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commit/galaxy-central: dan: Fix for uninstalling a Tool Shed Repository.
by Bitbucket 12 Oct '12

12 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f8869673cf8c/ changeset: f8869673cf8c user: dan date: 2012-10-12 21:35:41 summary: Fix for uninstalling a Tool Shed Repository. affected #: 1 file diff -r 7be1e88035efd985c886c9e2723aa49c08557274 -r f8869673cf8cac165cd738333b48f0b21f3de60e lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -451,6 +451,8 @@ tool_shed_repository = get_repository( trans, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) if relative_install_dir: + if tool_path: + relative_install_dir = os.path.join( tool_path, relative_install_dir ) repository_install_dir = os.path.abspath( relative_install_dir ) else: repository_install_dir = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for installing tool shed repositories broken in 7890:18ab38e43d8b due to removal of ToolBoxSearch.enabled property.
by Bitbucket 12 Oct '12

12 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7be1e88035ef/ changeset: 7be1e88035ef user: dan date: 2012-10-12 19:25:20 summary: Fix for installing tool shed repositories broken in 7890:18ab38e43d8b due to removal of ToolBoxSearch.enabled property. affected #: 1 file diff -r f37d6fdc76107abac84672a228f1b0433a8a8624 -r 7be1e88035efd985c886c9e2723aa49c08557274 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -165,9 +165,7 @@ app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict # Write the current in-memory version of the integrated_tool_panel.xml file to disk. app.toolbox.write_integrated_tool_panel_config_file() - if app.toolbox_search.enabled: - # If search support for tools is enabled, index the new installed tools. - app.toolbox_search = ToolBoxSearch( app.toolbox ) + app.toolbox_search = ToolBoxSearch( app.toolbox ) def alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=False, override=True ): """ Parse a proprietary datatypes config (a datatypes_conf.xml file included in an installed tool shed repository) and @@ -1884,9 +1882,7 @@ # Update the config_elems of the in-memory shed_tool_conf_dict. shed_tool_conf_dict[ 'config_elems' ] = config_elems trans.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict - if trans.app.toolbox_search.enabled: - # If search support for tools is enabled, index tools. - trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox ) + trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox ) if uninstall: # Write the current in-memory version of the integrated_tool_panel.xml file to disk. trans.app.toolbox.write_integrated_tool_panel_config_file() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for managing user preferences in the Tool Shed.
by Bitbucket 12 Oct '12

12 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f37d6fdc7610/ changeset: f37d6fdc7610 user: dan date: 2012-10-12 16:48:05 summary: Fix for managing user preferences in the Tool Shed. affected #: 3 files diff -r 09bed8d782ce793d6cd4251ab1376f7650c885c9 -r f37d6fdc76107abac84672a228f1b0433a8a8624 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -735,7 +735,7 @@ message=message, status=status ) else: - return trans.fill_template( '/webapps/community/user/info.mako', + return trans.fill_template( '/webapps/community/user/manage_info.mako', cntrller=cntrller, user=user, email=email, diff -r 09bed8d782ce793d6cd4251ab1376f7650c885c9 -r f37d6fdc76107abac84672a228f1b0433a8a8624 templates/webapps/community/user/info.mako --- a/templates/webapps/community/user/info.mako +++ /dev/null @@ -1,9 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/user/info.mako" import="render_user_info" /> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -${render_user_info()} diff -r 09bed8d782ce793d6cd4251ab1376f7650c885c9 -r f37d6fdc76107abac84672a228f1b0433a8a8624 templates/webapps/community/user/manage_info.mako --- /dev/null +++ b/templates/webapps/community/user/manage_info.mako @@ -0,0 +1,9 @@ +<%inherit file="/base.mako"/> +<%namespace file="/user/info.mako" import="render_user_info" /> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +${render_user_info()} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Change show_info.mako to manage_info.mako
by Bitbucket 12 Oct '12

12 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/09bed8d782ce/ changeset: 09bed8d782ce user: dan date: 2012-10-12 16:13:19 summary: Change show_info.mako to manage_info.mako affected #: 3 files diff -r 6711bdada4fac2522ddcab31e32559efe94537a5 -r 09bed8d782ce793d6cd4251ab1376f7650c885c9 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -721,7 +721,7 @@ user_info_forms = self.get_all_forms( trans, filter=dict( deleted=False ), form_type=trans.app.model.FormDefinition.types.USER_INFO ) - return trans.fill_template( '/webapps/galaxy/user/show_info.mako', + return trans.fill_template( '/webapps/galaxy/user/manage_info.mako', cntrller=cntrller, user=user, email=email, diff -r 6711bdada4fac2522ddcab31e32559efe94537a5 -r 09bed8d782ce793d6cd4251ab1376f7650c885c9 templates/webapps/galaxy/user/manage_info.mako --- /dev/null +++ b/templates/webapps/galaxy/user/manage_info.mako @@ -0,0 +1,95 @@ +<%inherit file="/base.mako"/> +<%namespace file="/user/info.mako" import="render_user_info" /> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +${render_user_info()} + +%if user.values or user_info_forms: + <p></p> + <div class="toolForm"> + <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > + <div class="toolFormTitle">User information</div> + %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1: + <div class="form-row"> + <label>User type:</label> + ${user_type_fd_id_select_field.get_html()} + </div> + %else: + <input type="hidden" name="user_type_fd_id" value="${trans.security.encode_id( user_type_form_definition.id )}"/> + %endif + %for field in widgets: + <div class="form-row"> + <label>${field['label']}:</label> + ${field['widget'].get_html()} + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + <div class="form-row"> + <input type="submit" name="edit_user_info_button" value="Save"/> + </div> + </form> + </div> + <p></p> +%endif + +<p/> + +<div class="toolForm"> + <form name="user_addresses" id="user_addresses" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > + <div class="toolFormTitle">User Addresses</div> + <div class="toolFormBody"> + %if user.addresses: + <div class="form-row"> + <div class="grid-header"> + %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ): + %if i > 0: + <span>|</span> + %endif + %if show_filter == filter: + <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}"><b>${filter}</b></a></span> + %else: + <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}">${filter}</a></span> + %endif + %endfor + </div> + </div> + <table class="grid"> + <tbody> + %for index, address in enumerate(addresses): + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td> + <div class="form-row"> + <label>${address.desc}:</label> + ${address.get_html()} + </div> + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + %if not address.deleted: + <a class="action-button" href="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Edit</a> + <a class="action-button" href="${h.url_for( controller='user', action='delete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Delete</a> + %else: + <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Undelete</a> + %endif + </li> + </ul> + </div> + </td> + </tr> + %endfor + </tbody> + </table> + %endif + <div class="form-row"> + <input type="submit" value="Add a new address"> + </div> + </div> + </form> +</div> diff -r 6711bdada4fac2522ddcab31e32559efe94537a5 -r 09bed8d782ce793d6cd4251ab1376f7650c885c9 templates/webapps/galaxy/user/show_info.mako --- a/templates/webapps/galaxy/user/show_info.mako +++ /dev/null @@ -1,95 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/user/info.mako" import="render_user_info" /> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -${render_user_info()} - -%if user.values or user_info_forms: - <p></p> - <div class="toolForm"> - <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > - <div class="toolFormTitle">User information</div> - %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1: - <div class="form-row"> - <label>User type:</label> - ${user_type_fd_id_select_field.get_html()} - </div> - %else: - <input type="hidden" name="user_type_fd_id" value="${trans.security.encode_id( user_type_form_definition.id )}"/> - %endif - %for field in widgets: - <div class="form-row"> - <label>${field['label']}:</label> - ${field['widget'].get_html()} - <div class="toolParamHelp" style="clear: both;"> - ${field['helptext']} - </div> - <div style="clear: both"></div> - </div> - %endfor - <div class="form-row"> - <input type="submit" name="edit_user_info_button" value="Save"/> - </div> - </form> - </div> - <p></p> -%endif - -<p/> - -<div class="toolForm"> - <form name="user_addresses" id="user_addresses" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > - <div class="toolFormTitle">User Addresses</div> - <div class="toolFormBody"> - %if user.addresses: - <div class="form-row"> - <div class="grid-header"> - %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ): - %if i > 0: - <span>|</span> - %endif - %if show_filter == filter: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}"><b>${filter}</b></a></span> - %else: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}">${filter}</a></span> - %endif - %endfor - </div> - </div> - <table class="grid"> - <tbody> - %for index, address in enumerate(addresses): - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td> - <div class="form-row"> - <label>${address.desc}:</label> - ${address.get_html()} - </div> - <div class="form-row"> - <ul class="manage-table-actions"> - <li> - %if not address.deleted: - <a class="action-button" href="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Edit</a> - <a class="action-button" href="${h.url_for( controller='user', action='delete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Delete</a> - %else: - <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Undelete</a> - %endif - </li> - </ul> - </div> - </td> - </tr> - %endfor - </tbody> - </table> - %endif - <div class="form-row"> - <input type="submit" value="Add a new address"> - </div> - </div> - </form> -</div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for managing user info.
by Bitbucket 12 Oct '12

12 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6711bdada4fa/ changeset: 6711bdada4fa user: dan date: 2012-10-12 16:10:18 summary: Fix for managing user info. affected #: 3 files diff -r 18ab38e43d8bf4e95b64b1939f243c370fdad2d9 -r 6711bdada4fac2522ddcab31e32559efe94537a5 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -721,7 +721,7 @@ user_info_forms = self.get_all_forms( trans, filter=dict( deleted=False ), form_type=trans.app.model.FormDefinition.types.USER_INFO ) - return trans.fill_template( '/webapps/galaxy/user/info.mako', + return trans.fill_template( '/webapps/galaxy/user/show_info.mako', cntrller=cntrller, user=user, email=email, diff -r 18ab38e43d8bf4e95b64b1939f243c370fdad2d9 -r 6711bdada4fac2522ddcab31e32559efe94537a5 templates/webapps/galaxy/user/info.mako --- a/templates/webapps/galaxy/user/info.mako +++ /dev/null @@ -1,95 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/user/info.mako" import="render_user_info" /> -<%namespace file="/message.mako" import="render_msg" /> - -%if message: - ${render_msg( message, status )} -%endif - -${render_user_info()} - -%if user.values or