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commit/galaxy-central: dan: Some web sanitization for Data Managers and Biostar redirect.
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c1d4e82df5cb/ Changeset: c1d4e82df5cb Branch: next-stable User: dan Date: 2014-12-04 21:14:28+00:00 Summary: Some web sanitization for Data Managers and Biostar redirect. Affected #: 4 files diff -r b51526d2f9b42a0bc64b55584e435ceebe7ceb31 -r c1d4e82df5cbf8a6d551221a0d4013d658ad4748 lib/galaxy/webapps/galaxy/controllers/data_manager.py --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -7,6 +7,8 @@ pkg_resources.require( "Paste" ) import paste.httpexceptions +from galaxy.web.framework.helpers import escape + #set up logger import logging log = logging.getLogger( __name__ ) @@ -18,8 +20,8 @@ not_is_admin = not trans.user_is_admin() if not_is_admin and not trans.app.config.enable_data_manager_user_view: raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) - message = kwd.get( 'message' ) - status = kwd.get( 'status', 'info' ) + message = escape( kwd.get( 'message', '' ) ) + status = escape( kwd.get( 'status', 'info' ) ) return trans.fill_template( "data_manager/index.mako", data_managers=trans.app.data_managers, tool_data_tables=trans.app.tool_data_tables, view_only=not_is_admin, message=message, status=status ) @web.expose @@ -27,8 +29,8 @@ not_is_admin = not trans.user_is_admin() if not_is_admin and not trans.app.config.enable_data_manager_user_view: raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) - message = kwd.get( 'message' ) - status = kwd.get( 'status', 'info' ) + message = escape( kwd.get( 'message', '' ) ) + status = escape( kwd.get( 'status', 'info' ) ) data_manager_id = kwd.get( 'id', None ) data_manager = trans.app.data_managers.get_manager( data_manager_id ) if data_manager is None: @@ -41,8 +43,8 @@ not_is_admin = not trans.user_is_admin() if not_is_admin and not trans.app.config.enable_data_manager_user_view: raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) - message = kwd.get( 'message' ) - status = kwd.get( 'status', 'info' ) + message = escape( kwd.get( 'message', '' ) ) + status = escape( kwd.get( 'status', 'info' ) ) job_id = kwd.get( 'id', None ) try: job_id = trans.security.decode_id( job_id ) @@ -62,7 +64,7 @@ data_manager_json = loads( open( hda.get_file_name() ).read() ) except Exception, e: data_manager_json = {} - error_messages.append( "Unable to obtain data_table info for hda (%s): %s" % ( hda.id, e ) ) + error_messages.append( escape( "Unable to obtain data_table info for hda (%s): %s" % ( hda.id, e ) ) ) values = [] for key, value in data_manager_json.get( 'data_tables', {} ).iteritems(): values.append( ( key, value ) ) @@ -74,8 +76,8 @@ not_is_admin = not trans.user_is_admin() if not_is_admin and not trans.app.config.enable_data_manager_user_view: raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) - message = kwd.get( 'message' ) - status = kwd.get( 'status', 'info' ) + message = escape( kwd.get( 'message', '' ) ) + status = escape( kwd.get( 'status', 'info' ) ) data_table_name = kwd.get( 'table_name', None ) if not data_table_name: return trans.response.send_redirect( web.url_for( controller="data_manager", action="index" ) ) diff -r b51526d2f9b42a0bc64b55584e435ceebe7ceb31 -r c1d4e82df5cbf8a6d551221a0d4013d658ad4748 templates/webapps/galaxy/biostar/post_redirect.mako --- a/templates/webapps/galaxy/biostar/post_redirect.mako +++ b/templates/webapps/galaxy/biostar/post_redirect.mako @@ -18,7 +18,7 @@ <p>If you are not automatically forwarded, click the button below:<p><form id="postRedirectForm" action="${post_url}" method="post" > %for input_name, input_value in form_inputs.items(): - <input type="hidden" name="${input_name}" value="${input_value | h}"> + <input type="hidden" name="${input_name | h}" value="${input_value | h}"> %endfor <input type="submit" name="GalaxySubmitPostRedirectForm" id='GalaxySubmitPostRedirectForm' value="Click Here"></form> diff -r b51526d2f9b42a0bc64b55584e435ceebe7ceb31 -r c1d4e82df5cbf8a6d551221a0d4013d658ad4748 templates/webapps/galaxy/data_manager/manage_data_table.mako --- a/templates/webapps/galaxy/data_manager/manage_data_table.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_table.mako @@ -14,9 +14,9 @@ <% column_name_list = data_table.get_column_name_list() %><table class="tabletip"><thead> - <tr><th colspan="${len (column_name_list) }" style="font-size: 120%;"> + <tr><th colspan="${ len( column_name_list ) | h}" style="font-size: 120%;"> Data Manager: ${ data_table.name | h } - <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="reload_tool_data_tables", table_name=data_table.name ) }" title="Reload ${data_table.name} tool data table" data-placement="bottom"> + <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="reload_tool_data_tables", table_name=data_table.name ) }" title="Reload ${data_table.name | h} tool data table" data-placement="bottom"><span class="fa fa-refresh"></span></a></th></tr> diff -r b51526d2f9b42a0bc64b55584e435ceebe7ceb31 -r c1d4e82df5cbf8a6d551221a0d4013d658ad4748 templates/webapps/galaxy/data_manager/view_job.mako --- a/templates/webapps/galaxy/data_manager/view_job.mako +++ b/templates/webapps/galaxy/data_manager/view_job.mako @@ -26,8 +26,8 @@ </thead><tbody><tr><td>Name:</td><td>${hda.name | h}</td></tr> - <tr><td>Created:</td><td>${hda.create_time.strftime(trans.app.config.pretty_datetime_format)}</td></tr> - <tr><td>Filesize:</td><td>${nice_size(hda.dataset.file_size)}</td></tr> + <tr><td>Created:</td><td>${hda.create_time.strftime(trans.app.config.pretty_datetime_format) | h}</td></tr> + <tr><td>Filesize:</td><td>${nice_size(hda.dataset.file_size) | h}</td></tr><tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr><tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr><tr><td>View complete info:</td><td><a href="${h.url_for( controller='dataset', action='show_params', dataset_id=trans.security.encode_id( hda.id ))}">${ hda.id | h }</a></td></tr> @@ -47,7 +47,7 @@ %for j, table_row in enumerate( json_table ): <tbody> %if len_json_table > 1: - <tr><td><strong>Entry #${j}</strong></td><td></td></tr> + <tr><td><strong>Entry #${j | h}</strong></td><td></td></tr> %endif %for name, value in table_row.iteritems(): <tr><td>${name | h}:</td><td>${value | h}</td></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Some web sanitization for Data Managers and Biostar redirect.
