='user', action='login', message=message, status=status ) else: - center_url = h.url_for( controller='tool', action='browse_tool_categories', message=message, status=status ) + center_url = h.url_for( controller='tool', action='browse_categories', message=message, status=status ) %> <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"> </iframe> </%def> diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/tool/browse_tool.mako --- a/templates/webapps/community/tool/browse_tool.mako Fri Apr 30 13:09:29 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -<%namespace file="/message.mako" import="render_msg" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/community/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="title()">Browse Tool</%def> - -<h2>Galaxy Tool</h2> - -%if message: - ${render_msg( message, status )} -%endif - -%if not tools: - There are no tools -%else: - <table class="grid"> - <thead> - <tr> - <th>Name</th> - <th>Description</th> - </tr> - </thead> - <tbody> - <tr class="formRow id="toolRow"> - <td><a href="${h.url_for( controller='tool', action='browse', id=trans.security.encode_id( tool.id ) )}">${tool.name}</a></td> - <td>${tool.description}</td> - </tr> - </tbody> - </table> -%endif diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 13:09:29 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Fri Apr 30 14:08:23 2010 -0400 @@ -123,7 +123,7 @@ <div class="toolParamHelp" style="clear: both;"> Tools must be approved before they are made available to others in the community. After you have submitted your tool to be published, you will no longer be able to modify it, so make sure the information above is - correct and has been saved before submitting for approval. + correct and and save any changes before submitting for approval. </div> </div> </form> diff -r c642fbb301fc -r db4f8befcd89 templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Fri Apr 30 13:09:29 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Fri Apr 30 14:08:23 2010 -0400 @@ -49,6 +49,14 @@ <h2>View Tool: ${tool.name} <em>${tool.description}</em></h2> +%if cntrller=='admin' and tool.is_waiting(): + <p> + <ul class="manage-table-actions"> + <li><a class="action-button" href="${h.url_for( controller='admin', action='set_tool_state', state=trans.model.Tool.states.APPROVED, id=trans.security.encode_id( tool.id ), cntrller=cntrller )}"><span>Approve</span></a></li> + </ul> + </p> +%endif + %if message: ${render_msg( message, status )} %endif

1 0

[hg] galaxy 3721: merge
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c642fbb301fc changeset: 3721:c642fbb301fc user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Apr 30 13:09:29 2010 -0400 description: merge diffstat: lib/galaxy/datatypes/interval.py | 5 +- lib/galaxy/web/base/controller.py | 12 +- lib/galaxy/web/controllers/dataset.py | 12 +- tools/ngs_rna/tophat_wrapper.py | 216 +++++++++++++++---- tools/ngs_rna/tophat_wrapper.xml | 364 +++++++++++++++++++++++++++++---- 5 files changed, 503 insertions(+), 106 deletions(-) diffs (733 lines): diff -r 20ba52b9d504 -r c642fbb301fc lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Fri Apr 30 13:08:33 2010 -0400 +++ b/lib/galaxy/datatypes/interval.py Fri Apr 30 13:09:29 2010 -0400 @@ -831,9 +831,12 @@ except: return False -class Gtf( Tabular ): +class Gtf( Gff ): """Tab delimited data in Gtf format""" file_ext = "gtf" + + def sniff( self, filename ): + return False class Wiggle( Tabular, _RemoteCallMixin ): """Tab delimited data in wiggle format""" diff -r 20ba52b9d504 -r c642fbb301fc lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py Fri Apr 30 13:08:33 2010 -0400 +++ b/lib/galaxy/web/base/controller.py Fri Apr 30 13:09:29 2010 -0400 @@ -122,10 +122,14 @@ """ Get an HDA object by id. """ # DEPRECATION: We still support unencoded ids for backward compatibility try: - dataset_id = int( dataset_id ) - except ValueError: - dataset_id = trans.security.decode_id( dataset_id ) - data = trans.sa_session.query( trans.model.HistoryDatasetAssociation ).get( dataset_id ) + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + if data is None: + raise ValueError( 'Invalid reference dataset id: %s.' % dataset_id ) + except: + try: + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) + except: + data = None if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid dataset id: %s." % str( dataset_id ) ) if check_ownership: diff -r 20ba52b9d504 -r c642fbb301fc lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Fri Apr 30 13:08:33 2010 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Fri Apr 30 13:09:29 2010 -0400 @@ -307,10 +307,14 @@ composite_extensions.append('html') # for archiving composite datatypes # DEPRECATION: We still support unencoded ids for backward compatibility try: - dataset_id = int( dataset_id ) - except ValueError: - dataset_id = trans.security.decode_id( dataset_id ) - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + if data is None: + raise ValueError( 'Invalid reference dataset id: %s.' % dataset_id ) + except: + try: + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( int( dataset_id ) ) + except: + data = None if not data: raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) current_user_roles = trans.get_current_user_roles() diff -r 20ba52b9d504 -r c642fbb301fc tools/ngs_rna/tophat_wrapper.py --- a/tools/ngs_rna/tophat_wrapper.py Fri Apr 30 13:08:33 2010 -0400 +++ b/tools/ngs_rna/tophat_wrapper.py Fri Apr 30 13:09:29 2010 -0400 @@ -1,6 +1,6 @@ #!