galaxy-commits May 2010

galaxy-commits@lists.galaxyproject.org

2 participants
158 discussions

[hg] galaxy 3700: Encode HDA id for edit link in history panel.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c2a80b197ba5 changeset: 3700:c2a80b197ba5 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Apr 27 10:12:59 2010 -0400 description: Encode HDA id for edit link in history panel. diffstat: lib/galaxy/web/controllers/root.py | 3 ++- templates/root/history_common.mako | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diffs (25 lines): diff -r ba5b796311f3 -r c2a80b197ba5 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Apr 27 09:32:38 2010 -0400 +++ b/lib/galaxy/web/controllers/root.py Tue Apr 27 10:12:59 2010 -0400 @@ -253,7 +253,8 @@ history = trans.get_history() # TODO: hid handling data = history.datasets[ int( hid ) - 1 ] - elif id is not None: + elif id is not None: + id = trans.security.decode_id( id ) data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) else: trans.log_event( "Problem loading dataset id %s with history id %s." % ( str( id ), str( hid ) ) ) diff -r ba5b796311f3 -r c2a80b197ba5 templates/root/history_common.mako --- a/templates/root/history_common.mako Tue Apr 27 09:32:38 2010 -0400 +++ b/templates/root/history_common.mako Tue Apr 27 10:12:59 2010 -0400 @@ -47,7 +47,7 @@ %endif ></a> %if for_editing: - <a class="icon-button edit tooltip" title="Edit attributes" href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main"></a> + <a class="icon-button edit tooltip" title="Edit attributes" href="${h.url_for( controller='root', action='edit', id=trans.security.encode_id( data.id ) )}" target="galaxy_main"></a> %endif %endif %if for_editing:

1 0

[hg] galaxy 3699: Rename the tool_browser controller and add a l...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/ba5b796311f3 changeset: 3699:ba5b796311f3 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Apr 27 09:32:38 2010 -0400 description: Rename the tool_browser controller and add a link to the masthead. diffstat: lib/galaxy/webapps/community/buildapp.py | 2 +- lib/galaxy/webapps/community/controllers/admin.py | 2 +- lib/galaxy/webapps/community/controllers/tool.py | 161 +++++++++++++++ lib/galaxy/webapps/community/controllers/tool_browser.py | 161 --------------- lib/galaxy/webapps/community/controllers/upload.py | 4 +- templates/webapps/community/base_panels.mako | 1 + templates/webapps/community/index.mako | 4 +- templates/webapps/community/tool/browse_tool.mako | 2 +- templates/webapps/community/tool/view_tool.mako | 6 +- 9 files changed, 172 insertions(+), 171 deletions(-) diffs (441 lines): diff -r 83102f27fd1d -r ba5b796311f3 lib/galaxy/webapps/community/buildapp.py --- a/lib/galaxy/webapps/community/buildapp.py Mon Apr 26 17:02:37 2010 -0400 +++ b/lib/galaxy/webapps/community/buildapp.py Tue Apr 27 09:32:38 2010 -0400 @@ -76,7 +76,7 @@ add_controllers( webapp, app ) # These two routes handle our simple needs at the moment webapp.add_route( '/:controller/:action', action='index' ) - webapp.add_route( '/:action', controller='tool_browser', action='index' ) + webapp.add_route( '/:action', controller='tool', action='index' ) webapp.finalize_config() # Wrap the webapp in some useful middleware if kwargs.get( 'middleware', True ): diff -r 83102f27fd1d -r ba5b796311f3 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Mon Apr 26 17:02:37 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Tue Apr 27 09:32:38 2010 -0400 @@ -461,7 +461,7 @@ if 'operation' in kwargs: operation = kwargs['operation'].lower() if operation == "browse": - return trans.response.send_redirect( web.url_for( controller='tool_browser', + return trans.response.send_redirect( web.url_for( controller='tool', action='browse_tool', **kwargs ) ) elif operation == "edit tool": diff -r 83102f27fd1d -r ba5b796311f3 lib/galaxy/webapps/community/controllers/tool.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/webapps/community/controllers/tool.py Tue Apr 27 09:32:38 2010 -0400 @@ -0,0 +1,161 @@ +import sys, os, operator, string, shutil, re, socket, urllib, time, logging, mimetypes + +from galaxy.web.base.controller import * +from galaxy.webapps.community import model +from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.model.orm import * +from common import * + +log = logging.getLogger( __name__ ) + +# States for passing messages +SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" + +class ToolListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.name + class CategoryColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + if tool.categories: + return tool.categories + return 'not set' + class StateColumn( grids.GridColumn ): + def get_value( self, trans, grid, tool ): + state = tool.state() + if state == tool.states.NEW: + return '<div class="count-box state-color-queued">%s</div>' % state + if state == tool.states.WAITING: + return '<div class="count-box state-color-running">%s</div>' % state + if state == tool.states.APPROVED: + return '<div class="count-box state-color-ok">%s</div>' % state + if state == tool.states.REJECTED or state == tool.states.ERROR: + return '<div class="count-box state-color-error">%s</div>' % state + return state + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column.""" + accepted_filter_labels_and_vals = [ model.Tool.states.NEW, + model.Tool.states.WAITING, + model.Tool.states.APPROVED, + model.Tool.states.REJECTED, + model.Tool.states.DELETED, + "All" ] + accepted_filters = [] + for val in accepted_filter_labels_and_vals: + label = val.lower() + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args ) ) + return accepted_filters + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.user.email + # 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="Edit Tool", id=item.id, webapp="community" ) ), + attach_popup=True, + filterable="advanced" ), + CategoryColumn( "Category", + key="category", + model_class=model.Category, + link=( lambda item: dict( operation="View Tool", id=item.id, webapp="community" ) ), + 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" ) ) + global_actions = [ + grids.GridAction( "Upload tool", dict( controller='upload', action='upload', type='tool' ) ) + ] + operations = [ + grids.GridOperation( "Add to category", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( controller="common", action="add_category", webapp="community" ) ), + grids.GridOperation( "Remove from category", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( controller="common", action="remove_category", webapp="community" ) ), + grids.GridOperation( "View versions", condition=( lambda item: not item.deleted ), allow_multiple=False ) + ] + standard_filters = [ + 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 ): + return query.filter( self.model_class.deleted==False ) + +class ToolBrowserController( BaseController ): + + tool_list_grid = ToolListGrid() + + @web.expose + def index( 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/index.mako', message=message, status=status ) + @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_browser', + action='browse_tool', + **kwargs ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='tool_browser', + action='view_tool', + **kwargs ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='tool_browser', + **kwargs ) ) + # Render the list view + return self.tool_list_grid( trans, **kwargs ) + @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 ) + @web.expose + def download_tool( self, trans, id=None, **kwd ): + params = util.Params( kwd ) + tool = None + # Get the tool + tool = None + if id is not None: + id = trans.app.security.decode_id( id ) + tool = trans.sa_session.query( trans.model.Tool ).get( id ) + if tool is None: + return trans.response.send_redirect( web.url_for( controller='tool_browser', + action='browse_tools', + message='Please select a Tool to edit (the tool ID provided was invalid)', + status='error' ) ) + + trans.response.set_content_type(tool.mimetype) + trans.response.headers['Content-Length'] = int( os.stat( tool.file_name ).st_size ) + trans.response.headers['Content-Disposition'] = 'attachment; filename=%s' % tool.download_file_name + return open( tool.file_name ) diff -r 83102f27fd1d -r ba5b796311f3 lib/galaxy/webapps/community/controllers/tool_browser.py --- a/lib/galaxy/webapps/community/controllers/tool_browser.py Mon Apr 26 17:02:37 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,161 +0,0 @@ -import sys, os, operator, string, shutil, re, socket, urllib, time, logging, mimetypes - -from galaxy.web.base.controller import * -from galaxy.webapps.community import model -from galaxy.web.framework.helpers import time_ago, iff, grids -from galaxy.model.orm import * -from common import * - -log = logging.getLogger( __name__ ) - -# States for passing messages -SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" - -class ToolListGrid( grids.Grid ): - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool ): - return tool.name - class CategoryColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool ): - if tool.categories: - return tool.categories - return 'not set' - class StateColumn( grids.GridColumn ): - def get_value( self, trans, grid, tool ): - state = tool.state() - if state == tool.states.NEW: - return '<div class="count-box state-color-queued">%s</div>' % state - if state == tool.states.WAITING: - return '<div class="count-box state-color-running">%s</div>' % state - if state == tool.states.APPROVED: - return '<div class="count-box state-color-ok">%s</div>' % state - if state == tool.states.REJECTED or state == tool.states.ERROR: - return '<div class="count-box state-color-error">%s</div>' % state - return state - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column.""" - accepted_filter_labels_and_vals = [ model.Tool.states.NEW, - model.Tool.states.WAITING, - model.Tool.states.APPROVED, - model.Tool.states.REJECTED, - model.Tool.states.DELETED, - "All" ] - accepted_filters = [] - for val in accepted_filter_labels_and_vals: - label = val.lower() - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args ) ) - return accepted_filters - class UserColumn( grids.TextColumn ): - def get_value( self, trans, grid, tool ): - return tool.user.email - # 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="Edit Tool", id=item.id, webapp="community" ) ), - attach_popup=True, - filterable="advanced" ), - CategoryColumn( "Category", - key="category", - model_class=model.Category, - link=( lambda item: dict( operation="View Tool", id=item.id, webapp="community" ) ), - 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" ) ) - global_actions = [ - grids.GridAction( "Upload tool", dict( controller='upload', action='upload', type='tool' ) ) - ] - operations = [ - grids.GridOperation( "Add to category", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( controller="common", action="add_category", webapp="community" ) ), - grids.GridOperation( "Remove from category", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( controller="common", action="remove_category", webapp="community" ) ), - grids.GridOperation( "View versions", condition=( lambda item: not item.deleted ), allow_multiple=False ) - ] - standard_filters = [ - 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 ): - return query.filter( self.model_class.deleted==False ) - -class ToolBrowserController( BaseController ): - - tool_list_grid = ToolListGrid() - - @web.expose - def index( 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/index.mako', message=message, status=status ) - @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_browser', - action='browse_tool', - **kwargs ) ) - elif operation == "view tool": - return trans.response.send_redirect( web.url_for( controller='tool_browser', - action='view_tool', - **kwargs ) ) - elif operation == "edit tool": - return trans.response.send_redirect( web.url_for( controller='common', - action='edit_tool', - cntrller='tool_browser', - **kwargs ) ) - # Render the list view - return self.tool_list_grid( trans, **kwargs ) - @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 ) - @web.expose - def download_tool( self, trans, id=None, **kwd ): - params = util.Params( kwd ) - tool = None - # Get the tool - tool = None - if id is not None: - id = trans.app.security.decode_id( id ) - tool = trans.sa_session.query( trans.model.Tool ).get( id ) - if tool is None: - return trans.response.send_redirect( web.url_for( controller='tool_browser', - action='browse_tools', - message='Please select a Tool to edit (the tool ID provided was invalid)', - status='error' ) ) - - trans.response.set_content_type(tool.mimetype) - trans.response.headers['Content-Length'] = int( os.stat( tool.file_name ).st_size ) - trans.response.headers['Content-Disposition'] = 'attachment; filename=%s' % tool.download_file_name - return open( tool.file_name ) diff -r 83102f27fd1d -r ba5b796311f3 lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Mon Apr 26 17:02:37 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Tue Apr 27 09:32:38 2010 -0400 @@ -62,10 +62,10 @@ os.link( uploaded_file.name, obj.file_name ) except OSError: shutil.copy( uploaded_file.name, obj.file_name ) - # We're setting cntrller to 'tool_browser' since that is the only controller from which we can upload + # We're setting cntrller to 'tool' since that is the only controller from which we can upload return trans.response.send_redirect( web.url_for( controller='common', action='edit_tool', - cntrller='tool_browser', + cntrller='tool', id=trans.app.security.encode_id( obj.id ), message='Uploaded %s' % meta.message, status='done' ) ) diff -r 83102f27fd1d -r ba5b796311f3 templates/webapps/community/base_panels.mako --- a/templates/webapps/community/base_panels.mako Mon Apr 26 17:02:37 2010 -0400 +++ b/templates/webapps/community/base_panels.mako Tue Apr 27 09:32:38 2010 -0400 @@ -26,6 +26,7 @@ <td class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a></td> </%def> + ${tab( "tools", "Tools", h.url_for( controller='/tool', action='index', webapp='community' ) )} ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index', webapp='community' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} <td class="tab"> diff -r 83102f27fd1d -r ba5b796311f3 templates/webapps/community/index.mako --- a/templates/webapps/community/index.mako Mon Apr 26 17:02:37 2010 -0400 +++ b/templates/webapps/community/index.mako Tue Apr 27 09:32:38 2010 -0400 @@ -29,7 +29,7 @@ </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='tool_browser', action='browse_tools' )}" target="galaxy_main">Browse tools</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='tool', action='browse_tools' )}" target="galaxy_main">Browse tools</a></div> </div> </div> <div class="toolSectionPad"></div> @@ -51,7 +51,7 @@ if trans.app.config.require_login and not trans.user: center_url = h.url_for( controller='user', action='login', message=message, status=status ) else: - center_url = h.url_for( controller='tool_browser', action='browse_tools', message=message, status=status ) + center_url = h.url_for( controller='tool', action='browse_tools', message=message, status=status ) %> <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"> </iframe> </%def> diff -r 83102f27fd1d -r ba5b796311f3 templates/webapps/community/tool/browse_tool.mako --- a/templates/webapps/community/tool/browse_tool.mako Mon Apr 26 17:02:37 2010 -0400 +++ b/templates/webapps/community/tool/browse_tool.mako Tue Apr 27 09:32:38 2010 -0400 @@ -29,7 +29,7 @@ </thead> <tbody> <tr class="formRow id="toolRow"> - <td><a href="${h.url_for( controller='tool_browser', action='browse', id=trans.security.encode_id( tool.id ) )}">${tool.name}</a></td> + <td><a href="${h.url_for( controller='tool', action='browse', id=trans.security.encode_id( tool.id ) )}">${tool.name}</a></td> <td>${tool.description}</td> </tr> </tbody> diff -r 83102f27fd1d -r ba5b796311f3 templates/webapps/community/tool/view_tool.mako --- a/templates/webapps/community/tool/view_tool.mako Mon Apr 26 17:02:37 2010 -0400 +++ b/templates/webapps/community/tool/view_tool.mako Tue Apr 27 09:32:38 2010 -0400 @@ -19,7 +19,7 @@ <div class="toolFormTitle">${tool.name} <em>${tool.description}</em> ${tool.version} (ID: ${tool.tool_id})</div> <div class="toolFormBody"> <div class="form-row"> - Uploaded by <a href="${h.url_for(controller='tool_browser', action='user_tools')}">${tool.user.username}</a> on ${tool.create_time.strftime('%B %d, %Y')} + Uploaded by <a href="${h.url_for(controller='tool', action='user_tools')}">${tool.user.username}</a> on ${tool.create_time.strftime('%B %d, %Y')} <div style="clear: both"></div> </div> <div class="form-row"> @@ -36,12 +36,12 @@ </div> <div class="form-row"> <label>Download:</label> - <a href="${h.url_for(controller='tool_browser', action='download_tool', id=trans.app.security.encode_id( tool.id ))}"><img src="${h.url_for('/static/images/silk/page_white_compressed.png')}"> ${tool.tool_id}_${tool.version}</a> + <a href="${h.url_for(controller='tool', action='download_tool', id=trans.app.security.encode_id( tool.id ))}"><img src="${h.url_for('/static/images/silk/page_white_compressed.png')}"> ${tool.tool_id}_${tool.version}</a> <div style="clear: both"></div> </div> %if trans.user.id == tool.user_id: <div class="form-row"> - <em>This is your tool. You may <a href="${h.url_for(controller='tool_browser', action='edit_tool', id=trans.app.security.encode_id( tool.id ) )}">edit it</a>.</em> + <em>This is your tool. You may <a href="${h.url_for(controller='tool', action='edit_tool', id=trans.app.security.encode_id( tool.id ) )}">edit it</a>.</em> <div style="clear: both"></div> </div> %endif