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7272cc7b9ea1/ Changeset: 7272cc7b9ea1 User: dan Date: 2014-12-04 21:14:28+00:00 Summary: Some web sanitization for Data Managers and Biostar redirect. Affected #: 4 files diff -r 636d3594e201ebb2d085c33c6de32577d65bd866 -r 7272cc7b9ea1fd64646fa6d7e6fb5924fd8618f8 lib/galaxy/webapps/galaxy/controllers/data_manager.py --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -7,6 +7,8 @@ pkg_resources.require( "Paste" ) import paste.httpexceptions +from galaxy.web.framework.helpers import escape + #set up logger import logging log = logging.getLogger( __name__ ) @@ -18,8 +20,8 @@ not_is_admin = not trans.user_is_admin() if not_is_admin and not trans.app.config.enable_data_manager_user_view: raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) - message = kwd.get( 'message' ) - status = kwd.get( 'status', 'info' ) + message = escape( kwd.get( 'message', '' ) ) + status = escape( kwd.get( 'status', 'info' ) ) return trans.fill_template( "data_manager/index.mako", data_managers=trans.app.data_managers, tool_data_tables=trans.app.tool_data_tables, view_only=not_is_admin, message=message, status=status ) @web.expose @@ -27,8 +29,8 @@ not_is_admin = not trans.user_is_admin() if not_is_admin and not trans.app.config.enable_data_manager_user_view: raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) - message = kwd.get( 'message' ) - status = kwd.get( 'status', 'info' ) + message = escape( kwd.get( 'message', '' ) ) + status = escape( kwd.get( 'status', 'info' ) ) data_manager_id = kwd.get( 'id', None ) data_manager = trans.app.data_managers.get_manager( data_manager_id ) if data_manager is None: @@ -41,8 +43,8 @@ not_is_admin = not trans.user_is_admin() if not_is_admin and not trans.app.config.enable_data_manager_user_view: raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) - message = kwd.get( 'message' ) - status = kwd.get( 'status', 'info' ) + message = escape( kwd.get( 'message', '' ) ) + status = escape( kwd.get( 'status', 'info' ) ) job_id = kwd.get( 'id', None ) try: job_id = trans.security.decode_id( job_id ) @@ -62,7 +64,7 @@ data_manager_json = loads( open( hda.get_file_name() ).read() ) except Exception, e: data_manager_json = {} - error_messages.append( "Unable to obtain data_table info for hda (%s): %s" % ( hda.id, e ) ) + error_messages.append( escape( "Unable to obtain data_table info for hda (%s): %s" % ( hda.id, e ) ) ) values = [] for key, value in data_manager_json.get( 'data_tables', {} ).iteritems(): values.append( ( key, value ) ) @@ -74,8 +76,8 @@ not_is_admin = not trans.user_is_admin() if not_is_admin and not trans.app.config.enable_data_manager_user_view: raise paste.httpexceptions.HTTPUnauthorized( "This Galaxy instance is not configured to allow non-admins to view the data manager." ) - message = kwd.get( 'message' ) - status = kwd.get( 'status', 'info' ) + message = escape( kwd.get( 'message', '' ) ) + status = escape( kwd.get( 'status', 'info' ) ) data_table_name = kwd.get( 'table_name', None ) if not data_table_name: return trans.response.send_redirect( web.url_for( controller="data_manager", action="index" ) ) diff -r 636d3594e201ebb2d085c33c6de32577d65bd866 -r 7272cc7b9ea1fd64646fa6d7e6fb5924fd8618f8 templates/webapps/galaxy/biostar/post_redirect.mako --- a/templates/webapps/galaxy/biostar/post_redirect.mako +++ b/templates/webapps/galaxy/biostar/post_redirect.mako @@ -18,7 +18,7 @@ <p>If you are not automatically forwarded, click the button below:<p><form id="postRedirectForm" action="${post_url}" method="post" > %for input_name, input_value in form_inputs.items(): - <input type="hidden" name="${input_name}" value="${input_value | h}"> + <input type="hidden" name="${input_name | h}" value="${input_value | h}"> %endfor <input type="submit" name="GalaxySubmitPostRedirectForm" id='GalaxySubmitPostRedirectForm' value="Click Here"></form> diff -r 636d3594e201ebb2d085c33c6de32577d65bd866 -r 7272cc7b9ea1fd64646fa6d7e6fb5924fd8618f8 templates/webapps/galaxy/data_manager/manage_data_table.mako --- a/templates/webapps/galaxy/data_manager/manage_data_table.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_table.mako @@ -14,9 +14,9 @@ <% column_name_list = data_table.get_column_name_list() %><table class="tabletip"><thead> - <tr><th colspan="${len (column_name_list) }" style="font-size: 120%;"> + <tr><th colspan="${ len( column_name_list ) | h}" style="font-size: 120%;"> Data Manager: ${ data_table.name | h } - <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="reload_tool_data_tables", table_name=data_table.name ) }" title="Reload ${data_table.name} tool data table" data-placement="bottom"> + <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="reload_tool_data_tables", table_name=data_table.name ) }" title="Reload ${data_table.name | h} tool data table" data-placement="bottom"><span class="fa fa-refresh"></span></a></th></tr> diff -r 636d3594e201ebb2d085c33c6de32577d65bd866 -r 7272cc7b9ea1fd64646fa6d7e6fb5924fd8618f8 templates/webapps/galaxy/data_manager/view_job.mako --- a/templates/webapps/galaxy/data_manager/view_job.mako +++ b/templates/webapps/galaxy/data_manager/view_job.mako @@ -26,8 +26,8 @@ </thead><tbody><tr><td>Name:</td><td>${hda.name | h}</td></tr> - <tr><td>Created:</td><td>${hda.create_time.strftime(trans.app.config.pretty_datetime_format)}</td></tr> - <tr><td>Filesize:</td><td>${nice_size(hda.dataset.file_size)}</td></tr> + <tr><td>Created:</td><td>${hda.create_time.strftime(trans.app.config.pretty_datetime_format) | h}</td></tr> + <tr><td>Filesize:</td><td>${nice_size(hda.dataset.file_size) | h}</td></tr><tr><td>Tool Exit Code:</td><td>${job.exit_code | h}</td></tr><tr><td>Full Path:</td><td>${hda.file_name | h}</td></tr><tr><td>View complete info:</td><td><a href="${h.url_for( controller='dataset', action='show_params', dataset_id=trans.security.encode_id( hda.id ))}">${ hda.id | h }</a></td></tr> @@ -47,7 +47,7 @@ %for j, table_row in enumerate( json_table ): <tbody> %if len_json_table > 1: - <tr><td><strong>Entry #${j}</strong></td><td></td></tr> + <tr><td><strong>Entry #${j | h}</strong></td><td></td></tr> %endif %for name, value in table_row.iteritems(): <tr><td>${name | h}:</td><td>${value | h}</td></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 11 new changesets