user_info_forms: - <p></p> - <div class="toolForm"> - <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > - <div class="toolFormTitle">User information</div> - %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1: - <div class="form-row"> - <label>User type:</label> - ${user_type_fd_id_select_field.get_html()} - </div> - %else: - <input type="hidden" name="user_type_fd_id" value="${trans.security.encode_id( user_type_form_definition.id )}"/> - %endif - %for field in widgets: - <div class="form-row"> - <label>${field['label']}:</label> - ${field['widget'].get_html()} - <div class="toolParamHelp" style="clear: both;"> - ${field['helptext']} - </div> - <div style="clear: both"></div> - </div> - %endfor - <div class="form-row"> - <input type="submit" name="edit_user_info_button" value="Save"/> - </div> - </form> - </div> - <p></p> -%endif - -<p/> - -<div class="toolForm"> - <form name="user_addresses" id="user_addresses" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > - <div class="toolFormTitle">User Addresses</div> - <div class="toolFormBody"> - %if user.addresses: - <div class="form-row"> - <div class="grid-header"> - %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ): - %if i > 0: - <span>|</span> - %endif - %if show_filter == filter: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}"><b>${filter}</b></a></span> - %else: - <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}">${filter}</a></span> - %endif - %endfor - </div> - </div> - <table class="grid"> - <tbody> - %for index, address in enumerate(addresses): - <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> - <td> - <div class="form-row"> - <label>${address.desc}:</label> - ${address.get_html()} - </div> - <div class="form-row"> - <ul class="manage-table-actions"> - <li> - %if not address.deleted: - <a class="action-button" href="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Edit</a> - <a class="action-button" href="${h.url_for( controller='user', action='delete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Delete</a> - %else: - <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Undelete</a> - %endif - </li> - </ul> - </div> - </td> - </tr> - %endfor - </tbody> - </table> - %endif - <div class="form-row"> - <input type="submit" value="Add a new address"> - </div> - </div> - </form> -</div> diff -r 18ab38e43d8bf4e95b64b1939f243c370fdad2d9 -r 6711bdada4fac2522ddcab31e32559efe94537a5 templates/webapps/galaxy/user/show_info.mako --- /dev/null +++ b/templates/webapps/galaxy/user/show_info.mako @@ -0,0 +1,95 @@ +<%inherit file="/base.mako"/> +<%namespace file="/user/info.mako" import="render_user_info" /> +<%namespace file="/message.mako" import="render_msg" /> + +%if message: + ${render_msg( message, status )} +%endif + +${render_user_info()} + +%if user.values or user_info_forms: + <p></p> + <div class="toolForm"> + <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='edit_info', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > + <div class="toolFormTitle">User information</div> + %if user_type_fd_id_select_field and len( user_type_fd_id_select_field.options ) > 1: + <div class="form-row"> + <label>User type:</label> + ${user_type_fd_id_select_field.get_html()} + </div> + %else: + <input type="hidden" name="user_type_fd_id" value="${trans.security.encode_id( user_type_form_definition.id )}"/> + %endif + %for field in widgets: + <div class="form-row"> + <label>${field['label']}:</label> + ${field['widget'].get_html()} + <div class="toolParamHelp" style="clear: both;"> + ${field['helptext']} + </div> + <div style="clear: both"></div> + </div> + %endfor + <div class="form-row"> + <input type="submit" name="edit_user_info_button" value="Save"/> + </div> + </form> + </div> + <p></p> +%endif + +<p/> + +<div class="toolForm"> + <form name="user_addresses" id="user_addresses" action="${h.url_for( controller='user', action='new_address', cntrller=cntrller, user_id=trans.security.encode_id( user.id ) )}" method="post" > + <div class="toolFormTitle">User Addresses</div> + <div class="toolFormBody"> + %if user.addresses: + <div class="form-row"> + <div class="grid-header"> + %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ): + %if i > 0: + <span>|</span> + %endif + %if show_filter == filter: + <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}"><b>${filter}</b></a></span> + %else: + <span class="filter"><a href="${h.url_for( controller='user', action='manage_user_info', cntrller=cntrller, show_filter=filter, user_id=trans.security.encode_id( user.id ) )}">${filter}</a></span> + %endif + %endfor + </div> + </div> + <table class="grid"> + <tbody> + %for index, address in enumerate(addresses): + <tr class="libraryRow libraryOrFolderRow" id="libraryRow"> + <td> + <div class="form-row"> + <label>${address.desc}:</label> + ${address.get_html()} + </div> + <div class="form-row"> + <ul class="manage-table-actions"> + <li> + %if not address.deleted: + <a class="action-button" href="${h.url_for( controller='user', action='edit_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Edit</a> + <a class="action-button" href="${h.url_for( controller='user', action='delete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Delete</a> + %else: + <a class="action-button" href="${h.url_for( controller='user', action='undelete_address', cntrller=cntrller, address_id=trans.security.encode_id( address.id ), user_id=trans.security.encode_id( user.id ) )}">Undelete</a> + %endif + </li> + </ul> + </div> + </td> + </tr> + %endfor + </tbody> + </table> + %endif + <div class="form-row"> + <input type="submit" value="Add a new address"> + </div> + </div> + </form> +</div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Remove Whoosh handling for Python version 2.4 and remove minscore when searching.