1 0

[hg] galaxy 3698: Community space fixes and enhancements: separa...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/83102f27fd1d changeset: 3698:83102f27fd1d user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Apr 26 17:02:37 2010 -0400 description: Community space fixes and enhancements: separate the ToolListGrids into both controllers, add a new common controller for common methods across admin and tool_browser, first pass of tool category and tool state features. diffstat: lib/galaxy/web/controllers/requests_admin.py | 2 +- lib/galaxy/webapps/community/controllers/admin.py | 137 +++++++- lib/galaxy/webapps/community/controllers/common.py | 166 ++++++++++ lib/galaxy/webapps/community/controllers/tool_browser.py | 119 +++---- lib/galaxy/webapps/community/controllers/upload.py | 26 +- lib/galaxy/webapps/community/model/__init__.py | 68 ++- lib/galaxy/webapps/community/model/mapping.py | 28 +- lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py | 14 +- templates/webapps/community/admin/category/category_create.mako | 35 -- templates/webapps/community/admin/category/category_rename.mako | 44 -- templates/webapps/community/admin/category/grid.mako | 1 - templates/webapps/community/admin/category/role.mako | 118 ------- templates/webapps/community/admin/index.mako | 2 +- templates/webapps/community/category/add_to_category.mako | 24 + templates/webapps/community/category/create_category.mako | 35 ++ templates/webapps/community/category/grid.mako | 1 + templates/webapps/community/category/rename_category.mako | 44 ++ templates/webapps/community/tool/edit_tool.mako | 99 ++--- templates/webapps/community/upload/upload.mako | 15 + 19 files changed, 617 insertions(+), 361 deletions(-) diffs (1285 lines): diff -r 054527415fac -r 83102f27fd1d lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Mon Apr 26 15:40:52 2010 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Mon Apr 26 17:02:37 2010 -0400 @@ -48,7 +48,7 @@ elif request.state() == request.states.COMPLETE: return '<div class="count-box state-color-ok">%s</div>' % request.state() return request.state() - def filter( self, db_session, user, query, column_filter ): + def filter( self, trans, user, query, column_filter ): """ Modify query to filter request by state. """ if column_filter == "All": return query diff -r 054527415fac -r 83102f27fd1d lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py Mon Apr 26 15:40:52 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/admin.py Mon Apr 26 17:02:37 2010 -0400 @@ -1,8 +1,8 @@ from galaxy.web.base.controller import * -#from galaxy.web.controllers.admin import get_user, get_group, get_role 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 import logging log = logging.getLogger( __name__ ) @@ -294,7 +294,7 @@ webapp = "community" title = "Categories" model_class = model.Category - template='/webapps/community/admin/category/grid.mako' + template='/webapps/community/category/grid.mako' default_sort_key = "name" columns = [ NameColumn( "Name", @@ -346,15 +346,133 @@ def build_initial_query( self, session ): return session.query( self.model_class ) +# States for passing messages +SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" + +class ToolListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.name + 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 ) + return rval + return 'not set' + class StateColumn( grids.GridColumn ): + def get_value( self, trans, grid, tool ): + state = tool.state() + if state == tool.states.NEW: + return '<div class="count-box state-color-queued">%s</div>' % state + if state == tool.states.WAITING: + return '<div class="count-box state-color-running">%s</div>' % state + if state == tool.states.APPROVED: + return '<div class="count-box state-color-ok">%s</div>' % state + if state == tool.states.REJECTED or state == tool.states.ERROR: + return '<div class="count-box state-color-error">%s</div>' % state + return state + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column.""" + accepted_filter_labels_and_vals = [ model.Tool.states.NEW, + model.Tool.states.WAITING, + model.Tool.states.APPROVED, + model.Tool.states.REJECTED, + model.Tool.states.DELETED, + "All" ] + accepted_filters = [] + for val in accepted_filter_labels_and_vals: + label = val.lower() + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args ) ) + return accepted_filters + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.user.email + # 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="Edit Tool", id=item.id, webapp="community" ) ), + attach_popup=True, + filterable="advanced" ), + CategoryColumn( "Category", + key="category", + model_class=model.Category, + 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" ) + ] + 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( "Add to category", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( controller="common", action="add_category", cntrller="admin", webapp="community" ) ), + grids.GridOperation( "Remove from category", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( controller="common", action="remove_category", cntrller="admin", webapp="community" ) ), + grids.GridOperation( "View versions", condition=( lambda item: not item.deleted ), allow_multiple=False ) + ] + standard_filters = [ + 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 ): + return query.filter( self.model_class.deleted==False ) + class AdminCommunity( BaseController, Admin ): user_list_grid = UserListGrid() role_list_grid = RoleListGrid() group_list_grid = GroupListGrid() category_list_grid = CategoryListGrid() + tool_list_grid = ToolListGrid() @web.expose @web.require_admin + 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_browser', + action='browse_tool', + **kwargs ) ) + elif operation == "edit tool": + return trans.response.send_redirect( web.url_for( controller='common', + action='edit_tool', + cntrller='admin', + **kwargs ) ) + # Render the list view + return self.tool_list_grid( trans, **kwargs ) + @web.expose + @web.require_admin def categories( self, trans, **kwargs ): if 'operation' in kwargs: operation = kwargs['operation'].lower() @@ -401,7 +519,7 @@ webapp=webapp, message=util.sanitize_text( message ), status='error' ) ) - return trans.fill_template( '/webapps/community/admin/category/category_create.mako', + return trans.fill_template( '/webapps/community/category/create_category.mako', webapp=webapp, message=message, status=status ) @@ -442,7 +560,7 @@ webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) - return trans.fill_template( '/webapps/community/admin/category/category_rename.mako', + return trans.fill_template( '/webapps/community/category/rename_category.mako', category=category, webapp=webapp, message=message, @@ -546,14 +664,3 @@ webapp=webapp, message=util.sanitize_text( message ), status='done' ) ) - -## ---- Utility methods ------------------------------------------------------- - -def get_category( trans, id ): - """Get a User from the database by id.""" - # Load user from database - id = trans.security.decode_id( id ) - category = trans.sa_session.query( trans.model.Category ).get( id ) - if not category: - return trans.show_error_message( "Category not found for id (%s)" % str( id ) ) - return category diff -r 054527415fac -r 83102f27fd1d lib/galaxy/webapps/community/controllers/common.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/webapps/community/controllers/common.py Mon Apr 26 17:02:37 2010 -0400 @@ -0,0 +1,166 @@ +from galaxy.web.base.controller import * +#from galaxy.web.controllers.admin import get_user, get_group, get_role +from galaxy.webapps.community import model +from galaxy.model.orm import * +from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.web.form_builder import SelectField +import logging +log = logging.getLogger( __name__ ) + +class CommunityCommon( BaseController ): + @web.expose + def edit_tool( self, trans, cntrller, id=None, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + # Get the tool + tool = None + if id is not None: + encoded_id = id + id = trans.app.security.decode_id( id ) + tool = trans.sa_session.query( trans.model.Tool ).get( id ) + if tool is None: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message='Please select a Tool to edit (the tool ID provided was invalid)', + status='error' ) ) + 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' + elif params.save_button: + tool.user_description = util.restore_text( params.description ) + categories = [] + set_categories( trans, tool, util.listify( params.category_id ) ) + trans.sa_session.add( tool ) + trans.sa_session.flush() + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message="Saved categories and description for tool '%s'" % tool.name, + status='done' ) ) + categories = trans.sa_session.query( trans.model.Category ).order_by( trans.model.Category.table.c.name ).all() + return trans.fill_template( '/webapps/community/tool/edit_tool.mako', + cntrller=cntrller, + encoded_id = encoded_id, + tool=tool, + categories=categories, + message=message, + status=status ) + @web.expose + def view_tool( self, trans, cntrller, id=None, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + # Get the tool + tool = None + if id is not None: + id = trans.app.security.decode_id( id ) + tool = trans.sa_session.query( trans.model.Tool ).get( id ) + if tool is None: + return trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + message='Please select a Tool to edit (the tool ID provided was invalid)', + status='error' ) ) + return trans.fill_template( '/webapps/community/tool/view_tool.mako', + tool=tool, + message=message, + status=status ) + @web.expose + def add_category( self, trans, cntrller, **kwd ): + # TODO: we currently assume we are setting a tool category, so this method may need + # tweaking if / when we decide to set history or workflow categories + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) + id = params.get( 'id', None ) + # TODO: redirect if no id + tool = trans.sa_session.query( trans.model.Tool ).get( trans.security.decode_id( id ) ) + if params.get( 'add_category_button', False ): + category_ids = util.listify( params.get( 'category_id', '' ) ) + # TODO: redirect if no category_id + message = "The tool '%s' has been added to the categories: " % ( tool.name ) + for category_id in category_ids: + category = trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( category_id ) ) + tca = trans.app.model.ToolCategoryAssociation( tool, category ) + trans.sa_session.add( tca ) + trans.sa_session.flush() + message += " %s " % category.name + trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + use_panels=use_panels, + cntrller=cntrller, + message=util.sanitize_text( message ), + status=status ) ) + category_select_list = SelectField( 'category_id', multiple=True ) + for category in get_unassociated_categories( trans, tool ): + category_select_list.add_option( category.name, trans.security.encode_id( category.id ) ) + return trans.fill_template( '/webapps/community/category/add_to_category.mako', + cntrller=cntrller, + id=id, + category_select_list=category_select_list, + use_panels=use_panels ) + @web.expose + def remove_category( self, trans, cntrller, **kwd ): + # TODO: we currently assume we are setting a tool category, so this method may need + # tweaking if / when we decide to set history or workflow categories + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + use_panels = util.string_as_bool( params.get( 'use_panels', False ) ) + id = params.get( 'id', None ) + # TODO: redirect if no id + tool = trans.sa_session.query( trans.model.Tool ).get( trans.security.decode_id( id ) ) + category_id = params.get( 'category_id', None ) + category = trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( category_id ) ) + # TODO: redirect if no category_id + for tca in tool.categories: + if tca.category == category: + trans.sa_session.delete( tca ) + trans.sa_session.flush() + break + message = "The tool '%s' has been removed from the category '%s'" % ( tool.name, category.name ) + trans.response.send_redirect( web.url_for( controller=cntrller, + action='browse_tools', + use_panels=use_panels, + cntrller=cntrller, + message=util.sanitize_text( message ), + status=status ) ) + +## ---- Utility methods ------------------------------------------------------- + +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 ) +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 + # tweaking if / when we decide to set history or workflow categories + associated_categories = [] + for tca in obj.categories: + associated_categories.append( tca.category ) + categories = [] + for category in get_categories( trans ): + if category not in associated_categories: + categories.append( category ) + return categories +def get_category( trans, id ): + """Get a Category from the database by id.""" + # Load user from database + id = trans.security.decode_id( id ) + category = trans.sa_session.query( trans.model.Category ).get( id ) + if not category: + return trans.show_error_message( "Category not found for id (%s)" % str( id ) ) + return category +def set_categories( trans, obj, category_ids, delete_existing_assocs=True ): + if delete_existing_assocs: + for assoc in obj.categories: + trans.sa_session.delete( assoc ) + trans.sa_session.flush() + for category_id in category_ids: + # TODO: we currently assume we are setting a tool category, so this method may need + # tweaking if / when we decide to set history or workflow categories + category = trans.sa_session.query( trans.model.Category ).get( category_id ) + obj.categories.append( trans.model.ToolCategoryAssociation( obj, category ) ) diff -r 054527415fac -r 83102f27fd1d lib/galaxy/webapps/community/controllers/tool_browser.py --- a/lib/galaxy/webapps/community/controllers/tool_browser.py Mon Apr 26 15:40:52 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/tool_browser.py