/usr/bin/env python -import optparse, os, shutil, sys, tempfile +import optparse, os, shutil, subprocess, sys, tempfile, fileinput def stop_err( msg ): sys.stderr.write( "%s\n" % msg ) @@ -9,72 +9,184 @@ def __main__(): #Parse Command Line parser = optparse.OptionParser() - parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) - parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) + parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' ) + parser.add_option( '-C', '--coverage-output', dest='coverage_output_file', help='Coverage output file; formate is WIG.' ) + parser.add_option( '-J', '--junctions-output', dest='junctions_output_file', help='Junctions output file; formate is BED.' ) + parser.add_option( '-H', '--hits-output', dest='accepted_hits_output_file', help='Accepted hits output file; formate is SAM.' ) + parser.add_option( '', '--own-file', dest='own_file', help='' ) + parser.add_option( '-D', '--indexes-path', dest='index_path', help='Indexes directory; location of .ebwt and .fa files.' ) + parser.add_option( '-r', '--mate-inner-dist', dest='mate_inner_dist', help='This is the expected (mean) inner distance between mate pairs. \ + For, example, for paired end runs with fragments selected at 300bp, \ + where each end is 50bp, you should set -r to be 200. There is no default, \ + and this parameter is required for paired end runs.') + parser.add_option( '', '--mate-std-dev', dest='mate_std_dev', help='Standard deviation of distribution on inner distances between male pairs.' ) parser.add_option( '-a', '--min-anchor-length', dest='min_anchor_length', help='The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction.' ) + parser.add_option( '-m', '--splice-mismatches', dest='splice_mismatches', help='The maximum number of mismatches that can appear in the anchor region of a spliced alignment.' ) parser.add_option( '-i', '--min-intron-length', dest='min_intron_length', help='The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart.' ) parser.add_option( '-I', '--max-intron-length', dest='max_intron_length', help='The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read.' ) - parser.add_option( '-s', '--solexa-quals', dest='solexa_quals', help='Use the Solexa scale for quality values in FASTQ files.' ) - parser.add_option( '-S', '--solexa.3-quals', dest='solexa_quals', - help='As of the Illumina GA pipeline version 1.3, quality scores are encoded in Phred-scaled base-64. Use this option for FASTQ files from pipeline 1.3 or later.' ) - parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' ) - parser.add_option( '-C', '--coverage-output', dest='coverage_output_file', help='Coverage output file; formate is WIG.' ) - parser.add_option( '-J', '--junctions-output', dest='junctions_output_file', help='Junctions output file; formate is BED.' ) - parser.add_option( '-H', '--hits-output', dest='accepted_hits_output_file', help='Accepted hits output file; formate is SAM.' ) - parser.add_option( '-D', '--indexes-dir', dest='indexes_directory', help='Indexes directory; location of .ebwt and .fa files.' ) - parser.add_option( '-r', '--mate-inner-dist', dest='mate_inner_dist', help='This is the expected (mean) inner distance between mate pairs. \ - For, example, for paired end runs with fragments selected at 300bp, \ - where each end is 50bp, you should set -r to be 200. There is no default, \ - and this parameter is required for paired end runs.') + parser.add_option( '-F', '--junction_filter', dest='junction_filter', help='Filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)' ) + parser.add_option( '-g', '--max_multihits', dest='max_multihits', help='Maximum number of alignments to be allowed' ) + parser.add_option( '', '--microexon-search', action="store_true", dest='microexon_search', help='With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.') + parser.add_option( '', '--closure-search', action="store_true", dest='closure_search', help='Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (<= 50bp)') + parser.add_option( '', '--no-closure-search', action="store_false", dest='closure_search' ) + parser.add_option( '', '--coverage-search', action="store_true", dest='coverage_search', help='Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.') + parser.add_option( '', '--no-coverage-search', action="store_false", dest='coverage_search' ) + parser.add_option( '', '--min-segment-intron', dest='min_segment_intron', help='Minimum intron length that may be found during split-segment search' ) + parser.add_option( '', '--max-segment-intron', dest='max_segment_intron', help='Maximum intron length that may be found during split-segment search' ) + parser.add_option( '', '--min-closure-exon', dest='min_closure_exon', help='Minimum length for exonic hops in potential splice