by Bitbucket 12 Oct '12

12 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/18ab38e43d8b/ changeset: 18ab38e43d8b user: jgoecks date: 2012-10-12 04:37:44 summary: Remove Whoosh handling for Python version 2.4 and remove minscore when searching. affected #: 1 file diff -r d9e8a7eee7aac7e0ed15fce27592eb0182144889 -r 18ab38e43d8bf4e95b64b1939f243c370fdad2d9 lib/galaxy/tools/search/__init__.py --- a/lib/galaxy/tools/search/__init__.py +++ b/lib/galaxy/tools/search/__init__.py @@ -1,19 +1,13 @@ from galaxy.eggs import require from galaxy.web.framework.helpers import to_unicode -# Whoosh is compatible with Python 2.5+ Try to import Whoosh and set flag to indicate whether tool search is enabled. -try: - require( "Whoosh" ) +require( "Whoosh" ) - from whoosh.filedb.filestore import RamStorage - from whoosh.fields import Schema, STORED, ID, KEYWORD, TEXT - from whoosh.index import Index - from whoosh.scoring import BM25F - from whoosh.qparser import MultifieldParser - tool_search_enabled = True - schema = Schema( id = STORED, title = TEXT, description = TEXT, help = TEXT ) -except ImportError, e: - tool_search_enabled = False - schema = None +from whoosh.filedb.filestore import RamStorage +from whoosh.fields import Schema, STORED, ID, KEYWORD, TEXT +from whoosh.index import Index +from whoosh.scoring import BM25F +from whoosh.qparser import MultifieldParser +schema = Schema( id = STORED, title = TEXT, description = TEXT, help = TEXT ) class ToolBoxSearch( object ): """ @@ -26,9 +20,7 @@ Create a searcher for `toolbox`. """ self.toolbox = toolbox - self.enabled = tool_search_enabled - if tool_search_enabled: - self.build_index() + self.build_index() def build_index( self ): self.storage = RamStorage() @@ -40,13 +32,11 @@ writer.commit() def search( self, query, return_attribute='id' ): - if not tool_search_enabled: - return [] # Change field boosts for searcher to place more weight on title, description than help. searcher = self.index.searcher( \ weighting=BM25F( field_B={ 'title_B' : 3, 'description_B' : 2, 'help_B' : 1 } \ ) ) # Set query to search title, description, and help. parser = MultifieldParser( [ 'title', 'description', 'help' ], schema = schema ) - results = searcher.search( parser.parse( query ), minscore=2.0 ) + results = searcher.search( parser.parse( query ) ) return [ result[ return_attribute ] for result in results ] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: scatterplot.js: fixes after testing; utils/LazyDataLoader.js: basic lazy ajax loading object;
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d9e8a7eee7aa/ changeset: d9e8a7eee7aa user: carlfeberhard date: 2012-10-11 23:25:51 summary: scatterplot.js: fixes after testing; utils/LazyDataLoader.js: basic lazy ajax loading object; affected #: 3 files diff -r 419d87dd65149285d6c9f0043ea898b365d2dbde -r d9e8a7eee7aac7e0ed15fce27592eb0182144889 static/scripts/utils/LazyDataLoader.js --- /dev/null +++ b/static/scripts/utils/LazyDataLoader.js @@ -0,0 +1,183 @@ +/* +TODO: + ?? superclass dataloader, subclass lazydataloader?? + +*/ +//============================================================================== +/** + * Object to progressively load JSON data from a REST url, delaying some time between loading chunks + * + * Data from ajax loading is aggregated in a list, with one element for each ajax response. + * It's up to the calling code to combine the results in a meaningful, correct way + * + * example: + * var loader = new scatterplot.LazyDataLoader({ + * //logger : console, + * url : ( apiDatasetsURL + '/' + hda.id + '?data_type=raw_data' + * + '&columns=[10,14]' ), + * total : hda.metadata_data_lines, + * size : 500, + * + * initialize : function( config ){ + * // ... do some stuff + * }, + * + * buildUrl : function( start, size ){ + * // change the formation of start, size in query string + * return loader.url + '&' + jQuery.param({ + * start_val: start, + * max_vals: size + * }); + * }, + * + * loadedPartialEvent : 'loader.partial', + * loadedAllEvent : 'loader.all', + * }); + * $( loader ).bind( 'loader.partial', function( event, data ){ + * console.info( 'partial load complete:', event, data ); + * // ... do stuff with new data + * }); + * $( loader ).bind( 'loader.all', function( event, data ){ + * console.info( 'final load complete:', event, data ); + * // ... do stuff with all data + * }); + * + * loader.load( function( dataArray ){ console.debug( 'FINISHED!', x, y, z ); } ); + */ +function LazyDataLoader( config ){ + // for now assume: + // get, async, and params sent via url query string + // we want json + // we know the size of the data on the server beforehand + var loader = this; + + jQuery.extend( loader, LoggableMixin ); + jQuery.extend( loader, { + + //NOTE: the next two need to be sent in config (required) + // total size of data on server + total : undefined, + // url of service to get the data + url : undefined, + + // holds the interval id for the current load delay + currentIntervalId : undefined, + + // optional events to trigger when partial, last data are loaded + // loadedPartialEvent will be sent: the ajax response data, start value, and size + loadedPartialEvent : undefined, + // loadedAllEvent will be sent: the final loader's data array and the total + loadedAllEvent : undefined, + + // each load call will add an element to this array + // it's the responsibility of the code using this to combine them properly + data : [], + // ms btwn recursive loads + delay : 500, + // starting line, element, whatever + start : 0, + // size to fetch per load + size : 1000, + + // loader init func: extends loader with config and calls config.init if there + //@param {object} config : object containing variables to override (or additional) + initialize : function( config ){ + jQuery.extend( loader, config ); + + // call the custom initialize function if any + // only dangerous if the user tries LazyDataLoader.prototype.init + if( config.hasOwnProperty( 'initialize' ) ){ + config.initialize.call( loader, config ); + } + + // ensure necessary stuff + if( !loader.total ){ throw( loader + ' requires a total (total size of the data)' ); } + if( !loader.url ){ throw( loader + ' requires a url' ); } + + this.log( this + ' initialized:', loader ); + }, + + // returns query string formatted start and size (for the next fetch) appended to the loader.url + //OVERRIDE: to change how params are passed, param names, etc. + //@param {int} start : the line/row/datum indicating where in the dataset the next load begins + //@param {int} size : the number of lines/rows/data to get on the next load + buildUrl : function( start, size ){ + // currently VERY SPECIFIC to using data_providers.py start_val, max_vals params + return loader.url + '&' + jQuery.param({ + start_val: start, + max_vals: size + }); + }, + + //OVERRIDE: to handle ajax errors differently + ajaxErrorFn : function( xhr, status, error ){ + alert( loader + ' ERROR:' + status + '\n' + error ); + }, + + // interface to begin load (and first recursive call) + //@param {Function} callback : function to execute when all data is loaded. callback is passed loader.data + load : function( callback ){ + + // subsequent recursive calls + function loadHelper( start, size ){ + loader.log( loader + '.loadHelper, start:', start, 'size:', size ); + var url = loader.buildUrl( start, size ); + loader.log( '\t url:', url ); + + jQuery.ajax({ + url : loader.buildUrl( start, size ), + dataType : 'json', + error : function( xhr, status, error ){ + loader.log( '\t ajax error, status:', status, 'error:', error ); + if( loader.currentIntervalId ){ + clearInterval( loader.currentIntervalId ); + } + loader.ajaxErrorFn( xhr, status, error ); + }, + + success : function( response ){ + var next = start + size, + remainder = Math.min( loader.total - next, loader.size ); + loader.log( '\t ajax success, next:', next, 'remainder:', remainder ); + + // store the response as is in a new element + //TODO:?? store start, size as well? + loader.data.push( response ); + + // fire the partial load event + if( loader.loadedPartialEvent ){ + loader.log( '\t firing:', loader.loadedPartialEvent ); + $( loader ).trigger( loader.loadedPartialEvent, response, start, size ); + } + + // if we haven't gotten everything yet, + // set up for next recursive call and set the timer + if( remainder > 0 ){ + loader.currentIntervalId = setTimeout( + function(){ loadHelper( next, remainder ); }, + loader.delay + ); + loader.log( '\t currentIntervalId:', loader.currentIntervalId ); + + // otherwise (base-case), don't do anything + } else { + loader.log( loader + '.loadHelper, has finished:', loader.data ); + if( loader.loadedAllEvent ){ + loader.log( '\t firing:', loader.loadedAllEvent ); + $( loader ).trigger( loader.loadedAllEvent, loader.data, loader.total ); + } + if( callback ){ callback( loader.data ); } + } + } + }); + } + loadHelper( loader.start, Math.min( loader.total, loader.size ) ); + }, + + toString : function(){ return 'LazyDataLoader'; } + }); + + loader.initialize( config ); + return loader; +} + diff -r 419d87dd65149285d6c9f0043ea898b365d2dbde -r d9e8a7eee7aac7e0ed15fce27592eb0182144889 static/scripts/viz/scatterplot.js --- a/static/scripts/viz/scatterplot.js +++ b/static/scripts/viz/scatterplot.js @@ -1,6 +1,8 @@ define([ "../libs/underscore", + "../mvc/base-mvc", + "../utils/LazyDataLoader", "../templates/compiled/template-visualization-scatterplotControlForm", "../templates/compiled/template-visualization-statsTable", "../templates/compiled/template-visualization-chartSettings", @@ -14,7 +16,7 @@ /* ============================================================================= todo: outside this: - BUG: visualization menu doesn't disappear + BUG: setting width, height in plot controls doesn't re-interpolate data locations!! BUG?: get metadata_column_names (from datatype if necessary) BUG: single vis in popupmenu should have tooltip with that name NOT 'Visualizations' @@ -78,7 +80,7 @@ PADDING = 8, X_LABEL_TOO_LONG_AT = 5; - //this.debugging = true; + this.debugging = true; this.log = function(){ if( this.debugging && console && console.debug ){ var args = Array.prototype.slice.call( arguments ); @@ -102,8 +104,8 @@ yNumTicks : 10, xAxisLabelBumpY : 40, yAxisLabelBumpX : -35, - width : 320, - height : 320, + width : 500, + height : 500, //TODO: anyway to make this a sub-obj? marginTop : 50, marginRight : 50, @@ -120,7 +122,7 @@ }; this.config = _.extend( {}, this.defaults, config ); - this.updateConfig = function( newConfig ){ + this.updateConfig = function( newConfig, rerender ){ _.extend( this.config, newConfig ); }; @@ -148,9 +150,10 @@ this.yAxis = this.content.append( 'g' ).attr( 'class', 'axis' ).attr( 'id', 'y-axis' ); this.yAxisLabel = this.yAxis.append( 'text' ).attr( 'class', 'axis-label' ).attr( 'id', 'y-axis-label' ); - this.log( 'built svg:', d3.selectAll( 'svg' ) ); + //this.log( 'built svg:', d3.selectAll( 'svg' ) ); this.adjustChartDimensions = function( top, right, bottom, left ){ + //this.log( this + '.adjustChartDimensions', arguments ); top = top || 0; right = right || 0; bottom = bottom || 0; @@ -171,6 +174,7 @@ // ........................................................ data and scales this.preprocessData = function( data, min, max ){ + //this.log( this + '.preprocessData', arguments ); //TODO: filter by min, max if set // set a cap on the data, limit to first n points @@ -178,7 +182,7 @@ }; this.setUpDomains = function( xCol, yCol, meta ){ - this.log( 'setUpDomains' ); + //this.log( this + '.setUpDomains', arguments ); // configuration takes priority, otherwise meta (from the server) if passed, last-resort: compute it here this.xMin = this.config.xMin || ( meta )?( meta[0].min ):( d3.min( xCol ) ); this.xMax = this.config.xMax || ( meta )?( meta[0].max ):( d3.max( xCol ) ); @@ -187,6 +191,7 @@ }; this.setUpScales = function(){ + //this.log( this + '.setUpScales', arguments ); // Interpolation for x, y based on data domains this.xScale = d3.scale.linear() .domain([ this.xMin, this.xMax ]) @@ -198,6 +203,7 @@ // ........................................................ axis and ticks this.setUpXAxis = function(){ + //this.log( this + '.setUpXAxis', arguments ); // origin: bottom, left //TODO: incoporate top, right this.xAxisFn = d3.svg.axis() @@ -228,13 +234,14 @@ }; this.setUpYAxis = function(){ + //this.log( this + '.setUpYAxis', arguments ); this.yAxisFn = d3.svg.axis() .scale( this.yScale ) .ticks( this.config.yNumTicks ) .orient( 'left' ); this.yAxis// = content.select( 'g#y-axis' ) .call( this.yAxisFn ); - this.log( 'yAxis:', this.yAxis ); + //this.log( 'yAxis:', this.yAxis ); // get the tick labels for the y axis var yTickLabels = this.yAxis.selectAll( 'text' ).filter( function( e, i ){ return i !== 0; } ); @@ -259,7 +266,7 @@ if( this.config.marginLeft < neededY ){ var adjusting = ( neededY ) - this.config.marginLeft; adjusting = ( adjusting < 0 )?( 0 ):( adjusting ); - this.log( 'adjusting:', adjusting ); + //this.log( 'adjusting:', adjusting ); // update dimensions, translations this.adjustChartDimensions( 0, 0, 0, adjusting ); @@ -278,6 +285,7 @@ // ........................................................ grid lines this.renderGrid = function(){ + //this.log( this + '.renderGrid', arguments ); // VERTICAL // select existing this.vGridLines = this.content.selectAll( 'line.v-grid-line' ) @@ -328,51 +336,70 @@ }; + // initial render or complete re-render (REPLACE datapoints) this.renderDatapoints = function( xCol, yCol, ids ){ - // initial render, complete re-render (REPLACE datapoints) + this.log( this + '.renderDatapoints', arguments ); + var count = 0; this.datapoints = this.addDatapoints( xCol, yCol, ids, ".glyph" ); // glyphs that need to be removed: transition to from normal state to 'exit' state, remove from DOM this.datapoints.exit() + .each( function(){ count += 1; } ) .transition().duration( this.config.entryAnimDuration ) .attr( "cy", this.config.height ) .attr( "r", 0 ) .remove(); + this.log( count, ' glyphs removed' ); - this.log( this.datapoints, 'glyphs rendered' ); + //this.log( this.datapoints.length, ' glyphs in the graph' ); }; + // adding points to existing this.addDatapoints = function( newXCol, newYCol, ids, selectorForExisting ){ + this.log( this + '.addDatapoints', arguments ); // ADD datapoints to plot that's already rendered // if selectorForExisting === undefined (as in not passed), addDatapoints won't update existing // pass in the class ( '.glyph' ) to update exising datapoints var plot = this, + count = 0, xPosFn = function( d, i ){ + //if( d ){ this.log( 'x.data:', newXCol[ i ], 'plotted:', plot.xScale( newXCol[ i ] ) ); } return plot.xScale( newXCol[ i ] ); }, yPosFn = function( d, i ){ + //if( d ){ this.log( 'y.data:', newYCol[ i ], 'plotted:', plot.yScale( newYCol[ i ] ) ); } return plot.yScale( newYCol[ i ] ); }; // select all existing glyphs and compare to incoming data // enter() will yield those glyphs that need to be added - var newDatapoints = this.content.selectAll( selectorForExisting ).data( newXCol ); + var newDatapoints = this.content.selectAll( selectorForExisting ); + this.log( 'existing datapoints:', newDatapoints ); + newDatapoints = newDatapoints.data( newXCol ); // enter - new data to be added as glyphs: give them a 'entry' position and style + count = 0; newDatapoints.enter() - .append( "svg:circle" ) + .append( 'svg:circle' ) + .each( function(){ count += 1; } ) .classed( "glyph", true ) - // start all bubbles small... .attr( "cx", xPosFn ) .attr( "cy", yPosFn ) + // start all bubbles small... .attr( "r", 0 ); + this.log( count, ' new glyphs created' ); // for all existing glyphs and those that need to be added: transition anim to final state + count = 0; newDatapoints // ...animate to final position .transition().duration( this.config.entryAnimDuration ) - .attr( "r", this.config.datapointSize ); + .each( function(){ count += 1; } ) + .attr( "cx", xPosFn ) + .attr( "cy", yPosFn ) + .attr( "r", plot.config.datapointSize ); + this.log( count, ' existing glyphs transitioned' ); // attach ids if( ids ){ @@ -419,21 +446,22 @@ }; this.render = function( columnData, meta ){ + this.log( this + '.render', arguments ); //pre: columns passed are numeric //pre: at least two columns are passed //assume: first column is x, second column is y, any remaining aren't used var xCol = columnData[0], yCol = columnData[1], ids = ( columnData.length > 2 )?