Mon Apr 26 17:02:37 2010 -0400 @@ -4,6 +4,7 @@ from galaxy.webapps.community import model from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.model.orm import * +from common import * log = logging.getLogger( __name__ ) @@ -13,15 +14,41 @@ class ToolListGrid( grids.Grid ): class NameColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - if tool.name: - return tool.name - return 'not set' + return tool.name class CategoryColumn( grids.TextColumn ): def get_value( self, trans, grid, tool ): - if tool.category: - return tool.category + if tool.categories: + return tool.categories return 'not set' - + class StateColumn( grids.GridColumn ): + def get_value( self, trans, grid, tool ): + state = tool.state() + if state == tool.states.NEW: + return '<div class="count-box state-color-queued">%s</div>' % state + if state == tool.states.WAITING: + return '<div class="count-box state-color-running">%s</div>' % state + if state == tool.states.APPROVED: + return '<div class="count-box state-color-ok">%s</div>' % state + if state == tool.states.REJECTED or state == tool.states.ERROR: + return '<div class="count-box state-color-error">%s</div>' % state + return state + def get_accepted_filters( self ): + """ Returns a list of accepted filters for this column.""" + accepted_filter_labels_and_vals = [ model.Tool.states.NEW, + model.Tool.states.WAITING, + model.Tool.states.APPROVED, + model.Tool.states.REJECTED, + model.Tool.states.DELETED, + "All" ] + accepted_filters = [] + for val in accepted_filter_labels_and_vals: + label = val.lower() + args = { self.key: val } + accepted_filters.append( grids.GridColumnFilter( label, args ) ) + return accepted_filters + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, tool ): + return tool.user.email # Grid definition title = "Tools" model_class = model.Tool @@ -31,9 +58,15 @@ NameColumn( "Name", key="name", model_class=model.Tool, - link=( lambda item: dict( operation="View Tool", id=item.id, webapp="community" ) ), - attach_popup=False, + link=( lambda item: dict( operation="Edit Tool", id=item.id, webapp="community" ) ), + attach_popup=True, filterable="advanced" ), + CategoryColumn( "Category", + key="category", + model_class=model.Category, + link=( lambda item: dict( operation="View Tool", id=item.id, webapp="community" ) ), + attach_popup=False, + filterable="advanced" ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ) ] @@ -46,6 +79,14 @@ grids.GridAction( "Upload tool", dict( controller='upload', action='upload', type='tool' ) ) ] operations = [ + grids.GridOperation( "Add to category", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( controller="common", action="add_category", webapp="community" ) ), + grids.GridOperation( "Remove from category", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( controller="common", action="remove_category", webapp="community" ) ), grids.GridOperation( "View versions", condition=( lambda item: not item.deleted ), allow_multiple=False ) ] standard_filters = [ @@ -84,8 +125,9 @@ action='view_tool', **kwargs ) ) elif operation == "edit tool": - return trans.response.send_redirect( web.url_for( controller='tool_browser', + return trans.response.send_redirect( web.url_for( controller='common', action='edit_tool', + cntrller='tool_browser', **kwargs ) ) # Render the list view return self.tool_list_grid( trans, **kwargs ) @@ -99,65 +141,6 @@ message=message, status=status ) @web.expose - def view_tool( self, trans, id=None, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - # Get the tool - tool = None - if id is not None: - id = trans.app.security.decode_id( id ) - tool = trans.sa_session.query( trans.model.Tool ).get( id ) - if tool is None: - return trans.response.send_redirect( web.url_for( controller='tool_browser', - action='browse_tools', - message='Please select a Tool to edit (the tool ID provided was invalid)', - status='error' ) ) - return trans.fill_template( '/webapps/community/tool/view_tool.mako', - tool=tool, - message=message, - status=status ) - @web.expose - def edit_tool( self, trans, id=None, **kwd ): - params = util.Params( kwd ) - message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) - # Get the tool - tool = None - if id is not None: - id = trans.app.security.decode_id( id ) - tool = trans.sa_session.query( trans.model.Tool ).get( id ) - if tool is None: - return trans.response.send_redirect( web.url_for( controller='tool_browser', - action='browse_tools', - message='Please select a Tool to edit (the tool ID provided was invalid)', - status='error' ) ) - if tool.user_id != trans.user.id: - return trans.response.send_redirect( web.url_for( controller='tool_browser', - action='view_tool', - message='You are not the owner of this tool and therefore cannot edit it', - status='error' ) ) - 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' - elif params.save_button: - tool.user_description = util.restore_text( params.description ) - categories = [] - tool.set_categories( trans, util.listify( params.category ) ) - trans.sa_session.add( tool ) - trans.sa_session.flush() - return trans.response.send_redirect( web.url_for( controller='tool_browser', - action='browse_tools', - message='Saved categories and description for %s' % tool.name, - status='done' ) ) - categories = trans.sa_session.query( trans.model.Category ).order_by( trans.model.Category.table.c.name ).all() - return trans.fill_template( '/webapps/community/tool/edit_tool.mako', - tool=tool, - categories=categories, - message=message, - status=status ) - @web.expose def download_tool( self, trans, id=None, **kwd ): params = util.Params( kwd ) tool = None diff -r 054527415fac -r 83102f27fd1d lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Mon Apr 26 15:40:52 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Mon Apr 26 17:02:37 2010 -0400 @@ -1,9 +1,9 @@ import sys, os, shutil, logging, urllib2 - from galaxy.web.base.controller import * 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 log = logging.getLogger( __name__ ) @@ -17,6 +17,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + category_ids = util.listify( params.get( 'category_id', '' ) ) uploaded_file = None if params.file_data == '' and params.url.strip() == '': message = 'No files were entered on the upload form.' @@ -35,22 +36,36 @@ if params.upload_button and uploaded_file: datatype = trans.app.datatypes_registry.get_datatype_by_extension( params.upload_type ) if datatype is None: - message = 'An unknown filetype was selected. This should not be possble, please report the error.' + message = 'An unknown file type was selected. This should not be possible, please report the error.' status = 'error' else: try: + # Initialize the tool object meta = datatype.verify( uploaded_file ) meta.user = trans.user meta.guid = trans.app.security.get_new_guid() obj = datatype.create_model_object( meta ) trans.sa_session.add( obj ) + if isinstance( obj, trans.app.model.Tool ): + if category_ids: + for category_id in category_ids: + category = trans.app.model.Category.get( trans.security.decode_id( category_id ) ) + # Initialize the tool category + tca = trans.app.model.ToolCategoryAssociation( obj, category ) + trans.sa_session.add( tca ) + # Initialize the tool event + event = trans.app.model.Event( trans.app.model.Tool.states.NEW ) + tea = trans.app.model.ToolEventAssociation( obj, event ) + trans.sa_session.add_all( ( event, tea ) ) trans.sa_session.flush() try: os.link( uploaded_file.name, obj.file_name ) except OSError: shutil.copy( uploaded_file.name, obj.file_name ) - return trans.response.send_redirect( web.url_for( controller='tool_browser', + # We're setting cntrller to 'tool_browser' since that is the only controller from which we can upload + return trans.response.send_redirect( web.url_for( controller='common', action='edit_tool', + cntrller='tool_browser', id=trans.app.security.encode_id( obj.id ), message='Uploaded %s' % meta.message, status='done' ) ) @@ -62,8 +77,11 @@ status = 'error' uploaded_file.close() 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', message=message, status=status, selected_upload_type=selected_upload_type, - upload_types=trans.app.datatypes_registry.get_datatypes_for_select_list() ) + upload_types=trans.app.datatypes_registry.get_datatypes_for_select_list(), + selected_categories=selected_categories, + categories=get_categories( trans ) ) diff -r 054527415fac -r 83102f27fd1d lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py Mon Apr 26 15:40:52 2010 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Mon Apr 26 17:02:37 2010 -0400 @@ -87,6 +87,12 @@ class Tool( object ): file_path = '/tmp' + states = Bunch( NEW = 'new', + ERROR = 'error', + DELETED = 'deleted', + WAITING = 'waiting for approval', + APPROVED = 'approved', + REJECTED = 'rejected' ) 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 @@ -124,15 +130,27 @@ self.description = datatype_bunch.description self.version = datatype_bunch.version self.user_id = datatype_bunch.user.id - def set_categories( self, trans, categories, delete_existing_assocs=True ): - if delete_existing_assocs: - for a in self.categories: - trans.sa_session.delete( a ) - trans.sa_session.flush() - for category in categories: - if not isinstance( category, Category ): - category = trans.sa_session.query( Category ).get( int( category ) ) - self.categories.append( ToolCategoryAssociation( self, category ) ) + def state( self ): + if self.events: + return self.events[0].event.state + return None + def last_comment( self ): + if self.events: + if self.events[0].comment: + return self.events[0].comment + else: + return '' + return 'No comment' + def is_new( self ): + return self.state() == self.states.NEW + def is_error( self ): + return self.state() == self.states.ERROR + def is_deleted( self ): + return self.state() == self.states.DELETED + def is_approved( self ): + return self.state() == self.states.APPROVED + def is_rejected( self ): + return self.state() == self.states.REJECTED @property def extension( self ): # if instantiated via a query, this unmapped property won't exist @@ -162,6 +180,27 @@ def mimetype( self ): return mimetypes.guess_type( self.download_file_name )[0] +class Event( object ): + def __init__( self, state=None, comment='' ): + self.state = state + self.comment = comment + +class ToolEventAssociation( object ): + def __init__( self, tool=None, event=None ): + self.tool = tool + self.event = event + +class Category( object ): + def __init__( self, name=None, description=None, deleted=False ): + self.name = name + self.description = description + self.deleted = deleted + +class ToolCategoryAssociation( object ): + def __init__( self, tool=None, category=None ): + self.tool = tool + self.category = category + class Tag ( object ): def __init__( self, id=None, type=None, parent_id=None, name=None ): self.id = id @@ -170,12 +209,6 @@ self.name = name def __str__ ( self ): return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % ( self.id, self.type, self.parent_id, self.name ) - -class Category( object ): - def __init__( self, name=None, description=None, deleted=False ): - self.name = name - self.description = description - self.deleted = deleted class ItemTagAssociation ( object ): def __init__( self, id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None ): @@ -193,11 +226,6 @@ class ToolAnnotationAssociation( object ): pass -class ToolCategoryAssociation( object ): - def __init__( self, tool=None, category=None ): - self.tool = tool - self.category = category - ## ---- Utility methods ------------------------------------------------------- def directory_hash_id( id ): diff -r 054527415fac -r 83102f27fd1d lib/galaxy/webapps/community/model/mapping.py --- a/lib/galaxy/webapps/community/model/mapping.py Mon Apr 26 15:40:52 2010 -0400 +++ b/lib/galaxy/webapps/community/model/mapping.py Mon Apr 26 17:02:37 2010 -0400 @@ -112,7 +112,7 @@ Column( "version", TrimmedString( 255 ) ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "external_filename" , TEXT ), - Column( "deleted", Boolean, default=False ) ) + Column( "deleted", Boolean, index=True, default=False ) ) Category.table = Table( "category", metadata, Column( "id", Integer, primary_key=True ), @@ -127,6 +127,18 @@ Column( "tool_id", Integer, ForeignKey( "tool.id" ), index=True ), Column( "category_id", Integer, ForeignKey( "category.id" ), index=True ) ) +Event.table = Table( 'event', metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "state", TrimmedString( 255 ), index=True ), + Column( "comment", TEXT ) ) + +ToolEventAssociation.table = Table( "tool_event_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "tool_id", Integer, ForeignKey( "tool.id" ), index=True ), + Column( "event_id", Integer, ForeignKey( "event.id" ), index=True ) ) + Tag.table = Table( "tag", metadata, Column( "id", Integer, primary_key=True ), Column( "type", Integer ), @@ -202,7 +214,17 @@ assign_mapper( context, Tool, Tool.table, properties = dict( categories=relation( ToolCategoryAssociation ), + events=relation( ToolEventAssociation ), user=relation( User.mapper ) + ) ) + +assign_mapper( context, Event, Event.table, + properties=None ) + +assign_mapper( context, ToolEventAssociation, ToolEventAssociation.table, + properties=dict( + tool=relation( Tool ), + event=relation( Event ) ) ) @@ -211,8 +233,8 @@ assign_mapper( context, ToolCategoryAssociation, ToolCategoryAssociation.table, properties=dict( - category=relation(Category), - tool=relation(Tool) + category=relation( Category ), + tool=relation( Tool ) ) ) diff -r 054527415fac -r 83102f27fd1d lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py --- a/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Mon Apr 26 15:40:52 2010 -0400 +++ b/lib/galaxy/webapps/community/model/migrate/versions/0001_initial_tables.py Mon Apr 26 17:02:37 2010 -0400 @@ -89,7 +89,19 @@ Column( "version", TrimmedString( 