graph' ) + parser.add_option( '', '--min-closure-intron', dest='min_closure_intron', help='Minimum intron length that may be found during closure search' ) + parser.add_option( '', '--max-closure-intron', dest='max_closure_intron', help='Maximum intron length that may be found during closure search' ) + parser.add_option( '', '--min-coverage-intron', dest='min_coverage_intron', help='Minimum intron length that may be found during coverage search' ) + parser.add_option( '', '--max-coverage-intron', dest='max_coverage_intron', help='Maximum intron length that may be found during coverage search' ) + parser.add_option( '', '--seg-mismatches', dest='seg_mismatches', help='Number of mismatches allowed in each segment alignment for reads mapped independently' ) + parser.add_option( '', '--seg-length', dest='seg_length', help='Minimum length of read segments' ) + + # Wrapper options. + parser.add_option( '-1', '--input1', dest='input1', help='The (forward or single-end) reads file in Sanger FASTQ format' ) + parser.add_option( '-2', '--input2', dest='input2', help='The reverse reads file in Sanger FASTQ format' ) + parser.add_option( '', '--single-paired', dest='single_paired', help='' ) + parser.add_option( '', '--settings', dest='settings', help='' ) + (options, args) = parser.parse_args() - # Make temp directory for output. + #sys.stderr.write('*'*50+'\n'+str(options)+'\n'+'*'*50+'\n') + + # Creat bowtie index if necessary. + tmp_index_dir = tempfile.mkdtemp() + if options.own_file != 'None': + index_path = os.path.join( tmp_index_dir, os.path.split( options.own_file )[1] ) + cmd_index = 'bowtie-build -f %s %s' % ( options.own_file, index_path ) + try: + tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name + tmp_stderr = open( tmp, 'wb' ) + proc = subprocess.Popen( args=cmd_index, shell=True, cwd=tmp_index_dir, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr + except Exception, e: + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + stop_err( 'Error indexing reference sequence\n' + str( e ) ) + else: + index_path = options.index_path + + # Build tophat command. tmp_output_dir = tempfile.mkdtemp() - - # Build command. - - # Base. - cmd = "tophat -o %s " % ( tmp_output_dir ) - - # Add options. - if options.mate_inner_dist: - cmd += ( " -r %i" % int ( options.mate_inner_dist ) ) - - # Add index prefix. - cmd += " " + options.indexes_directory - - # Add input files. - cmd += " " + options.input1 - if options.mate_inner_dist: - # Using paired-end reads. - cmd += " " + options.input2 - - # Route program output to file. - cmd += " > %s" % tmp_output_dir + "/std_out.txt" - # Route program error output to file. - cmd += " 2> %s" % tmp_output_dir + "/std_err.txt" - - # Run. + cmd = 'tophat -o %s %s %s %s' + reads = options.input1 + if options.input2 != 'None': + reads += ' ' + options.input2 + opts = '-p %s' % options.num_threads + if options.single_paired == 'paired': + opts += ' -r %s' % options.mate_inner_dist + if options.settings == 'preSet': + cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) + else: + try: + if int( options.min_anchor_length ) >= 3: + opts += ' -a %s' % options.min_anchor_length + else: + raise Exception, 'Minimum anchor length must be 3 or greater' + opts += ' -m %s' % options.splice_mismatches + opts += ' -i %s' % options.min_intron_length + opts += ' -I %s' % options.max_intron_length + if float( options.junction_filter ) != 0.0: + opts += ' -F %s' % options.junction_filter + opts += ' -g %s' % options.max_multihits + if options.coverage_search: + opts += ' --coverage-search --min-coverage-intron %s --max-coverage-intron %s' % ( options.min_coverage_intron, options.max_coverage_intron ) + else: + opts += ' --no-coverage-search' + if options.closure_search: + opts += ' --closure-search --min-closure-exon %s --min-closure-intron %s --max-closure-intron %s' % ( options.min_closure_exon, options.min_closure_intron, options.max_closure_intron ) + else: + opts += ' --no-closure-search' + if options.microexon_search: + opts += ' --microexon-search' + if options.single_paired == 'paired': + opts += ' --mate-std-dev %s' % options.mate_std_dev + cmd = cmd % ( tmp_output_dir, opts, index_path, reads ) + except Exception, e: + # Clean up temp dirs + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + if os.path.exists( tmp_output_dir ): + shutil.rmtree( tmp_output_dir ) + stop_err( 'Something is wrong with the alignment parameters and the alignment could not be run\n' + str( e ) ) + print cmd + + # Run try: - os.system( cmd ) + tmp_out = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_stdout = open( tmp_out, 'wb' ) + tmp_err = tempfile.NamedTemporaryFile( dir=tmp_output_dir ).name + tmp_stderr = open( tmp_err, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, cwd=tmp_output_dir, stdout=tmp_stdout, stderr=tmp_stderr ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp_err, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stdout.close() + tmp_stderr.close() + if returncode != 0: + raise Exception, stderr except Exception, e: + # Clean up temp dirs + if os.path.exists( tmp_output_dir ): + shutil.rmtree( tmp_output_dir ) stop_err( 'Error in tophat:\n' + str( e ) ) # TODO: look