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

11 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6eccc509c109/ Changeset: 6eccc509c109 Branch: next-stable User: dannon Date: 2014-12-04 16:38:16+00:00 Summary: Sanitize all user fields in cloud/index.mako Affected #: 1 file diff -r 29b2c328b89b6634c9a3f9a21c2349105a7e485a -r 6eccc509c109c87889d80ba745d97cfa425e0ce4 templates/webapps/galaxy/cloud/index.mako --- a/templates/webapps/galaxy/cloud/index.mako +++ b/templates/webapps/galaxy/cloud/index.mako @@ -218,7 +218,7 @@ </div> %if share_string: - <input type='hidden' name='share_string' value='${share_string}'/> + <input id="dbremove_share_string" type='hidden' name='share_string' value='${share_string | h}'/> %else: <div class="form-row" style="display:none;"> @@ -228,11 +228,11 @@ %endif %if ami: - <input type='hidden' name='ami' value='${ami}'/> + <input type='hidden' name='ami' value='${ami | h}'/> %endif %if bucket_default: - <input type='hidden' name='bucket_default' value='${bucket_default}'/> + <input type='hidden' name='bucket_default' value='${bucket_default | h}'/> %endif <div class="form-row"> https://bitbucket.org/galaxy/galaxy-central/commits/90d3d1205ef0/ Changeset: 90d3d1205ef0 Branch: next-stable User: dannon Date: 2014-12-04 16:51:46+00:00 Summary: Remove unused cloud/run.mako; all functionality is rolled into cloud/index. Affected #: 1 file diff -r 6eccc509c109c87889d80ba745d97cfa425e0ce4 -r 90d3d1205ef0211ce2f459e2832c6bad2737d924 templates/webapps/galaxy/cloud/run.mako --- a/templates/webapps/galaxy/cloud/run.mako +++ /dev/null @@ -1,41 +0,0 @@ -<%inherit file="/webapps/galaxy/base_panels.mako"/> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.active_view="shared" - self.message_box_visible=False -%> -</%def> - - -<%def name="center_panel()"> - <div style="overflow: auto; height: 100%;"> - <div class="page-container" style="padding: 10px;"> - <h2>Launching a Galaxy Cloud Instance</h2> -%if error: - <p>${error}</p> -%elif instance: - %if kp_material: - <h3>Very Important Key Pair Information</h3> - <p>A new key pair named '${kp_name}' has been created in your AWS - account and will be used to access this instance via ssh. It is - <strong>very important</strong> that you save the following private key - as it is not saved on this Galaxy instance and will be permanently lost - once you leave this page. To do this, save the following key block as - a plain text file named '${kp_name}'.</p> - <pre>${kp_material}</pre> - %endif - <p>The instance '${instance.id} has been successfully launched using the - '${instance.image_id}' AMI.<br/> Access it at <a - href="http://${instance.public_dns_name}">http://${instance.public_dns_name}</a></p> - <p>SSH access is available using your private key '${kp_name}'.</p> -%else: - <p> Unknown failure, no instance. Please refer to your AWS console at <a - href="https://console.aws.amazon.com">https://console.aws.amazon.com</a></p> -%endif - </div> - </div> -</%def> - https://bitbucket.org/galaxy/galaxy-central/commits/54e5ea026a4a/ Changeset: 54e5ea026a4a Branch: next-stable User: dannon Date: 2014-12-04 17:05:07+00:00 Summary: Don't trust user email rendered into page unescaped for Raven. Affected #: 1 file diff -r 90d3d1205ef0211ce2f459e2832c6bad2737d924 -r 54e5ea026a4aaad0f4fd1228c63c77c15327afa4 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -45,7 +45,7 @@ <script> Raven.config('${app.config.sentry_dsn_public}').install(); %if trans.user: - Raven.setUser( { email: "${trans.user.email}" } ); + Raven.setUser( { email: "${trans.user.email | h}" } ); %endif </script> %endif https://bitbucket.org/galaxy/galaxy-central/commits/3ecb6b58e88a/ Changeset: 3ecb6b58e88a Branch: next-stable User: dannon Date: 2014-12-04 17:05:23+00:00 Summary: Trim trailing whitespace. Affected #: 1 file diff -r 54e5ea026a4aaad0f4fd1228c63c77c15327afa4 -r 3ecb6b58e88aeac8db48253e585df2aa429f39dc templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -13,7 +13,7 @@ self.body_class="" self.require_javascript=False %> - + <%def name="init()"> ## Override </%def> @@ -62,7 +62,7 @@ 'libs/require', "mvc/ui" )} - + <script type="text/javascript"> ## global configuration object var galaxy_config = @@ -112,14 +112,14 @@ 'galaxy.panels' )} <script type="text/javascript"> - + ensure_dd_helper(); - + %if self.has_left_panel: var lp = new Panel( { panel: $("#left"), center: $("#center"), drag: $("#left > .unified-panel-footer > .drag" ), toggle: $("#left > .unified-panel-footer > .panel-collapse" ) } ); force_left_panel = function( x ) { lp.force_panel( x ) }; %endif - + %if self.has_right_panel: var rp = new Panel( { panel: $("#right"), center: $("#center"), drag: $("#right > .unified-panel-footer > .drag" ), toggle: $("#right > .unified-panel-footer > .panel-collapse" ), right: true } ); window.handle_minwidth_hint = function( x ) { rp.handle_minwidth_hint( x ) }; @@ -134,7 +134,7 @@ ga('create', '${app.config.ga_code}', 'auto'); ga('send', 'pageview'); %endif - + </script> ## Handle AJAX (actually hidden iframe) upload tool <script type="text/javascript"> @@ -300,7 +300,7 @@ ## Document <html> - ${self.init()} + ${self.init()} <head> %if app.config.brand: <title>${self.title()} / ${app.config.brand}</title> @@ -316,7 +316,7 @@ ${self.javascripts()} ${self.javascript_app()} </head> - + <% body_class = self.body_class if self.message_box_visible: https://bitbucket.org/galaxy/galaxy-central/commits/738a4cbb6ed3/ Changeset: 738a4cbb6ed3 Branch: next-stable User: dannon Date: 2014-12-04 18:07:03+00:00 Summary: Cleanup of show_params while looking for bugs. Affected #: 1 file diff -r 3ecb6b58e88aeac8db48253e585df2aa429f39dc -r 738a4cbb6ed3189a80202f4be53726542b516239 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -932,7 +932,7 @@ @web.expose def show_params( self, trans, dataset_id=None, from_noframe=None, **kwd ): """ - Show the parameters used for an HDA + Show the parameters used for the job associated with an HDA """ hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) if not hda: @@ -961,19 +961,31 @@ toolbox = self.get_toolbox() tool = toolbox.get_tool( job.tool_id ) assert tool is not None, 'Requested tool has not been loaded.' - #Load parameter