( columnData[2] ):( undefined ); - this.log( 'renderScatterplot', xCol.length, yCol.length, this.config ); + //this.log( this + '.render', xCol.length, yCol.length, this.config ); //pre: xCol.len == yCol.len xCol = this.preprocessData( xCol ); yCol = this.preprocessData( yCol ); - //this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); + this.log( 'xCol len', xCol.length, 'yCol len', yCol.length ); this.setUpDomains( xCol, yCol, meta ); - this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); + //this.log( 'xMin, xMax, yMin, yMax:', this.xMin, this.xMax, this.yMin, this.yMax ); this.setUpScales(); this.adjustChartDimensions(); @@ -515,7 +543,7 @@ this.$chartSettingsPanel = this._render_chartSettings(); this.$statsPanel = this.$el.find( '.tab-pane#chart-stats' ); - this.$el.find( 'ul.nav' ).find( 'a[href="#chart-settings"]' ).tab( 'show' ); + //this.$el.find( 'ul.nav' ).find( 'a[href="#chart-settings"]' ).tab( 'show' ); return this; }, @@ -523,6 +551,7 @@ var chartControl = this, $chartSettingsPanel = this.$el.find( '.tab-pane#chart-settings' ), // limits for controls (by control/chartConfig id) + //TODO: move into TwoVarScatterplot controlRanges = { 'maxDataPoints' : { min: 1000, max: 30000, step: 100 }, 'datapointSize' : { min: 2, max: 10, step: 1 }, @@ -559,7 +588,6 @@ }); //TODO: anim checkbox - //TODO: labels -> renderPlot return $chartSettingsPanel; }, @@ -639,7 +667,7 @@ columns = []; this.log( 'columnSelections:', columnSelections ); - //TODO: ?? could be moved into getColumnVals; + //TODO: move this data/chart settings form crap out this.log( columnSelections.X.val, columnSelections.Y.val ); this.xColIndex = columnSelections.X.colIndex; this.yColIndex = columnSelections.Y.colIndex; @@ -650,15 +678,18 @@ columns.push( columnSelections.ID.colIndex ); } - this.log( columnSelections.X.colName, columnSelections.Y.colName ); - this.plot.xLabel = this.chartConfig.xLabel = columnSelections.X.colName; - this.plot.xLabel = this.chartConfig.yLabel = columnSelections.Y.colName; + // update labels using chartSettings inputs (if not at defaults), otherwise the selects' colName + var chartSettingsXLabel = this.$chartSettingsPanel.find( 'input#X-axis-label' ).val(), + chartSettingsYLabel = this.$chartSettingsPanel.find( 'input#Y-axis-label' ).val(); + this.chartConfig.xLabel = ( chartSettingsXLabel === 'X' )? + ( columnSelections.X.colName ):( chartSettingsXLabel ); + this.chartConfig.yLabel = ( chartSettingsYLabel === 'Y' )? + ( columnSelections.Y.colName ):( chartSettingsYLabel ); + //this.log( 'this.chartConfig:', this.chartConfig ); + view.plot.updateConfig( this.chartConfig, false ); - //TODO: alter directly - view.plot.updateConfig( this.chartConfig, false ); //TODO: validate columns - minimally: we can assume either set by selectors or via a good query string //TODO: other vals: max, start, page - //TODO: chart config // fetch the data, sending chosen columns to the server var params = { @@ -705,6 +736,7 @@ //============================================================================== return { + LazyDataLoader : LazyDataLoader, TwoVarScatterplot : TwoVarScatterplot, ScatterplotControlForm : ScatterplotControlForm };}); diff -r 419d87dd65149285d6c9f0043ea898b365d2dbde -r d9e8a7eee7aac7e0ed15fce27592eb0182144889 templates/visualization/scatterplot.mako --- a/templates/visualization/scatterplot.mako +++ b/templates/visualization/scatterplot.mako @@ -209,7 +209,7 @@ var hda = ${h.to_json_string( hda )}, historyID = '${historyID}' apiDatasetsURL = "${h.url_for( controller='/api/datasets' )}"; - + var settingsForm = new scatterplot.ScatterplotControlForm({ dataset : hda, el : $( '#chart-settings-form' ), @@ -243,3 +243,4 @@ <div id="test"></div></%def> + Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix minor typos in db_shell.py
by Bitbucket 11 Oct '12

11 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/419d87dd6514/ changeset: 419d87dd6514 user: dan date: 2012-10-11 22:43:37 summary: Fix minor typos in db_shell.py affected #: 1 file diff -r 26a72076eb75683e1fe1dca95e1a356f501d9393 -r 419d87dd65149285d6c9f0043ea898b365d2dbde scripts/db_shell.py --- a/scripts/db_shell.py +++ b/scripts/db_shell.py @@ -1,14 +1,14 @@ # This script allows easy access to Galaxy's database layer via the -# Galaxy models. For example:q -# % python -i scripts/db_shel.py +# Galaxy models. For example: +# % python -i scripts/db_shell.py # >>> new_user = User("admin(a)gmail.com") # >>> new_user.set_password # >>> sa_session.add(new_user) # >>> sa_session.commit() # >>> sa_session.query(User).all() # -# You can also use this script as a library, for instance see https://gist.github.com/1979583q -# TODO: This script overlaps alot wth manage_db.py and create_db.py, +# You can also use this script as a library, for instance see https://gist.github.com/1979583 +# TODO: This script overlaps a lot with manage_db.py and create_db.py, # these should maybe be refactored to remove duplication. import sys, os.path, logging Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 4 new changesets
by Bitbucket 11 Oct '12

11 Oct '12