for errors in program output. - # Copy output files from tmp directory to specified files. + # Postprocessing: copy output files from tmp directory to specified files. Also need to remove header lines from SAM file. try: - shutil.copyfile( tmp_output_dir + "/coverage.wig", options.coverage_output_file ) - shutil.copyfile( tmp_output_dir + "/junctions.bed", options.junctions_output_file ) - shutil.copyfile( tmp_output_dir + "/accepted_hits.sam", options.accepted_hits_output_file ) - except Exception, e: - stop_err( 'Error in tophat:\n' + str( e ) ) - - # Clean up temp dirs - if os.path.exists( tmp_output_dir ): - shutil.rmtree( tmp_output_dir ) + try: + shutil.copyfile( tmp_output_dir + "/coverage.wig", options.coverage_output_file ) + shutil.copyfile( tmp_output_dir + "/junctions.bed", options.junctions_output_file ) + + # Remove headers from SAM file in place. + in_header = True # Headers always at start of file. + for line in fileinput.input( tmp_output_dir + "/accepted_hits.sam", inplace=1 ): + if in_header and line.startswith("@"): + continue + else: + in_header = False + sys.stdout.write( line ) + + # Copy SAM File. + shutil.copyfile( tmp_output_dir + "/accepted_hits.sam", options.accepted_hits_output_file ) + except Exception, e: + stop_err( 'Error in tophat:\n' + str( e ) ) + finally: + # Clean up temp dirs + if os.path.exists( tmp_index_dir ): + shutil.rmtree( tmp_index_dir ) + if os.path.exists( tmp_output_dir ): + shutil.rmtree( tmp_output_dir ) if __name__=="__main__": __main__() diff -r 20ba52b9d504 -r c642fbb301fc tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml Fri Apr 30 13:08:33 2010 -0400 +++ b/tools/ngs_rna/tophat_wrapper.xml Fri Apr 30 13:09:29 2010 -0400 @@ -1,24 +1,104 @@ -<tool id="tophat" name="Tophat" version="1.0.13"> +<tool id="tophat" name="Tophat" version="1.0.0"> <description>Find splice junctions using RNA-seq data</description> <command interpreter="python"> - tophat_wrapper.py + tophat_wrapper.py + ## Change this to accomodate the number of threads you have available. --num-threads="4" - --coverage-output=$coverage - --junctions-output=$junctions + + ## Provide outputs. + --coverage-output=$coverage + --junctions-output=$junctions --hits-output=$accepted_hits + + ## Handle reference file. #if $refGenomeSource.genomeSource == "history": - --indexes-dir=$refGenomeSource.ownFile + --own-file=$refGenomeSource.ownFile + --indexes-path="None" #else: - --indexes-dir=$refGenomeSource.index.value + --own-file="None" + --indexes-path=$refGenomeSource.index.value #end if + + ## Are reads single-end or paired? + --single-paired=$singlePaired.sPaired + + ## First input file always required. + --input1=$singlePaired.input1 + + ## Set parms based on whether reads are single-end or paired. #if $singlePaired.sPaired == "single": - --input1=$singlePaired.input1 --input2="None" - #else: - -r $singlePaired.mean_inner_distance - --input1=$singlePaired.input1 - --input2=$singlePaired.input2 - #end if + -r "None" + --settings=$singlePaired.sParams.sSettingsType + #if $singlePaired.sParams.sSettingsType == "full": + --mate-std-dev="None" + -a $singlePaired.sParams.anchor_length + -m $singlePaired.sParams.splice_mismatches + -i $singlePaired.sParams.min_intron_length + -I $singlePaired.sParams.max_intron_length + -F $singlePaired.sParams.junction_filter + -g $singlePaired.sParams.max_multihits + --min-segment-intron $singlePaired.sParams.min_segment_intron + --max-segment-intron $singlePaired.sParams.max_segment_intron + --seg-mismatches=$singlePaired.sParams.seg_mismatches + --seg-length=$singlePaired.sParams.seg_length + #if $singlePaired.sParams.closure_search.use_search == "Yes": + --closure-search + --min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon + --min-closure-intron $singlePaired.sParams.closure_search.min_closure_intron + --max-closure-intron $singlePaired.sParams.closure_search.max_closure_intron + #else: + --no-closure-search + #end if + #if $singlePaired.sParams.coverage_search.use_search == "Yes": + --coverage-search + --min-coverage-intron $singlePaired.sParams.coverage_search.min_coverage_intron + --max-coverage-intron $singlePaired.sParams.coverage_search.max_coverage_intron + #else: + --no-coverage-search + #end if + ## No idea why the type conversion is necessary, but it seems to be. + #if str ($singlePaired.sParams.microexon_search) == "Yes": + --microexon-search + #end if + #end if + #else: + --input2=$singlePaired.input2 + -r $singlePaired.mate_inner_distance + --settings=$singlePaired.pParams.pSettingsType + #if $singlePaired.pParams.pSettingsType == "full": + --mate-std-dev=$singlePaired.pParams.mate_std_dev + -a $singlePaired.pParams.anchor_length + -m $singlePaired.pParams.splice_mismatches + -i $singlePaired.pParams.min_intron_length + -I $singlePaired.pParams.max_intron_length + -F $singlePaired.pParams.junction_filter + -g $singlePaired.pParams.max_multihits + --min-segment-intron $singlePaired.pParams.min_segment_intron + --max-segment-intron $singlePaired.pParams.max_segment_intron + --seg-mismatches=$singlePaired.pParams.seg_mismatches + --seg-length=$singlePaired.pParams.seg_length + #if $singlePaired.pParams.closure_search.use_search == "Yes": + --closure-search + --min-closure-exon $singlePaired.pParams.closure_search.min_closure_exon + --min-closure-intron $singlePaired.pParams.closure_search.min_closure_intron + --max-closure-intron $singlePaired.pParams.closure_search.max_closure_intron + #else: + --no-closure-search + #end if + #if $singlePaired.pParams.coverage_search.use_search == "Yes": + --coverage-search + --min-coverage-intron $singlePaired.pParams.coverage_search.min_coverage_intron + --max-coverage-intron $singlePaired.pParams.coverage_search.max_coverage_intron + #else: + --no-coverage-search + #end if + ## No idea why the type conversion is necessary, but it seems to be. + #if str ($singlePaired.pParams.microexon_search) == "Yes": + --microexon-search + #end if + #end if + #end if </command> <inputs> <conditional name="refGenomeSource"> @@ -27,56 +107,219 @@ <option value="history">Use one from the history</option> </param> <when value="indexed"> - <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> - <options from_file="bowtie_indices.loc"> - <column name="value" index="1" /> - <column name="name" index="0" /> - </options> - </param> - </when> + <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> + <options from_file="bowtie_indices.loc"> + <column name="value" index="1" /> + <column name="name" index="0" /> + </options> + </param> + </when> <when value="history"> <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> </when>  - </conditional>  + </conditional>  <conditional name="singlePaired"> <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> </param> <when value="single"> - <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <conditional name="sParams"> + <param name="sSettingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters."> + <option value="preSet">Use Defaults</option> + <option value="full">Full parameter list</option> + </param> + <when value="preSet" /> +  + <when value="full"> + <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /> + <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /> + <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /> + <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> + <param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /> + <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /> + <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> + <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> + <param name="seg_mismatches" type="integer" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /> + <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> +  + <conditional name="closure_search"> + <param name="use_search" type="select" label="Use Closure Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." /> + <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" /> + <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" /> + </when> + <when value="No" /> + </conditional> +  + <conditional name="coverage_search"> + <param name="use_search" type="select" label="Use Coverage Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" /> + <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /> + </when> + <when value="No" /> + </conditional> + <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + </when>  + </conditional>  </when> <when value="paired"> - <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> - <param format="fastqsanger" name="mean_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs"/> + <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/> + <param name="mate_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs" /> + <conditional name="pParams"> + <param name="pSettingsType" type="select" label="TopHat settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full parameter list"> + <option value="preSet">Commonly used</option> + <option value="full">Full parameter list</option> + </param> + <when value="preSet" /> +  + <when value="full"> + <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/> + <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." /> + <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" /> + <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." /> + <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." /> + <param name="junction_filter" type="float" value="0.15" label="Minimum isoform fraction: filter out junctions supported by too few alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" /> + <param name="max_multihits" type="integer" value="40" label="Maximum number of alignments to be allowed" /> + <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" /> + <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" /> + <param name="seg_mismatches" type="integer" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" /> + <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" /> +  + <conditional name="closure_search"> + <param name="use_search" type="select" label="Use Closure Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." /> + <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" /> + <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" /> + </when> + <when value="No" /> + </conditional> +  + <conditional