objects, if a parameter type has changed, it's possible for the value to no longer be valid + # Load parameter objects, if a parameter type has changed, it's possible for the value to no longer be valid try: params_objects = job.get_param_values( trans.app, ignore_errors=False ) except: params_objects = job.get_param_values( trans.app, ignore_errors=True ) - upgrade_messages = tool.check_and_update_param_values( job.get_param_values( trans.app, ignore_errors=True ), trans, update_values=False ) #use different param_objects here, since we want to display original values as much as possible + # use different param_objects in the following line, since we want to display original values as much as possible + upgrade_messages = tool.check_and_update_param_values( job.get_param_values( trans.app, + ignore_errors=True ), + trans, + update_values=False ) has_parameter_errors = True except: pass if job is None: return trans.show_error_message( "Job information is not available for this dataset." ) - #TODO: we should provide the basic values along with the objects, in order to better handle reporting of old values during upgrade - return trans.fill_template( "show_params.mako", inherit_chain=inherit_chain, history=trans.get_history(), hda=hda, job=job, tool=tool, params_objects=params_objects, upgrade_messages=upgrade_messages, has_parameter_errors=has_parameter_errors ) + # TODO: we should provide the basic values along with the objects, in order to better handle reporting of old values during upgrade + return trans.fill_template( "show_params.mako", + inherit_chain=inherit_chain, + history=trans.get_history(), + hda=hda, + job=job, + tool=tool, + params_objects=params_objects, + upgrade_messages=upgrade_messages, + has_parameter_errors=has_parameter_errors ) @web.expose def copy_datasets( self, trans, source_history=None, source_content_ids="", target_history_id=None, target_history_ids="", new_history_name="", do_copy=False, **kwd ): https://bitbucket.org/galaxy/galaxy-central/commits/84bf14a4e9de/ Changeset: 84bf14a4e9de Branch: next-stable User: dannon Date: 2014-12-04 18:10:37+00:00 Summary: Catch ValueError and actually log it instead of blowing up w/ invalid dataset_id. Raise httpexception. Affected #: 1 file diff -r 738a4cbb6ed3189a80202f4be53726542b516239 -r 84bf14a4e9de8bb7a27411933c28fdc237b75a52 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -934,9 +934,12 @@ """ Show the parameters used for the job associated with an HDA """ - hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + try: + hda = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + except ValueError: + hda = None if not hda: - raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) + raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % escape( str( dataset_id ) ) ) if not self._can_access_dataset( trans, hda ): return trans.show_error_message( "You are not allowed to access this dataset" ) @@ -967,8 +970,7 @@ except: params_objects = job.get_param_values( trans.app, ignore_errors=True ) # use different param_objects in the following line, since we want to display original values as much as possible - upgrade_messages = tool.check_and_update_param_values( job.get_param_values( trans.app, - ignore_errors=True ), + upgrade_messages = tool.check_and_update_param_values( job.get_param_values( trans.app, ignore_errors=True ), trans, update_values=False ) has_parameter_errors = True https://bitbucket.org/galaxy/galaxy-central/commits/502ee96ed98d/ Changeset: 502ee96ed98d Branch: next-stable User: dannon Date: 2014-12-04 19:04:52+00:00 Summary: Cleanup of search functionality while hunting bugs. Affected #: 3 files diff -r 84bf14a4e9de8bb7a27411933c28fdc237b75a52 -r 502ee96ed98d74e31844dc601599fd4c10006090 lib/galaxy/webapps/galaxy/controllers/search.py --- a/lib/galaxy/webapps/galaxy/controllers/search.py +++ b/lib/galaxy/webapps/galaxy/controllers/search.py @@ -1,4 +1,3 @@ - """ Contains a basic search interface for Galaxy """ @@ -8,7 +7,8 @@ log = logging.getLogger( __name__ ) + class SearchController( BaseUIController ): @web.expose def index(self, trans): - return trans.fill_template( "search/index.mako") + return trans.fill_template( "search/index.mako" ) diff -r 84bf14a4e9de8bb7a27411933c28fdc237b75a52 -r 502ee96ed98d74e31844dc601599fd4c10006090 templates/search/index.mako --- a/templates/search/index.mako +++ b/templates/search/index.mako @@ -17,9 +17,9 @@ ${parent.stylesheets()} <style> .searchResult { - border-style:dashed; - border-width:1px; - margin: 5px; + border-style:dashed; + border-width:1px; + margin: 5px; } </style> @@ -30,17 +30,17 @@ <script type="text/javascript"> var search_format_output = function(doc) { - var div_class = "historyItem"; - var a = $("<div class='" + div_class + "'>") - a.append($("<div>").append(doc['model_class'])); - b = a.append( $("<div class='historyItemTitle'><a href='/file/" + doc['id'] + "'>" + doc['name'] + "</a></div>") ); - if ('misc_blurb' in doc) { - b.append( $("<div>").append(doc["misc_blurb"]) ); - } - if ('peek' in doc) { - b.append( $("<pre class='peek'>").append( doc["peek"]) ); - } - return a; + var div_class = "historyItem"; + var a = $("<div class='" + div_class + "'>") + a.append($("<div>").append(doc['model_class'])); + b = a.append( $("<div class='historyItemTitle'><a href='/file/" + doc['id'] + "'>" + doc['name'] + "</a></div>") ); + if ('misc_blurb' in doc) { + b.append( $("<div>").append(doc["misc_blurb"]) ); + } + if ('peek' in doc) { + b.append( $("<pre class='peek'>").append( doc["peek"]) ); + } + return a; } </script> diff -r 84bf14a4e9de8bb7a27411933c28fdc237b75a52 -r 502ee96ed98d74e31844dc601599fd4c10006090 templates/search/search.mako --- a/templates/search/search.mako +++ b/templates/search/search.mako @@ -2,7 +2,7 @@ <%def name="search_init()"> ${h.js( - 'libs/jquery/jquery', + 'libs/jquery/jquery', )} </%def> @@ -12,54 +12,54 @@ <script type="text/javascript"> function doSearch(query) { - if (query.length > 1) { - var url = "/api/search"; - $.ajax({ - type : 'POST', - url: url, - data: JSON.stringify({"query" : query }), - contentType : 'application/json', - dataType : 'json', - success : function(data) { - var p = $("#output"); - p.empty(); - for(var i in data) { - var e = ${output_format}(data[i]); - p.append(e); - } - } - }); - } + if (query.length > 1) { + var url = "/api/search"; + $.ajax({ + type : 'POST', + url: url, + data: JSON.stringify({"query" : query }), + contentType : 'application/json', + dataType : 'json', + success : function(data) { + var p = $("#output"); + p.empty(); + for(var i in data) { + var e = ${output_format}(data[i]); + p.append(e); + } + } + }); + } }; $(document).ready( function() { - $("#search_button").click(function() { - doSearch($("#search_text").val()); - }); - $('#search_text').keyup(function(e){ - if(e.keyCode == 13) { - doSearch($("#search_text").val()); - } - }); - doSearch($("#search_text").val()); + $("#search_button").click(function() { + doSearch($("#search_text").val()); + }); + $('#search_text').keyup(function(e){ + if(e.keyCode == 13) { + doSearch($("#search_text").val()); + } + }); + doSearch($("#search_text").val()); }); var queryURL = function (query) { - var url = "/api/search" + encodeURIComponent(query); - url = url + "&field=" + $("#searchFields").val(); - if ($("#fileType").val() != "All") { - url = url + "&type=" + $("#fileType").val() - } - return url; + var url = "/api/search" + encodeURIComponent(query); + url = url + "&field=" + $("#searchFields").val(); + if ($("#fileType").val() != "All") { + url = url + "&type=" + $("#fileType").val() + } + return url; } </script><div id="search_box" style="margin: 20px;"> - <input type="text" id="search_text" size="90"/> + <input type="text" id="search_text" size="90"/></div><div style="margin: 20px;"> - <input type="button" id="search_button" value="Search"/> + <input type="button" id="search_button" value="Search"/></div><div id="output"></div> https://bitbucket.org/galaxy/galaxy-central/commits/02681fa23902/ Changeset: 02681fa23902 Branch: next-stable User: dannon Date: 2014-12-04 20:23:35+00:00 Summary: Fix search to work for at least datasets, hdas, etc. Affected #: 2 files diff -r 502ee96ed98d74e31844dc601599fd4c10006090 -r 02681fa23902d774892634cbbe5c9fbaf26f0846 templates/search/index.mako --- a/templates/search/index.mako +++ b/templates/search/index.mako @@ -1,52 +1,112 @@ - <%inherit file="/webapps/galaxy/base_panels.mako"/> -<%namespace file="/search/search.mako" import="search_init" /> -<%namespace file="/search/search.mako" import="search_dialog" /><%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.message_box_visible=False - self.active_view="shared" - self.overlay_visible=False -%> + <% + self.has_left_panel=False + self.has_right_panel=False + self.message_box_visible=False + self.active_view="shared" + self.overlay_visible=False + %></%def><%def name="stylesheets()"> -${parent.stylesheets()} -<style> -.searchResult { - border-style:dashed; - border-width:1px; - margin: 5px; -} -</style> + ${parent.stylesheets()} + <style> + .searchResult { + border-style:dashed; + border-width:1px; + margin: 5px; + } + </style> +</%def> + + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js( + "libs/jquery/jquery", + )} + <script type="text/javascript"> + + function search_format_output(doc) { + var div_class = "historyItem"; + var a = $("<div class='" + div_class + "'>") + a.append($("<div>").append(doc['model_class'])); + b = a.append( $("<div class='historyItemTitle'><a href='/file/" + doc['id'] + "'>" + doc['name'] + "</a></div>") ); + if ('misc_blurb' in doc) { + b.append( $("<div>").append(doc["misc_blurb"]) ); + } + if ('peek' in doc) { + b.append( $("<pre class='peek'>").append( doc["peek"]) ); + } + return a; + } + + function doSearch(query) { + if (query.length > 1) { + var url = "/api/search"; + $.ajax({ + type : 'POST', + url: url, + data: JSON.stringify({"query" : query }), + contentType : 'application/json', + dataType : 'json', + success : function(data) { + var p = $("#output"); + p.empty(); + _.each(data.results, function(doc){ + var div_class = "historyItem"; + var a = $("<div class='" + div_class + "'>") + a.append($("<div>").append(doc['model_class'])); + b = a.append( $("<div class='historyItemTitle'><a href='/file/" + doc['id'] + "'>" + doc['name'] + "</a></div>") ); + if ('misc_blurb' in doc) { + b.append( $("<div>").append(doc["misc_blurb"]) ); + } + if ('peek' in doc) { + b.append( $("<pre class='peek'>").append( doc["peek"]) ); + } + p.append(b); + }); + } + }); + } + }; + + + var queryURL = function (query) { + var url = "/api/search" + encodeURIComponent(query); + url = url + "&field=" + $("#searchFields").val(); + if ($("#fileType").val() != "All") { + url = url + "&type=" + $("#fileType").val() + } + return url; + } + + $(document).ready( function() { + $("#search_button").click(function() { + doSearch($("#search_text").val()); + }); + $('#search_text').keyup(function(e){ + if(e.keyCode == 13) { + doSearch($("#search_text").val()); + } + }); + doSearch($("#search_text").val()); + }); + </script></%def> + <%def name="center_panel()"> -${search_init()} -<script type="text/javascript"> -var search_format_output = function(doc) { - var div_class = "historyItem"; - var a = $("<div class='" + div_class + "'>") - a.append($("<div>").append(doc['model_class'])); - b = a.append( $("<div class='historyItemTitle'><a href='/file/" + doc['id'] + "'>" + doc['name'] + "</a></div>") ); - if ('misc_blurb' in doc) { - b.append( $("<div>").append(doc["misc_blurb"]) ); - } - if ('peek' in doc) { - b.append( $("<pre class='peek'>").append( doc["peek"]) ); - } - return a; -} + <div id="search_box" style="margin: 20px;"> + <input type="text" id="search_text" size="90"/> + </div> + <div style="margin: 20px;"> + <input type="button" id="search_button" value="Search"/> + </div> + <div id="output"></div> -</script> -<div style="overflow: auto; height: 100%"> -${search_dialog("search_format_output")} -</div></%def> - - diff -r 502ee96ed98d74e31844dc601599fd4c10006090 -r 02681fa23902d774892634cbbe5c9fbaf26f0846 templates/search/search.mako --- a/templates/search/search.mako +++ /dev/null @@ -1,68 +0,0 @@ - -<%def name="search_init()"> - - ${h.js( - 'libs/jquery/jquery', -)} - -</%def> - -<%def name="search_dialog(output_format)"> - -<script type="text/javascript"> - -function doSearch(query) { - if (query.length > 1) { - var url = "/api/search"; - $.ajax({ - type : 'POST', - url: url, - data: JSON.stringify({"query" : query }), - contentType : 'application/json', - dataType : 'json', - success : function(data) { - var p = $("#output"); - p.empty(); - for(var i in data) { - var e = ${output_format}(data[i]); - p.append(e); - } - } - }); - } -}; - -$(document).ready( function() { - $("#search_button").click(function() { - doSearch($("#search_text").val()); - }); - $('#search_text').keyup(function(e){ - if(e.keyCode == 13) { - doSearch($("#search_text").val()); - } - }); - doSearch($("#search_text").val()); -}); - -var queryURL = function (query) { - var url = "/api/search" + encodeURIComponent(query); - url = url + "&field=" + $("#searchFields").val(); - if ($("#fileType").val() != "All") { - url = url + "&type=" + $("#fileType").val() - } - return url; -} - -</script> - -<div id="search_box" style="margin: 20px;"> - <input type="text" id="search_text" size="90"/> -</div> -<div style="margin: 20px;"> - <input type="button" id="search_button" value="Search"/> -</div> - -<div id="output"></div> - - -</%def> https://bitbucket.org/galaxy/galaxy-central/commits/ead3e859dda1/ Changeset: ead3e859dda1 Branch: next-stable User: dannon Date: 2014-12-04 20:27:19+00:00 Summary: Disable search interface for right now -- I made it not broken in the previous commit, but nobody should be using this yet. Affected #: 1 file diff -r 02681fa23902d774892634cbbe5c9fbaf26f0846 -r ead3e859dda102520ea706bb3a566723af33a90f lib/galaxy/webapps/galaxy/controllers/search.py --- a/lib/galaxy/webapps/galaxy/controllers/search.py +++ b/lib/galaxy/webapps/galaxy/controllers/search.py @@ -9,6 +9,11 @@ class SearchController( BaseUIController ): + @web.expose def index(self, trans): - return trans.fill_template( "search/index.mako" ) + """ + Not ready for human consumption, yet. Power users can still use the + search API. + """ + return trans.show_message("Sorry, the search interface isn't quite ready for use, yet.") https://bitbucket.org/galaxy/galaxy-central/commits/a37ee286981b/ Changeset: a37ee286981b Branch: next-stable User: dannon Date: 2014-12-04 20:29:06+00:00 Summary: Tweak message and commentary for search controller. Affected #: 1 file diff -r ead3e859dda102520ea706bb3a566723af33a90f -r a37ee286981b363c0f8b644c3a40a7007648fffe lib/galaxy/webapps/galaxy/controllers/search.py --- a/lib/galaxy/webapps/galaxy/controllers/search.py +++ b/lib/galaxy/webapps/galaxy/controllers/search.py @@ -13,7 +13,7 @@ @web.expose def index(self, trans): """ - Not ready for human consumption, yet. Power users can still use the - search API. + Per the message, this is not ready for human consumption, yet. Power + users can still use the search API. """ - return trans.show_message("Sorry, the search interface isn't quite ready for use, yet.") + return trans.show_message("Sorry, the search interface isn't quite ready for use, yet. Watch the release notes and check back later!") https://bitbucket.org/galaxy/galaxy-central/commits/b51526d2f9b4/ Changeset: b51526d2f9b4 Branch: next-stable User: dannon Date: 2014-12-04 20:40:51+00:00 Summary: Merge. Affected #: 3 files diff -r a37ee286981b363c0f8b644c3a40a7007648fffe -r b51526d2f9b42a0bc64b55584e435ceebe7ceb31 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -125,6 +125,9 @@ // handle default value if (!field.skip) { + if (input.optional && field.validate && !field.validate()) { + value = 'None'; + } add (job_input_id, input.id, value); } } diff -r a37ee286981b363c0f8b644c3a40a7007648fffe -r b51526d2f9b42a0bc64b55584e435ceebe7ceb31 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -125,6 +125,9 @@ // handle default value if (!field.skip) { + if (input.optional && field.validate && !field.validate()) { + value = 'None'; + } add (job_input_id, input.id, value); } } diff -r a37ee286981b363c0f8b644c3a40a7007648fffe -r b51526d2f9b42a0bc64b55584e435ceebe7ceb31 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){if(q.optional&&p.validate&&!p.validate()){r="None"}c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/effaa3321792/ Changeset: effaa3321792 Branch: next-stable User: guerler Date: 2014-12-04 18:46:44+00:00 Summary: ToolForm: Adjust optional parameter submission Affected #: 3 files diff -r 29b2c328b89b6634c9a3f9a21c2349105a7e485a -r effaa332179242851638c008fab9010d04f3d48b client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -125,6 +125,9 @@ // handle default value if (!field.skip) { + if (input.optional && field.validate && !field.validate()) { + value = 'None'; + } add (job_input_id, input.id, value); } } diff -r 29b2c328b89b6634c9a3f9a21c2349105a7e485a -r effaa332179242851638c008fab9010d04f3d48b static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -125,6 +125,9 @@ // handle default value if (!field.skip) { + if (input.optional && field.validate && !field.validate()) { + value = 'None'; + } add (job_input_id, input.id, value); } } diff -r 29b2c328b89b6634c9a3f9a21c2349105a7e485a -r effaa332179242851638c008fab9010d04f3d48b static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){if(q.optional&&p.validate&&!p.validate()){r="None"}c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/636d3594e201/ Changeset: 636d3594e201 User: guerler Date: 2014-12-04 18:48:10+00:00 Summary: Merge Affected #: 3 files diff -r 66d38fa8edcbd9926f4eca9b875e2fe561d2d850 -r 636d3594e201ebb2d085c33c6de32577d65bd866 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -125,6 +125,9 @@ // handle default value if (!field.skip) { + if (input.optional && field.validate && !field.validate()) { + value = 'None'; + } add (job_input_id, input.id, value); } } diff -r 66d38fa8edcbd9926f4eca9b875e2fe561d2d850 -r 636d3594e201ebb2d085c33c6de32577d65bd866 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -125,6 +125,9 @@ // handle default value if (!field.skip) { + if (input.optional && field.validate && !field.validate()) { + value = 'None'; + } add (job_input_id, input.id, value); } } diff -r 66d38fa8edcbd9926f4eca9b875e2fe561d2d850 -r 636d3594e201ebb2d085c33c6de32577d65bd866 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){if(q.optional&&p.validate&&!p.validate()){r="None"}c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of 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: jmchilton: Test case for passing null to optional tool input.