255 ) ), Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "external_filename" , TEXT ), - Column( "deleted", Boolean, default=False ) ) + Column( "deleted", Boolean, index=True, default=False ) ) + +Event_table = Table( 'event', metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "state", TrimmedString( 255 ), index=True ), + Column( "comment", TEXT ) ) + +ToolEventAssociation_table = Table( "tool_event_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "tool_id", Integer, ForeignKey( "tool.id" ), index=True ), + Column( "event_id", Integer, ForeignKey( "event.id" ), index=True ) ) Category_table = Table( "category", metadata, Column( "id", Integer, primary_key=True ), diff -r 054527415fac -r 83102f27fd1d templates/webapps/community/admin/category/category_create.mako --- a/templates/webapps/community/admin/category/category_create.mako Mon Apr 26 15:40:52 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $(function(){ - $("input:text:first").focus(); - }) - </script> -</%def> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Create Role</div> - <div class="toolFormBody"> - <form name="create_category_form" id="create_category_form" action="${h.url_for( action='create_category' )}" method="post" > - <div class="form-row"> - <input name="webapp" type="hidden" value="${webapp}" size=40"/> - <label>Name:</label> - <input name="name" type="textfield" value="" size=40"/> - </div> - <div class="form-row"> - <label>Description:</label> - <input name="description" type="textfield" value="" size=40"/> - </div> - <div class="form-row"> - <input type="submit" name="create_category_button" value="Save"/> - </div> - </form> - </div> -</div> diff -r 054527415fac -r 83102f27fd1d templates/webapps/community/admin/category/category_rename.mako --- a/templates/webapps/community/admin/category/category_rename.mako Mon Apr 26 15:40:52 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 054527415fac -r 83102f27fd1d templates/webapps/community/admin/category/grid.mako --- a/templates/webapps/community/admin/category/grid.mako Mon Apr 26 15:40:52 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -<%inherit file="/grid_base.mako"/> diff -r 054527415fac -r 83102f27fd1d templates/webapps/community/admin/category/role.mako --- a/templates/webapps/community/admin/category/role.mako Mon Apr 26 15:40:52 2010 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,118 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $(function(){ - $("input:text:first").focus(); - }) - </script> -</%def> - -<%def name="render_select( name, options )"> - <select name="${name}" id="${name}" style="min-width: 250px; height: 150px;" multiple> - %for option in options: - <option value="${option[0]}">${option[1]}</option> - %endfor - </select> -</%def> - -<script type="text/javascript"> -$().ready(function() { - $('#users_add_button').click(function() { - return !$('#out_users option:selected').remove().appendTo('#in_users'); - }); - $('#users_remove_button').click(function() { - return !$('#in_users option:selected').remove().appendTo('#out_users'); - }); - $('#groups_add_button').click(function() { - return !$('#out_groups option:selected').remove().appendTo('#in_groups'); - }); - $('#groups_remove_button').click(function() { - return !$('#in_groups option:selected').remove().appendTo('#out_groups'); - }); - $('form#associate_role_user_group').submit(function() { - $('#in_users option').each(function(i) { - $(this).attr("selected", "selected"); - }); - $('#in_groups option').each(function(i) { - $(this).attr("selected", "selected"); - }); - }); -}); -</script> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">Role '${role.name}'</div> - <div class="toolFormBody"> - <form name="associate_role_user_group" id="associate_role_user_group" action="${h.url_for( action='manage_users_and_groups_for_role', id=trans.security.encode_id( role.id ) )}" method="post" > - <input name="webapp" type="hidden" value="${webapp}" size=40"/> - <div class="form-row"> - <div style="float: left; margin-right: 10px;"> - <label>Users associated with '${role.name}'</label> - ${render_select( "in_users", in_users )}<br/> - <input type="submit" id="users_remove_button" value=">>"/> - </div> - <div> - <label>Users not associated with '${role.name}'</label> - ${render_select( "out_users", out_users )}<br/> - <input type="submit" id="users_add_button" value="<<"/> - </div> - </div> - <div class="form-row"> - <div style="float: left; margin-right: 10px;"> - <label>Groups associated with '${role.name}'</label> - ${render_select( "in_groups", in_groups )}<br/> - <input type="submit" id="groups_remove_button" value=">>"/> - </div> - <div> - <label>Groups not associated with '${role.name}'</label> - ${render_select( "out_groups", out_groups )}<br/> - <input type="submit" id="groups_add_button" value="<<"/> - </div> - </div> - <div class="form-row"> - <input type="submit" name="role_members_edit_button" value="Save"/> - </div> - </form> - </div> -</div> -<br clear="left"/> -<br/> -%if len( library_dataset_actions ) > 0: - <h3>Data library datasets associated with role '${role.name}'</h3> - <table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"> - <tr> - <td> - <ul> - %for ctr, library, in enumerate( library_dataset_actions.keys() ): - <li> - <img src="${h.url_for( '/static/images/silk/book_open.png' )}" class="rowIcon"/> - ${library.name} - <ul> - %for folder_path, permissions in library_dataset_actions[ library ].items(): - <li> - <img src="/static/images/silk/folder_page.png" class="rowIcon"/> - ${folder_path} - <ul> - % for permission in permissions: - <ul> - <li>${permission}</li> - </ul> - %endfor - </ul> - </li> - %endfor - </ul> - </li> - %endfor - </ul> - </td> - </tr> - </table> -%endif diff -r 054527415fac -r 83102f27fd1d templates/webapps/community/admin/index.mako --- a/templates/webapps/community/admin/index.mako Mon Apr 26 15:40:52 2010 -0400 +++ b/templates/webapps/community/admin/index.mako Mon Apr 26 17:02:37 2010 -0400 @@ -85,7 +85,7 @@ </div> <div class="toolSectionBody"> <div class="toolSectionBg"> - <div class="toolTitle"><a href="${h.url_for( controller='tool_browser', action='browse_tools', webapp='community' )}" target="galaxy_main">Manage tools</a></div> + <div class="toolTitle"><a href="${h.url_for( controller='admin', action='browse_tools', webapp='community' )}" target="galaxy_main">Manage tools</a></div> </div> </div> <div class="toolSectionPad"></div> diff -r 054527415fac -r 83102f27fd1d templates/webapps/community/category/add_to_category.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/category/add_to_category.mako Mon Apr 26 17:02:37 2010 -0400 @@ -0,0 +1,24 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Select a category</div> + <div class="toolFormBody"> + <form id="select_category" name="select_category" action="${h.url_for( controller='common', action='add_category', cntrller=cntrller, id=id, use_panels=use_panels )}" method="post" > + <div class="form-row"> + <label>Category:</label> + ${category_select_list.get_html()} + </div> + <div class="toolParamHelp" style="clear: both;"> + Multi-select list - hold the appropriate key while clicking to select multiple columns + </div> + <div class="form-row"> + <input type="submit" name="add_category_button" value="Add tool to categories"/> + </div> + </form> + </div> +</div> diff -r 054527415fac -r 83102f27fd1d templates/webapps/community/category/create_category.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/category/create_category.mako Mon Apr 26 17:02:37 2010 -0400 @@ -0,0 +1,35 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<%def name="javascripts()"> + ${parent.javascripts()} + <script type="text/javascript"> + $(function(){ + $("input:text:first").focus(); + }) + </script> +</%def> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Create Role</div> + <div class="toolFormBody"> + <form name="create_category_form" id="create_category_form" action="${h.url_for( action='create_category' )}" method="post" > + <div class="form-row"> + <input name="webapp" type="hidden" value="${webapp}" size=40"/> + <label>Name:</label> + <input name="name" type="textfield" value="" size=40"/> + </div> + <div class="form-row"> + <label>Description:</label> + <input name="description" type="textfield" value="" size=40"/> + </div> + <div class="form-row"> + <input type="submit" name="create_category_button" value="Save"/> + </div> + </form> + </div> +</div> diff -r 054527415fac -r 83102f27fd1d templates/webapps/community/category/grid.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/category/grid.mako Mon Apr 26 17:02:37 2010 -0400 @@ -0,0 +1,1 @@ +<%inherit file="/grid_base.mako"/> diff -r 054527415fac -r 83102f27fd1d templates/webapps/community/category/rename_category.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/category/rename_category.mako Mon Apr 26 17:02:37 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='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 054527415fac -r 83102f27fd1d templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Mon Apr 26 15:40:52 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Mon Apr 26 17:02:37 2010 -0400 @@ -17,57 +17,56 @@ ${render_msg( message, status )} %endif -<form id="tool_edit_form" name="tool_edit_form" action="${h.url_for( controller='tool_browser', action='edit_tool' )}" enctype="multipart/form-data" method="post"> -<input type="hidden" name="id" value="${trans.app.security.encode_id( tool.id )}"/> -<div class="toolForm"> - <div class="toolFormTitle">Edit Tool</div> - <div class="toolFormBody"> - <div class="form-row"> - <label>Categories:</label> - <div class="form-row-input"> - <select name="category" multiple size=5 style="min-width: 250px;"> - %for category in categories: - %if category.id in [ tool_category.id for tool_category in tool.categories ]: - <option value="${category.id}" selected>${category.name}</option> - %else: - <option value="${category.id}">${category.name}</option> - %endif - %endfor - </select> +<form id="tool_edit_form" name="tool_edit_form" action="${h.url_for( controller='common', action='edit_tool' )}" enctype="multipart/form-data" method="post"> + <input type="hidden" name="id" value="${trans.app.security.encode_id( tool.id )}"/> + <input type="hidden" name="cntrller" value="${cntrller}"/> + <div class="toolForm"> + <div class="toolFormTitle">Edit Tool</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Categories:</label> + <div class="form-row-input"> + <select name="category_id" multiple size=5 style="min-width: 250px;"> + %for category in categories: + %if category.id in [ tool_category.id for tool_category in tool.categories ]: + <option value="${category.id}" selected>${category.name}</option> + %else: + <option value="${category.id}">${category.name}</option> + %endif + %endfor + </select> + </div> + <div style="clear: both"></div> </div> - <div style="clear: both"></div> + <div class="form-row"> + <label>Description:</label> + <div class="form-row-input"><textarea name="description" rows="5" cols="35">${tool.user_description}</textarea></div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" class="primary-button" name="save_button" value="Save"> + </div> + </div> </div> - <div class="form-row"> - <label>Description:</label> - <div class="form-row-input"><textarea name="description" rows="5" cols="35">${tool.user_description}</textarea></div> - <div style="clear: both"></div> + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Upload new version</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>File:</label> + <div class="form-row-input"><input type="file" name="file_data"/></div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>URL:</label> + <div class="form-row-input"><input type="text" name="url" style="width: 100%;"/></div> + <div class="toolParamHelp" style="clear: both;"> + Instead of uploading directly from your computer, you may instruct Galaxy to download the file from a Web or FTP address. + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <input type="submit" class="primary-button" name="save_button" value="Save"> + </div> </div> - <div class="form-row"> - <input type="submit" class="primary-button" name="save_button" value="Save"> - </div> - </div> -</div> - -<p/> - -<div class="toolForm"> - <div class="toolFormTitle">Upload new version</div> - <div class="toolFormBody"> - <div class="form-row"> - <label>File:</label> - <div class="form-row-input"><input type="file" name="file_data"/></div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>URL:</label> - <div class="form-row-input"><input type="text" name="url" style="width: 100%;"/></div> - <div class="toolParamHelp" style="clear: both;"> - Instead of uploading directly from your computer, you may instruct Galaxy to download the file from a Web or FTP address. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" class="primary-button" name="save_button" value="Save"> - </div> -</div> </form> diff -r 054527415fac -r 83102f27fd1d templates/webapps/community/upload/upload.mako --- a/templates/webapps/community/upload/upload.mako Mon Apr 26 15:40:52 2010 -0400 +++ b/templates/webapps/community/upload/upload.mako Mon Apr 26 17:02:37 2010 -0400 @@ -46,6 +46,21 @@ <div style="clear: both"></div> </div> <div class="form-row"> + <label>Category</label> + <div class="form-row-input"> + <select name="category_id"> + %for category in categories: + %if category.id in selected_categories: + <option value="${trans.security.encode_id( category.id )}" selected>${category.name}</option> + %else: + <option value="${trans.security.encode_id( category.id )}">${category.name}</option> + %endif + %endfor + </select> + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> <label>URL:</label> <div class="form-row-input"><input type="text" name="url" style="width: 100%;"/></div> <div class="toolParamHelp" style="clear: both;">