name="coverage_search"> + <param name="use_search" type="select" label="Use Coverage Search"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" /> + <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" /> + </when> + <when value="No" /> + </conditional> + <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer."> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + </when>  + </conditional>  </when> </conditional> </inputs> - + <outputs> - <data format="sam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> - <data format="wig" name="coverage" label="${tool.name} on ${on_string}: coverage"/> + <data format="sam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> + <data format="bedgraph" name="coverage" label="${tool.name} on ${on_string}: coverage"/> <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> </outputs> - + <tests> +  + +  <test> - <param name="genomeSource" value="indexed"/> - <param name="index" value="test_ref"/> + <param name="genomeSource" value="history"/> + <param name="ownFile" ftype="fasta" value="tophat_in3.fa"/> <param name="sPaired" value="paired"/> <param name="input1" ftype="fastqsanger" value="tophat_in1.fq"/> <param name="input2" ftype="fastqsanger" value="tophat_in2.fq"/> - <param name="mean_inner_distance" value="20"/> -  <output name="coverage" file="tophat_out2.wig"/> <output name="junctions" file="tophat_out3.bed"/> </test> - </tests> - +  +  + </tests> + <help> **Tophat Overview** @@ -104,11 +347,15 @@ **Outputs** -Tophat produces three output files:: +Tophat produces three output files: - coverage.wig -- coverage of reads - accepted_hits.sam -- reads that were mapped onto genome - junctions.bed -- splice junctions identified by Tophat +- coverage.wig -- A UCSC BedGraph_ wigglegram track, showing the depth of coverage at each position, including the spliced read alignments. +- accepted_hits.sam -- A list of read alignments in SAM_ format. +- junctions.bed -- A UCSC BED_ track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction. + +.. _BedGraph: http://genome.ucsc.edu/goldenPath/help/bedgraph.html +.. _SAM: http://samtools.sourceforge.net/ +.. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 ------- @@ -122,8 +369,35 @@ This is a list of implemented Tophat options:: - -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments - selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter - is required for paired end runs. + -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments + selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter + is required for paired end runs. + --mate-std-dev INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. + -a/--min-anchor-length INT The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced + alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one + read with this many bases on each side. This must be at least 3 and the default is 8. + -m/--splice-mismatches INT The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0. + -i/--min-intron-length INT The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70. + -I/--max-intron-length INT The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000. + -F/--min-isoform-fraction 0.0-1.0 TopHat filters out junctions supported by too few alignments. Suppose a junction spanning two exons, is supported by S reads. Let the average depth of coverage of + exon A be D, and assume that it is higher than B. If S / D is less than the minimum isoform fraction, the junction is not reported. A value of zero disables the + filter. The default is 0.15. + -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many + alignments. The default is 40. + --no-closure-search Disables the mate pair closure-based search for junctions. Currently, has no effect - closure search is off by default. + --closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (about or less than 50bp) + --no-coverage-search Disables the coverage based search for junctions. + --coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity. + --microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer. + --butterfly-search TopHat will use a slower but potentially more sensitive algorithm to find junctions in addition to its standard search. Consider using this if you expect that your experiment produced a lot of reads from pre-mRNA, that fall within the introns of your transcripts. + --segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2. + --segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25. + --min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50. + --min-closure-intron The minimum intron length that may be found during closure search. The default is 50. + --max-closure-intron The maximum intron length that may be found during closure search. The default is 5000. + --min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50. + --max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000. + --min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50. + --max-segment-intron The maximum intron length that may be found during split-segment search. The default is 500000. </help> </tool>

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