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/66d38fa8edcb/ Changeset: 66d38fa8edcb User: jmchilton Date: 2014-12-04 17:28:23+00:00 Summary: Test case for passing null to optional tool input. Affected #: 2 files diff -r c5d6eadac9c3d6784361b93ef81c87307b5a4f0f -r 66d38fa8edcbd9926f4eca9b875e2fe561d2d850 test/api/test_tools.py --- a/test/api/test_tools.py +++ b/test/api/test_tools.py @@ -106,6 +106,20 @@ output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output ) assert output1_content == "--ex1,ex2" + @skip_without_tool( "multi_select" ) + def test_multi_select_optional( self ): + history_id = self.dataset_populator.new_history() + inputs = { + "select_ex": ["--ex1"], + "select_optional": None, + } + response = self._run( "multi_select", history_id, inputs, assert_ok=True ) + output = response[ "outputs" ] + output1_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output[ 0 ] ) + output2_content = self.dataset_populator.get_history_dataset_content( history_id, dataset=output[ 1 ] ) + assert output1_content.strip() == "--ex1" + assert output2_content.strip() == "None", output2_content + @skip_without_tool( "multi_data_param" ) def test_multidata_param( self ): history_id = self.dataset_populator.new_history() diff -r c5d6eadac9c3d6784361b93ef81c87307b5a4f0f -r 66d38fa8edcbd9926f4eca9b875e2fe561d2d850 test/functional/tools/multi_select.xml --- a/test/functional/tools/multi_select.xml +++ b/test/functional/tools/multi_select.xml @@ -3,7 +3,7 @@ <configfiles><configfile name="config">${select_ex}</configfile></configfiles> - <command>cat $config > $output</command> + <command>cat $config > $output; echo '$select_optional' > $output2</command><inputs><param name="select_ex" type="select" display="checkboxes" multiple="true"><option value="--ex1">Ex1</option> @@ -12,9 +12,17 @@ <option value="--ex4">Ex4</option><option value="ex5">Ex5</option></param> + <param name="select_optional" type="select" optional="true"> + <option value="--ex1">Ex1</option> + <option value="ex2">Ex2</option> + <option value="--ex3">Ex3</option> + <option value="--ex4">Ex4</option> + <option value="ex5">Ex5</option> + </param></inputs><outputs><data format="txt" name="output" /> + <data format="txt" name="output2" /></outputs><tests><test> 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: guerler: ToolForm: Update error message again
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c5d6eadac9c3/ Changeset: c5d6eadac9c3 User: guerler Date: 2014-12-04 17:01:34+00:00 Summary: ToolForm: Update error message again Affected #: 3 files diff -r e4447035cdc08adba1d75363f694c5988716c554 -r c5d6eadac9c3d6784361b93ef81c87307b5a4f0f client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -314,7 +314,7 @@ // data column case 'data_column': - input_def.error_text = 'Referenced dataset has no matching columns.'; + input_def.error_text = 'Missing columns in referenced dataset.'; field = this._fieldSelect(input_def); break; diff -r e4447035cdc08adba1d75363f694c5988716c554 -r c5d6eadac9c3d6784361b93ef81c87307b5a4f0f static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -314,7 +314,7 @@ // data column case 'data_column': - input_def.error_text = 'Referenced dataset has no matching columns.'; + input_def.error_text = 'Missing columns in referenced dataset.'; field = this._fieldSelect(input_def); break; diff -r e4447035cdc08adba1d75363f694c5988716c554 -r c5d6eadac9c3d6784361b93ef81c87307b5a4f0f static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.error_text="Referenced dataset has no matching columns.";i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,type:h.type,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,error_text:h.error_text||"No options available",multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.error_text="Missing columns in referenced dataset.";i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,type:h.type,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,error_text:h.error_text||"No options available",multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Update error message for missing columns
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e4447035cdc0/ Changeset: e4447035cdc0 User: guerler Date: 2014-12-04 16:59:21+00:00 Summary: ToolForm: Update error message for missing columns Affected #: 3 files diff -r 6b526d404d1e48f7a9a771624a259dd8a503ea39 -r e4447035cdc08adba1d75363f694c5988716c554 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -314,7 +314,7 @@ // data column case 'data_column': - input_def.error_text = 'Referenced dataset contains no suitable columns'; + input_def.error_text = 'Referenced dataset has no matching columns.'; field = this._fieldSelect(input_def); break; diff -r 6b526d404d1e48f7a9a771624a259dd8a503ea39 -r e4447035cdc08adba1d75363f694c5988716c554 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -314,7 +314,7 @@ // data column case 'data_column': - input_def.error_text = 'Referenced dataset contains no suitable columns'; + input_def.error_text = 'Referenced dataset has no matching columns.'; field = this._fieldSelect(input_def); break; diff -r 6b526d404d1e48f7a9a771624a259dd8a503ea39 -r e4447035cdc08adba1d75363f694c5988716c554 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.error_text="Referenced dataset contains no suitable columns";i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,type:h.type,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,error_text:h.error_text||"No options available",multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.error_text="Referenced dataset has no matching columns.";i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,type:h.type,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,error_text:h.error_text||"No options available",multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Update error message