1 0

[hg] galaxy 3697: Community app: Add the "view tool" interface a...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/054527415fac changeset: 3697:054527415fac user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Apr 26 15:40:52 2010 -0400 description: Community app: Add the "view tool" interface and make tools downloadable. diffstat: lib/galaxy/webapps/community/config.py | 3 + lib/galaxy/webapps/community/controllers/tool_browser.py | 53 +++++++++++++- lib/galaxy/webapps/community/controllers/upload.py | 1 + lib/galaxy/webapps/community/datatypes/__init__.py | 2 +- lib/galaxy/webapps/community/model/__init__.py | 31 ++++++++- static/images/silk/page_white_compressed.png | 0 templates/webapps/community/tool/edit_tool.mako | 2 +- templates/webapps/community/tool/view_tool.mako | 49 +++++++++++++ 8 files changed, 134 insertions(+), 7 deletions(-) diffs (261 lines): diff -r 5002f66739e1 -r 054527415fac lib/galaxy/webapps/community/config.py --- a/lib/galaxy/webapps/community/config.py Mon Apr 26 13:53:48 2010 -0400 +++ b/lib/galaxy/webapps/community/config.py Mon Apr 26 15:40:52 2010 -0400 @@ -62,6 +62,9 @@ self.log_events = False self.cloud_controller_instance = False self.datatypes_config = kwargs.get( 'datatypes_config_file', 'community_datatypes_conf.xml' ) + # Proxy features + self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) + self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() diff -r 5002f66739e1 -r 054527415fac lib/galaxy/webapps/community/controllers/tool_browser.py --- a/lib/galaxy/webapps/community/controllers/tool_browser.py Mon Apr 26 13:53:48 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/tool_browser.py Mon Apr 26 15:40:52 2010 -0400 @@ -1,4 +1,4 @@ -import sys, os, operator, string, shutil, re, socket, urllib, time, logging +import sys, os, operator, string, shutil, re, socket, urllib, time, logging, mimetypes from galaxy.web.base.controller import * from galaxy.webapps.community import model @@ -31,7 +31,7 @@ NameColumn( "Name", key="name", model_class=model.Tool, - link=( lambda item: dict( operation="Edit Tool", id=item.id, webapp="community" ) ), + link=( lambda item: dict( operation="View Tool", id=item.id, webapp="community" ) ), attach_popup=False, filterable="advanced" ), # Columns that are valid for filtering but are not visible. @@ -79,6 +79,10 @@ return trans.response.send_redirect( web.url_for( controller='tool_browser', action='browse_tool', **kwargs ) ) + elif operation == "view tool": + return trans.response.send_redirect( web.url_for( controller='tool_browser', + action='view_tool', + **kwargs ) ) elif operation == "edit tool": return trans.response.send_redirect( web.url_for( controller='tool_browser', action='edit_tool', @@ -95,6 +99,25 @@ message=message, status=status ) @web.expose + def view_tool( self, trans, id=None, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + # Get the tool + tool = None + if id is not None: + id = trans.app.security.decode_id( id ) + tool = trans.sa_session.query( trans.model.Tool ).get( id ) + if tool is None: + return trans.response.send_redirect( web.url_for( controller='tool_browser', + action='browse_tools', + message='Please select a Tool to edit (the tool ID provided was invalid)', + status='error' ) ) + return trans.fill_template( '/webapps/community/tool/view_tool.mako', + tool=tool, + message=message, + status=status ) + @web.expose def edit_tool( self, trans, id=None, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -102,7 +125,6 @@ # Get the tool tool = None if id is not None: - encoded_id = id id = trans.app.security.decode_id( id ) tool = trans.sa_session.query( trans.model.Tool ).get( id ) if tool is None: @@ -110,6 +132,11 @@ action='browse_tools', message='Please select a Tool to edit (the tool ID provided was invalid)', status='error' ) ) + if tool.user_id != trans.user.id: + return trans.response.send_redirect( web.url_for( controller='tool_browser', + action='view_tool', + message='You are not the owner of this tool and therefore cannot edit it', + status='error' ) ) 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' @@ -126,8 +153,26 @@ status='done' ) ) categories = trans.sa_session.query( trans.model.Category ).order_by( trans.model.Category.table.c.name ).all() return trans.fill_template( '/webapps/community/tool/edit_tool.mako', - encoded_id = encoded_id, tool=tool, categories=categories, message=message, status=status ) + @web.expose + def download_tool( self, trans, id=None, **kwd ): + params = util.Params( kwd ) + tool = None + # Get the tool + tool = None + if id is not None: + id = trans.app.security.decode_id( id ) + tool = trans.sa_session.query( trans.model.Tool ).get( id ) + if tool is None: + return trans.response.send_redirect( web.url_for( controller='tool_browser', + action='browse_tools', + message='Please select a Tool to edit (the tool ID provided was invalid)', + status='error' ) ) + + trans.response.set_content_type(tool.mimetype) + trans.response.headers['Content-Length'] = int( os.stat( tool.file_name ).st_size ) + trans.response.headers['Content-Disposition'] = 'attachment; filename=%s' % tool.download_file_name + return open( tool.file_name ) diff -r 5002f66739e1 -r 054527415fac lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py Mon Apr 26 13:53:48 2010 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Mon Apr 26 15:40:52 2010 -0400 @@ -51,6 +51,7 @@ shutil.copy( uploaded_file.name, obj.file_name ) return trans.response.send_redirect( web.url_for( controller='tool_browser', action='edit_tool', + id=trans.app.security.encode_id( obj.id ), message='Uploaded %s' % meta.message, status='done' ) ) except datatypes.DatatypeVerificationError, e: diff -r 5002f66739e1 -r 054527415fac lib/galaxy/webapps/community/datatypes/__init__.py --- a/lib/galaxy/webapps/community/datatypes/__init__.py Mon Apr 26 13:53:48 2010 -0400 +++ b/lib/galaxy/webapps/community/datatypes/__init__.py Mon Apr 26 15:40:52 2010 -0400 @@ -99,7 +99,7 @@ def verify( self, file ): msg = '' try: - tar = tarfile.TarFile( fileobj = file ) + tar = tarfile.open( file.name ) except tarfile.ReadError: raise DatatypeVerificationError( 'The tool file is not a readable tar file' ) xml_names = filter( lambda x: x.lower().endswith( '.xml' ), tar.getnames() ) diff -r 5002f66739e1 -r 054527415fac lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py Mon Apr 26 13:53:48 2010 -0400 +++ b/lib/galaxy/webapps/community/model/__init__.py Mon Apr 26 15:40:52 2010 -0400 @@ -4,7 +4,7 @@ Naming: try to use class names that have a distinct plural form so that the relationship cardinalities are obvious (e.g. prefer Dataset to Data) """ -import os.path, os, errno, sys, codecs, operator, tempfile, logging, tarfile +import os.path, os, errno, sys, codecs, operator, tempfile, logging, tarfile, mimetypes from galaxy.util.bunch import Bunch from galaxy import util from galaxy.util.hash_util import * @@ -96,6 +96,7 @@ self.version = version or "1.0.0" self.user_id = user_id self.external_filename = external_filename + self.__extension = None def get_file_name( self ): if not self.external_filename: assert self.id is not None, "ID must be set before filename used (commit the object)" @@ -132,6 +133,34 @@ if not isinstance( category, Category ): category = trans.sa_session.query( Category ).get( int( category ) ) self.categories.append( ToolCategoryAssociation( self, category ) ) + @property + def extension( self ): + # if instantiated via a query, this unmapped property won't exist + if '_Tool__extension' not in dir( self ): + self.__extension = None + if self.__extension is None: + head = open( self.file_name, 'rb' ).read( 4 ) + try: + assert head[:3] == 'BZh' + assert int( head[-1] ) in range( 0, 10 ) + self.__extension = 'tar.bz2' + except AssertionError: + pass + if self.__extension is None: + try: + assert head[:2] == '\037\213' + self.__extension = 'tar.gz' + except: + pass + if self.__extension is None: + self.__extension = 'tar' + return self.__extension + @property + def download_file_name( self ): + return '%s_%s.%s' % ( self.tool_id, self.version, self.extension ) + @property + def mimetype( self ): + return mimetypes.guess_type( self.download_file_name )[0] class Tag ( object ): def __init__( self, id=None, type=None, parent_id=None, name=None ): diff -r 5002f66739e1 -r 054527415fac static/images/silk/page_white_compressed.png Binary file static/images/silk/page_white_compressed.png has changed diff -r 5002f66739e1 -r 054527415fac templates/webapps/community/tool/edit_tool.mako --- a/templates/webapps/community/tool/edit_tool.mako Mon Apr 26 13:53:48 2010 -0400 +++ b/templates/webapps/community/tool/edit_tool.mako Mon Apr 26 15:40:52 2010 -0400 @@ -18,7 +18,7 @@ %endif <form id="tool_edit_form" name="tool_edit_form" action="${h.url_for( controller='tool_browser', action='edit_tool' )}" enctype="multipart/form-data" method="post"> -<input type="hidden" name="id" value="${encoded_id}"/> +<input type="hidden" name="id" value="${trans.app.security.encode_id( tool.id )}"/> <div class="toolForm"> <div class="toolFormTitle">Edit Tool</div> <div class="toolFormBody"> diff -r 5002f66739e1 -r 054527415fac templates/webapps/community/tool/view_tool.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/webapps/community/tool/view_tool.mako Mon Apr 26 15:40:52 2010 -0400 @@ -0,0 +1,49 @@ +<%namespace file="/message.mako" import="render_msg" /> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/community/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="title()">View Tool</%def> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">${tool.name} <em>${tool.description}</em> ${tool.version} (ID: ${tool.tool_id})</div> + <div class="toolFormBody"> + <div class="form-row"> + Uploaded by <a href="${h.url_for(controller='tool_browser', action='user_tools')}">${tool.user.username}</a> on ${tool.create_time.strftime('%B %d, %Y')} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Categories:</label> + %for category in [ tca.category for tca in tool.categories ]: + ${category.name} + %endfor + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Description:</label> + ${tool.user_description} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Download:</label> + <a href="${h.url_for(controller='tool_browser', action='download_tool', id=trans.app.security.encode_id( tool.id ))}"><img src="${h.url_for('/static/images/silk/page_white_compressed.png')}"> ${tool.tool_id}_${tool.version}</a> + <div style="clear: both"></div> + </div> + %if trans.user.id == tool.user_id: + <div class="form-row"> + <em>This is your tool. You may <a href="${h.url_for(controller='tool_browser', action='edit_tool', id=trans.app.security.encode_id( tool.id ) )}">edit it</a>.</em> + <div style="clear: both"></div> + </div> + %endif + </div> +</div>

1 0

[hg] galaxy 3696: Fix indentations.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/5002f66739e1 changeset: 3696:5002f66739e1 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Apr 26 13:53:48 2010 -0400 description: Fix indentations. diffstat: templates/root/history_common.mako | 22 +++++++++++----------- 1 files changed, 11 insertions(+), 11 deletions(-) diffs (32 lines): diff -r 0ed61e8bd1d5 -r 5002f66739e1 templates/root/history_common.mako --- a/templates/root/history_common.mako Mon Apr 26 13:48:24 2010 -0400 +++ b/templates/root/history_common.mako Mon Apr 26 13:53:48 2010 -0400 @@ -127,17 +127,17 @@ ## icons. <div style="clear: both"></div> %endif - <div style="clear: both"></div> - %for display_app in data.datatype.get_display_types(): - <% target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> - %if len( display_links ) > 0: - | ${data.datatype.get_display_label(display_app)} - %for display_name, display_link in display_links: - <a target="${target_frame}" href="${display_link}">${_(display_name)}</a> - %endfor - %endif - %endfor - %endif + <div style="clear: both"></div> + %for display_app in data.datatype.get_display_types(): + <% target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> + %if len( display_links ) > 0: + | ${data.datatype.get_display_label(display_app)} + %for display_name, display_link in display_links: + <a target="${target_frame}" href="${display_link}">${_(display_name)}</a> + %endfor + %endif + %endfor + %endif %for display_app in data.get_display_applications( trans ).itervalues(): | ${display_app.name} %for link_app in display_app.links.itervalues():