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d2258c1bcbc9/ changeset: d2258c1bcbc9 user: dan date: 2012-10-11 22:36:45 summary: Unicode fixes for copying datasets. affected #: 1 file diff -r 7549962ac83381ab92ac806b168d45b0b4b9a107 -r d2258c1bcbc9344dc376c11fceeec039b1b23709 templates/dataset/copy_view.mako --- a/templates/dataset/copy_view.mako +++ b/templates/dataset/copy_view.mako @@ -57,7 +57,7 @@ %><option value="${trans.security.encode_id(hist.id)}" ${selected}> - ${i + 1}: ${h.truncate(hist.name, 30)}${current_history_text} + ${i + 1}: ${h.truncate(util.unicodify( hist.name ), 30)}${current_history_text} </option> %endfor </select> @@ -98,7 +98,7 @@ if encoded_id == target_history_id: selected = " selected='selected'" %> - <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate(hist.name, 30)}${source_history_text}</option> + <option value="${encoded_id}"${selected}>${i + 1}: ${h.truncate( util.unicodify( hist.name ), 30)}${source_history_text}</option> %endfor </select><br /><br /><a style="margin-left: 10px;" href="javascript:void(0);" id="select-multiple">Choose multiple histories</a> @@ -113,7 +113,7 @@ %><div class="form-row"><input type="checkbox" name="target_history_ids" id="hist_${encoded_id}" value="${encoded_id}"/> - <label for="hist_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${hist.name}${cur_history_text}</label> + <label for="hist_${encoded_id}" style="display: inline; font-weight:normal;">${i + 1}: ${ util.unicodify( hist.name ) }${cur_history_text}</label></div> %endfor </div> https://bitbucket.org/galaxy/galaxy-central/changeset/6ef979d7cab5/ changeset: 6ef979d7cab5 user: dan date: 2012-10-11 22:36:45 summary: Unicode fixes for Galaxy Forms. affected #: 1 file diff -r d2258c1bcbc9344dc376c11fceeec039b1b23709 -r 6ef979d7cab519ceef3727a069a55ec7c5a8c21f templates/form.mako --- a/templates/form.mako +++ b/templates/form.mako @@ -53,7 +53,7 @@ %endif <div class="form" style="margin: 1em"> - <div class="form-title">${form.title}</div> + <div class="form-title">${util.unicodify( form.title )}</div><div class="form-body"><% has_file_input = False https://bitbucket.org/galaxy/galaxy-central/changeset/5f67671bafdf/ changeset: 5f67671bafdf user: dan date: 2012-10-11 22:36:45 summary: Unicode fixes for sharing histories. affected #: 1 file diff -r 6ef979d7cab519ceef3727a069a55ec7c5a8c21f -r 5f67671bafdfb3fa4986f1059035bbf177f586f8 templates/history/share.mako --- a/templates/history/share.mako +++ b/templates/history/share.mako @@ -20,7 +20,7 @@ <tr><td><input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - ${history.name} + ${ util.unicodify( history.name )} </td><td> %if len( history.datasets ) < 1: @@ -81,7 +81,7 @@ %for history, hdas in no_change_needed.items(): <div class="form-row"><label>History</label> - ${history.name} + ${util.unicodify( history.name )} </div><div style="clear: both"></div><div class="form-row"> @@ -89,7 +89,7 @@ </div> %for hda in hdas: <div class="form-row"> - ${hda.name} + ${util.unicodify( hda.name )} %if hda.deleted: (deleted) %endif @@ -108,7 +108,7 @@ %for history, hdas in can_change.items(): <div class="form-row"><label>History</label> - ${history.name} + ${util.unicodify( history.name )} </div><div style="clear: both"></div><div class="form-row"> @@ -116,7 +116,7 @@ </div> %for hda in hdas: <div class="form-row"> - ${hda.name} + ${util.unicodify( hda.name )} %if hda.deleted: (deleted) %endif @@ -136,7 +136,7 @@ %for history, hdas in cannot_change.items(): <div class="form-row"><label>History</label> - ${history.name} + ${util.unicodify( history.name )} </div><div style="clear: both"></div><div class="form-row"> @@ -144,7 +144,7 @@ </div> %for hda in hdas: <div class="form-row"> - ${hda.name} + ${util.unicodify( hda.name )} %if hda.deleted: (deleted) %endif https://bitbucket.org/galaxy/galaxy-central/changeset/26a72076eb75/ changeset: 26a72076eb75 user: dan date: 2012-10-11 22:36:46 summary: Unicode fixes for workflow configuration menu. affected #: 1 file diff -r 5f67671bafdfb3fa4986f1059035bbf177f586f8 -r 26a72076eb75683e1fe1dca95e1a356f501d9393 templates/workflow/configure_menu.mako --- a/templates/workflow/configure_menu.mako +++ b/templates/workflow/configure_menu.mako @@ -31,7 +31,7 @@ %for i, workflow in enumerate( workflows ): <tr><td> - ${workflow.name} + ${util.unicodify( workflow.name )} </td><td>You</td><td>${len(workflow.latest_workflow.steps)}</td> @@ -53,7 +53,7 @@ <% workflow = association.stored_workflow %><tr><td> - ${workflow.name} + ${util.unicodify( workflow.name )} </td><td>${workflow.user.email}</td><td>${len(workflow.latest_workflow.steps)}</td> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 11 Oct '12

11 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3fc27b7125cc/ changeset: 3fc27b7125cc user: dan date: 2012-10-11 20:06:10 summary: Only allow errors to be viewed if the user can access the dataset. affected #: 1 file diff -r b27aa5db944d3c3a79c9bedf9d91fe2a2e89e01d -r 3fc27b7125ccca13354558e355832de8f1f5f51a lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -166,6 +166,8 @@ @web.expose def errors( self, trans, id ): hda = trans.sa_session.query( model.HistoryDatasetAssociation ).get( id ) + if not hda or not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): + return trans.show_error_message( "Either this dataset does not exist or you do not have permission to access it." ) return trans.fill_template( "dataset/errors.mako", hda=hda ) @web.expose def stdoutX( self, trans, dataset_id=None, **kwargs ): https://bitbucket.org/galaxy/galaxy-central/changeset/7549962ac833/ changeset: 7549962ac833 user: dan date: 2012-10-11 20:06:18 summary: Only copy the user on bug reports if the user can access the dataset. affected #: 1 file diff -r 3fc27b7125ccca13354558e355832de8f1f5f51a -r 7549962ac83381ab92ac806b168d45b0b4b9a107 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -248,7 +248,7 @@ # Check email a bit email = email.strip() parts = email.split() - if len( parts ) == 1 and len( email ) > 0: + if len( parts ) == 1 and len( email ) > 0 and trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): to = to_address + ", " + email else: to = to_address Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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