1 0

[hg] galaxy 3695: Rollback display links/peek ordering in histor...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0ed61e8bd1d5 changeset: 3695:0ed61e8bd1d5 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Apr 26 13:48:24 2010 -0400 description: Rollback display links/peek ordering in history datasets so that links appear above peek. diffstat: templates/root/history_common.mako | 41 ++++++++++++++++++------------------- 1 files changed, 20 insertions(+), 21 deletions(-) diffs (53 lines): diff -r 1a3bc21d3a8e -r 0ed61e8bd1d5 templates/root/history_common.mako --- a/templates/root/history_common.mako Mon Apr 26 09:58:21 2010 -0400 +++ b/templates/root/history_common.mako Mon Apr 26 13:48:24 2010 -0400 @@ -127,29 +127,28 @@ ## icons. <div style="clear: both"></div> %endif + <div style="clear: both"></div> + %for display_app in data.datatype.get_display_types(): + <% target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> + %if len( display_links ) > 0: + | ${data.datatype.get_display_label(display_app)} + %for display_name, display_link in display_links: + <a target="${target_frame}" href="${display_link}">${_(display_name)}</a> + %endfor + %endif + %endfor + %endif + %for display_app in data.get_display_applications( trans ).itervalues(): + | ${display_app.name} + %for link_app in display_app.links.itervalues(): + <a target="${link_app.url.get( 'target_frame', '_blank' )}" href="${link_app.get_display_url( data, trans )}">${_(link_app.name)}</a> + %endfor + %endfor + + </div> %if data.peek != "no peek": <div><pre id="peek${data.id}" class="peek">${_(data.display_peek())}</pre></div> - %endif - <div style="clear: both"></div> - %for display_app in data.datatype.get_display_types(): - <% target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> - %if len( display_links ) > 0: - | ${data.datatype.get_display_label(display_app)} - %for display_name, display_link in display_links: - <a target="${target_frame}" href="${display_link}">${_(display_name)}</a> - %endfor - %endif - %endfor - %endif - %for display_app in data.get_display_applications( trans ).itervalues(): - | ${display_app.name} - %for link_app in display_app.links.itervalues(): - <a target="${link_app.url.get( 'target_frame', '_blank' )}" href="${link_app.get_display_url( data, trans )}">${_(link_app.name)}</a> - %endfor - %endfor - - </div> - + %endif %else: <div>${_('Error: unknown dataset state "%s".') % data_state}</div> %endif

1 0

[hg] galaxy 3694: Add missing job_id substitutions to jobs/runne...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/1a3bc21d3a8e changeset: 3694:1a3bc21d3a8e user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Apr 26 09:58:21 2010 -0400 description: Add missing job_id substitutions to jobs/runners/pbs.py. diffstat: lib/galaxy/jobs/runners/pbs.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r df8fc06fdac9 -r 1a3bc21d3a8e lib/galaxy/jobs/runners/pbs.py --- a/lib/galaxy/jobs/runners/pbs.py Sun Apr 25 16:18:15 2010 -0400 +++ b/lib/galaxy/jobs/runners/pbs.py Mon Apr 26 09:58:21 2010 -0400 @@ -378,7 +378,7 @@ try: # recheck to make sure it wasn't a communication problem self.check_single_job( pbs_server_name, job_id ) - log.warning( "(%s/%s) job was not in state check list, but was found with individual state check" ) + log.warning( "(%s/%s) job was not in state check list, but was found with individual state check" % ( galaxy_job_id, job_id ) ) new_watched.append( pbs_job_state ) except: errno, text = pbs.error()

1 0

[hg] galaxy 3693: Fix multiple issues for history display. Fixes...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/df8fc06fdac9 changeset: 3693:df8fc06fdac9 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sun Apr 25 16:18:15 2010 -0400 description: Fix multiple issues for history display. Fixes include: (a) empty annotations hidden; (b) text 'import XXX' added next to import icon; (c) fix dataset display links; (d) fix dataset view links; and (e) fix peek placement. diffstat: lib/galaxy/datatypes/interval.py | 2 +- lib/galaxy/web/controllers/history.py | 2 -- templates/dataset/display.mako | 5 ++++- templates/display_base.mako | 2 +- templates/history/display.mako | 15 ++++++++++++--- templates/history/view.mako | 12 +----------- templates/page/history_annotation_table.mako | 2 +- templates/root/history.mako | 2 +- templates/root/history_common.mako | 28 ++++++++++++++++++++++------ templates/workflow/display.mako | 7 ++++++- 10 files changed, 49 insertions(+), 28 deletions(-) diffs (237 lines): diff -r 7151ae06bf7a -r df8fc06fdac9 lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Sat Apr 24 15:03:22 2010 -0400 +++ b/lib/galaxy/datatypes/interval.py Sun Apr 25 16:18:15 2010 -0400 @@ -235,7 +235,7 @@ # if our URL scheme is https. Making this work # requires additional hackery in your upstream proxy. # If UCSC ever supports https, remove this hack. - internal_url = "%s" % url_for( controller='dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) + internal_url = "%s" % url_for( controller='/dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) if base_url.startswith( 'https://' ): base_url = base_url.replace( 'https', 'http', 1 ) display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) diff -r 7151ae06bf7a -r df8fc06fdac9 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Sat Apr 24 15:03:22 2010 -0400 +++ b/lib/galaxy/web/controllers/history.py Sun Apr 25 16:18:15 2010 -0400 @@ -590,11 +590,9 @@ error( "Either you are not allowed to view this history or the owner of this history has not made it accessible." ) # View history. datasets = self.get_history_datasets( trans, history_to_view ) - user_owns_history = ( trans.get_user() == history_to_view.user ) return trans.stream_template_mako( "history/view.mako", history = history_to_view, datasets = datasets, - user_owns_history = user_owns_history, show_deleted = False ) @web.expose diff -r 7151ae06bf7a -r df8fc06fdac9 templates/dataset/display.mako --- a/templates/dataset/display.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/dataset/display.mako Sun Apr 25 16:18:15 2010 -0400 @@ -24,7 +24,10 @@ <%def name="render_item_links( data )"> ## Provide links to save data and import dataset. <a href="${h.url_for( controller='/dataset', action='display', dataset_id=trans.security.encode_id( data.id ), to_ext=data.ext )}" class="icon-button disk tooltip" title="Save dataset"></a> - <a href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( data.id ) )}" class="icon-button import tooltip" title="Import dataset"></a> + <a + href="${h.url_for( controller='/dataset', action='imp', dataset_id=trans.security.encode_id( data.id ) )}" + class="icon-button import tooltip" + title="Import dataset"></a> </%def> <%def name="render_item( data, data_to_render )"> diff -r 7151ae06bf7a -r df8fc06fdac9 templates/display_base.mako --- a/templates/display_base.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/display_base.mako Sun Apr 25 16:18:15 2010 -0400 @@ -114,7 +114,7 @@ <%def name="render_item_header( item )"> <h3>Galaxy ${get_class_display_name( item.__class__ )} '${get_item_name( item )| h}'</h3> - %if hasattr( item, "annotation"): + %if hasattr( item, "annotation") and item.annotation is not None: <div class="annotation">Annotation: ${item.annotation}</div> %endif <hr/> diff -r 7151ae06bf7a -r df8fc06fdac9 templates/history/display.mako --- a/templates/history/display.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/history/display.mako Sun Apr 25 16:18:15 2010 -0400 @@ -38,7 +38,12 @@ </%def> <%def name="render_item_links( history )"> - <a href="${h.url_for( controller='/history', action='imp', id=trans.security.encode_id(history.id) )}" class="icon-button import tooltip" title="Import history"></a> + <a + href="${h.url_for( controller='/history', action='imp', id=trans.security.encode_id(history.id) )}" + class="icon-button import" + ## Needed to overwide initial width so that link is floated left appropriately. + style="width: 100%" + title="Import history">Import history</a> </%def> <%def name="render_item( history, datasets )"> @@ -60,10 +65,14 @@ %if data.visible: <td> <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset=user_owns_history )} + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} </div> </td> - <td class="annotation">${data.annotation}</td> + <td class="annotation"> + %if hasattr( data, "annotation") and data.annotation is not None: + ${data.annotation} + %endif + </td> %endif </tr> %endfor diff -r 7151ae06bf7a -r df8fc06fdac9 templates/history/view.mako --- a/templates/history/view.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/history/view.mako Sun Apr 25 16:18:15 2010 -0400 @@ -64,11 +64,6 @@ </%def> <%def name="center_panel()"> - ## For now, turn off inline editing so that view is external only. - <% - user_owns_history = False - %> - ## Get URL to other histories owned by user that owns this history. <% ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. @@ -84,9 +79,7 @@ <div style="overflow: auto; height: 100%;"> ## Render view of history. <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> - %if not user_owns_history: <a href="${h.url_for( action='imp', id=trans.security.encode_id(history.id) )}">import and start using history</a> | - %endif <a href="${get_history_link( history )}">${_('refresh')}</a> %if show_deleted: | <a href="${h.url_for('history', show_deleted=False)}">${_('hide deleted')}</a> @@ -95,9 +88,6 @@ </div> <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - %if user_owns_history: - <div style="float: right"><a id="history-rename" title="Rename" class="icon-button edit" target="galaxy_main" href="${h.url_for( controller='history', action='rename' )}"></a></div> - %endif <div id="history-name">${history.get_display_name()}</div> </div> @@ -118,7 +108,7 @@ %for data in datasets: %if data.visible: <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset=user_owns_history )} + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} </div> %endif %endfor diff -r 7151ae06bf7a -r df8fc06fdac9 templates/page/history_annotation_table.mako --- a/templates/page/history_annotation_table.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/page/history_annotation_table.mako Sun Apr 25 16:18:15 2010 -0400 @@ -50,7 +50,7 @@ ##<td valign="top" class="annotation">Describe this step: why was it done? what data does it produce?</td> <td> <div class="historyItemContainer" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset = False )} + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = False )} </div> </td> </tr> diff -r 7151ae06bf7a -r df8fc06fdac9 templates/root/history.mako --- a/templates/root/history.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/root/history.mako Sun Apr 25 16:18:15 2010 -0400 @@ -387,7 +387,7 @@ %for data in reversed( datasets ): %if data.visible: <div class="historyItemContainer" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, user_owns_dataset = True )} + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = True )} </div> %endif %endfor diff -r 7151ae06bf7a -r df8fc06fdac9 templates/root/history_common.mako --- a/templates/root/history_common.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/root/history_common.mako Sun Apr 25 16:18:15 2010 -0400 @@ -1,6 +1,6 @@ <% _=n_ %> ## Render the dataset `data` as history item, using `hid` as the displayed id -<%def name="render_dataset( data, hid, show_deleted_on_refresh = False, user_owns_dataset = True )"> +<%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True )"> <a name="${trans.security.encode_id( data.id )}"></a> <% if data.state in ['no state','',None]: @@ -29,16 +29,28 @@ ## links should be enough. However the number of datasets being uploaded ## at a time is usually small so the impact of these images is also small. <img src="${h.url_for('/static/images/eye_icon_grey.png')}" width='16' height='16' alt='display data' title='display data' class='button display' border='0'> - %if user_owns_dataset: + %if for_editing: <img src="${h.url_for('/static/images/pencil_icon_grey.png')}" width='16' height='16' alt='edit attributes' title='edit attributes' class='button edit' border='0'> %endif %else: - <a class="icon-button display tooltip" title="Display data in browser" href="${h.url_for( controller='dataset', action='display', dataset_id=trans.security.encode_id( data.id ), preview=True, filename='' )}" target="galaxy_main"></a> - %if user_owns_dataset: + <% + dataset_id = trans.security.encode_id( data.id ) + if for_editing: + display_url = h.url_for( controller='dataset', action='display', dataset_id=dataset_id, preview=True, filename='' ) + else: + display_url = h.url_for( controller='dataset', action='display_by_username_and_slug', + username=data.history.user.username, slug=dataset_id ) + %> + <a class="icon-button display tooltip" title="Display data in browser" href="${display_url}" + %if for_editing: + target="galaxy_main" + %endif + ></a> + %if for_editing: <a class="icon-button edit tooltip" title="Edit attributes" href="${h.url_for( controller='root', action='edit', id=data.id )}" target="galaxy_main"></a> %endif %endif - %if user_owns_dataset: + %if for_editing: <a class="icon-button delete tooltip" title="Delete" href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${data.id}"></a> %endif </div> @@ -89,7 +101,7 @@ <% dataset_id=trans.security.encode_id( data.id ) %> %if data.has_data: <a href="${h.url_for( controller='dataset', action='display', dataset_id=dataset_id, to_ext=data.ext )}" title="Save" class="icon-button disk tooltip"></a> - %if user_owns_dataset: + %if for_editing: <a href="${h.url_for( controller='tool_runner', action='rerun', id=data.id )}" target="galaxy_main" title="Run this job again" class="icon-button arrow-circle tooltip"></a> %if app.config.get_bool( 'enable_tracks', False ) and data.ext in app.datatypes_registry.get_available_tracks(): <a class="icon-button vis-chart tooltip trackster" title="Visualize in Trackster" id="visualize_${hid}"></a> @@ -110,6 +122,10 @@ </div> %endif + %else: + ## When displaying datasets for viewing, this is often needed to prevent peek from overlapping + ## icons. + <div style="clear: both"></div> %endif %if data.peek != "no peek": <div><pre id="peek${data.id}" class="peek">${_(data.display_peek())}</pre></div> diff -r 7151ae06bf7a -r df8fc06fdac9 templates/workflow/display.mako --- a/templates/workflow/display.mako Sat Apr 24 15:03:22 2010 -0400 +++ b/templates/workflow/display.mako Sun Apr 25 16:18:15 2010 -0400 @@ -71,7 +71,12 @@ <%def name="render_item_links( workflow )"> - <a href="${h.url_for( controller='/workflow', action='imp', id=trans.security.encode_id(workflow.id) )}" class="icon-button import tooltip" title="Import workflow"></a> + <a + href="${h.url_for( controller='/workflow', action='imp', id=trans.security.encode_id(workflow.id) )}" + class="icon-button import" + ## Needed to overwide initial width so that link is floated left appropriately. + style="width: 100%" + title="Import workflow">Import workflow</a> </%def> <%def name="render_item( workflow, steps )">

1 0

[hg] galaxy 3692: Better labels for rna-seq tools' output datasets.
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/7151ae06bf7a changeset: 3692:7151ae06bf7a user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Sat Apr 24 15:03:22 2010 -0400 description: Better labels for rna-seq tools' output datasets. diffstat: tools/ngs_rna/cuffcompare_wrapper.py | 4 +++- tools/ngs_rna/cuffcompare_wrapper.xml | 6 +++--- tools/ngs_rna/cuffdiff_wrapper.py | 4 +++- tools/ngs_rna/cuffdiff_wrapper.xml | 22 +++++++++++----------- tools/ngs_rna/cufflinks_wrapper.py | 4 +++- tools/ngs_rna/cufflinks_wrapper.xml | 6 +++--- tools/ngs_rna/tophat_wrapper.xml | 6 +++--- 7 files changed, 29 insertions(+), 23 deletions(-) diffs (130 lines): diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffcompare_wrapper.py --- a/tools/ngs_rna/cuffcompare_wrapper.py Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.py Sat Apr 24 15:03:22 2010 -0400 @@ -33,11 +33,13 @@ if options.ignore_nonoverlap: cmd += " -R " + # Output/debugging. + print cmd + # Add input files. if type(args) is list: args = " ".join(args) cmd += " " + args - print cmd # Run command. try: diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffcompare_wrapper.xml --- a/tools/ngs_rna/cuffcompare_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -32,9 +32,9 @@ </inputs> <outputs> - <data format="gtf" name="transcripts_combined" label="Cuffcompare on data ${input1.hid} and data ${input2.hid}: combined transcripts"/> - <data format="tracking" name="transcripts_tracking" label="Cuffcompare on data ${input1.hid} and data ${input2.hid}: transcript tracking"/> - <data format="gtf" name="transcripts_accuracy" label="Cuffcompare on data ${input1.hid} and data ${input2.hid}: transcript accuracy"/> + <data format="gtf" name="transcripts_combined" label="${tool.name} on ${on_string}: combined transcripts"/> + <data format="tracking" name="transcripts_tracking" label="${tool.name} on ${on_string}: transcript tracking"/> + <data format="gtf" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy"/> </outputs> <tests> diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffdiff_wrapper.py --- a/tools/ngs_rna/cuffdiff_wrapper.py Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.py Sat Apr 24 15:03:22 2010 -0400 @@ -69,9 +69,11 @@ if options.max_mle_iterations: cmd += ( " --max-mle-iterations %i" % int ( options.max_mle_iterations ) ) + # Output/debugging. + print cmd + # Add inputs. cmd += " " + options.inputA + " " + options.input1 + " " + options.input2 - print cmd # Run command. try: diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -44,17 +44,17 @@ </inputs> <outputs> - <data format="tabular" name="isoforms_exp" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: isoform expression"/> - <data format="tabular" name="genes_exp" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: gene expression"/> - <data format="tabular" name="tss_groups_exp" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: TSS groups expression"/> - <data format="tabular" name="cds_exp_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: CDS Expression FPKM Tracking"/> - <data format="tabular" name="splicing_diff" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: splicing diff"/> - <data format="tabular" name="cds_diff" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: CDS diff"/> - <data format="tabular" name="promoters_diff" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: promoters diff"/> - <data format="tabular" name="tss_groups_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: TSS groups FPKM tracking" /> - <data format="tabular" name="cds_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: CDS FPKM tracking"/> - <data format="tabular" name="genes_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: gene FPKM tracking"/> - <data format="tabular" name="isoforms_fpkm_tracking" label="Cuffdiff on data ${gtf_input.hid}, data ${aligned_reads1.hid}, and data ${aligned_reads2.hid}: isoform FPKM tracking"/> + <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: isoform expression"/> + <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene expression"/> + <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups expression"/> + <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS Expression FPKM Tracking"/> + <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing diff"/> + <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS diff"/> + <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters diff"/> + <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" /> + <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking"/> + <data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking"/> + <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: isoform FPKM tracking"/> </outputs> <tests> diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cufflinks_wrapper.py --- a/tools/ngs_rna/cufflinks_wrapper.py Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.py Sat Apr 24 15:03:22 2010 -0400 @@ -62,9 +62,11 @@ if options.max_mle_iterations: cmd += ( " --max-mle-iterations %i" % int ( options.max_mle_iterations ) ) + # Output/debugging. + print cmd + # Add input files. cmd += " " + options.input - print cmd # Run command. try: diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -50,9 +50,9 @@ </inputs> <outputs> - <data format="expr" name="genes_expression" label="Cufflinks on data ${input.hid}: gene expression"/> - <data format="expr" name="transcripts_expression" label="Cufflinks on data ${input.hid}: transcript expression"/> - <data format="gtf" name="assembled_isoforms" label="Cufflinks on data ${input.hid}: assembled transcripts"/> + <data format="expr" name="genes_expression" label="${tool.name} on ${on_string}: gene expression"/> + <data format="expr" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression"/> + <data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts"/> </outputs> <tests> diff -r 0dd1676e5b6f -r 7151ae06bf7a tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml Fri Apr 23 17:04:39 2010 -0400 +++ b/tools/ngs_rna/tophat_wrapper.xml Sat Apr 24 15:03:22 2010 -0400 @@ -55,9 +55,9 @@ </inputs> <outputs> - <data format="sam" name="accepted_hits"/> - <data format="wig" name="coverage" /> - <data format="bed" name="junctions" /> + <data format="sam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits"/> + <data format="wig" name="coverage" label="${tool.name} on ${on_string}: coverage"/> + <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions"/> </outputs> <tests>

1 0

[hg] galaxy 3691: Some fixes for the async datasource tool contr...
by Nate Coraor 10 May '10

10 May '10

details: http://www.bx.psu.edu/hg/galaxy/rev/0dd1676e5b6f changeset: 3691:0dd1676e5b6f user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Apr 23 17:04:39 2010 -0400 description: Some fixes for the async datasource tool controller. diffstat: lib/galaxy/web/controllers/async.py | 4 ++-- 1 files changed, 2 insertions(+), 2 deletions(-) diffs (19 lines): diff -r 7ae394334e5c -r 0dd1676e5b6f lib/galaxy/web/controllers/async.py --- a/lib/galaxy/web/controllers/async.py Fri Apr 23 16:32:40 2010 -0400 +++ b/lib/galaxy/web/controllers/async.py Fri Apr 23 17:04:39 2010 -0400 @@ -108,8 +108,8 @@ data.name = GALAXY_NAME data.dbkey = GALAXY_BUILD data.info = GALAXY_INFO + trans.sa_session.add( data ) #Need to add data to session before setting state (setting state requires that the data object is in the session, but this may change) data.state = data.states.NEW - trans.sa_session.add( data ) open( data.file_name, 'wb' ).close() #create the file trans.history.add_dataset( data, genome_build=GALAXY_BUILD ) trans.sa_session.add( trans.history ) @@ -135,4 +135,4 @@ trans.sa_session.flush() - return trans.fill_template('tool_executed.tmpl', out_data={}, tool=tool, config=self.app.config ) + return trans.fill_template( 'tool_executed.mako', history=history, toolbox=toolbox, tool=tool, util=util, out_data={} )

1 0

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