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6b526d404d1e/ Changeset: 6b526d404d1e User: guerler Date: 2014-12-04 16:53:22+00:00 Summary: ToolForm: Update error message Affected #: 3 files diff -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 -r 6b526d404d1e48f7a9a771624a259dd8a503ea39 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -41,16 +41,16 @@ extensions = extensions.replace(',', ', '); var pos = extensions.lastIndexOf(', '); if (pos != -1) { - extensions = extensions.substr(0, pos) + " or " + extensions.substr(pos+1); + extensions = extensions.substr(0, pos) + ' or ' + extensions.substr(pos+1); } } - var hda_error = 'No dataset available'; + var hda_error = 'No dataset available.'; if (extensions) { - hda_error = 'No dataset of type ' + extensions + ' available.'; + hda_error = 'No ' + extensions + ' dataset available.'; } - var hdca_error = 'No dataset list available'; + var hdca_error = 'No dataset list available.'; if (extensions) { - hdca_error = 'No dataset list of type ' + extensions + ' available.'; + hdca_error = 'No ' + extensions + ' dataset list available.'; } // add single dataset selector diff -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 -r 6b526d404d1e48f7a9a771624a259dd8a503ea39 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -41,16 +41,16 @@ extensions = extensions.replace(',', ', '); var pos = extensions.lastIndexOf(', '); if (pos != -1) { - extensions = extensions.substr(0, pos) + " or " + extensions.substr(pos+1); + extensions = extensions.substr(0, pos) + ' or ' + extensions.substr(pos+1); } } - var hda_error = 'No dataset available'; + var hda_error = 'No dataset available.'; if (extensions) { - hda_error = 'No dataset of type ' + extensions + ' available.'; + hda_error = 'No ' + extensions + ' dataset available.'; } - var hdca_error = 'No dataset list available'; + var hdca_error = 'No dataset list available.'; if (extensions) { - hdca_error = 'No dataset list of type ' + extensions + ' available.'; + hdca_error = 'No ' + extensions + ' dataset list available.'; } // add single dataset selector diff -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 -r 6b526d404d1e48f7a9a771624a259dd8a503ea39 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(f,o){this.app=f;this.options=o;var n=this;this.setElement("<div/>");this.list={};var m=[];if(o.type=="data_collection"){this.mode="collection"}else{if(o.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var j=o.extensions.toString();if(j){j=j.replace(",",", ");var k=j.lastIndexOf(", ");if(k!=-1){j=j.substr(0,k)+" or "+j.substr(k+1)}}var h="No dataset available";if(j){h="No dataset of type "+j+" available."}var l="No dataset list available";if(j){l="No dataset list of type "+j+" available."}if(this.mode=="single"){m.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({error_text:h,onchange:function(){n.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,error_text:h,onchange:function(){n.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){m.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({error_text:l,onchange:function(){n.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){n.current=i;n.refresh();n.trigger("change")}});this.$batch=$(a.batchMode());if(_.size(this.list)>1){this.$el.append(c.wrap(this.button_type.$el))}for(var g in this.list){this.$el.append(this.list[g].field.$el)}this.$el.append(this.$batch);this.update(o.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(o.onchange){o.onchange(n.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(f,o){this.app=f;this.options=o;var n=this;this.setElement("<div/>");this.list={};var m=[];if(o.type=="data_collection"){this.mode="collection"}else{if(o.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var j=o.extensions.toString();if(j){j=j.replace(",",", ");var k=j.lastIndexOf(", ");if(k!=-1){j=j.substr(0,k)+" or "+j.substr(k+1)}}var h="No dataset available.";if(j){h="No "+j+" dataset available."}var l="No dataset list available.";if(j){l="No "+j+" dataset list available."}if(this.mode=="single"){m.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({error_text:h,onchange:function(){n.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,error_text:h,onchange:function(){n.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){m.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({error_text:l,onchange:function(){n.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){n.current=i;n.refresh();n.trigger("change")}});this.$batch=$(a.batchMode());if(_.size(this.list)>1){this.$el.append(c.wrap(this.button_type.$el))}for(var g in this.list){this.$el.append(this.list[g].field.$el)}this.$el.append(this.$batch);this.update(o.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(o.onchange){o.onchange(n.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: ToolForm: Add dataset types to error message
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6b397d3623e9/ Changeset: 6b397d3623e9 User: guerler Date: 2014-12-04 16:45:18+00:00 Summary: ToolForm: Add dataset types to error message Affected #: 15 files diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -340,7 +340,7 @@ buttons: { execute : new Ui.Button({ icon : 'fa-check', - tooltip : 'Execute the tool', + tooltip : 'Execute: ' + self.model.name, title : 'Execute', cls : 'btn btn-primary', floating : 'clear', diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -314,6 +314,7 @@ // data column case 'data_column': + input_def.error_text = 'Referenced dataset contains no suitable columns'; field = this._fieldSelect(input_def); break; @@ -425,6 +426,7 @@ return new SelectClass.View({ id : 'field-' + input_def.id, data : options, + error_text : input_def.error_text || 'No options available', multiple : input_def.multiple, searchable : input_def.searchable, onchange : function() { diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -35,10 +35,29 @@ this.current = this.mode; this.list = {}; + // error messages + var extensions = options.extensions.toString(); + if (extensions) { + extensions = extensions.replace(',', ', '); + var pos = extensions.lastIndexOf(', '); + if (pos != -1) { + extensions = extensions.substr(0, pos) + " or " + extensions.substr(pos+1); + } + } + var hda_error = 'No dataset available'; + if (extensions) { + hda_error = 'No dataset of type ' + extensions + ' available.'; + } + var hdca_error = 'No dataset list available'; + if (extensions) { + hdca_error = 'No dataset list of type ' + extensions + ' available.'; + } + // add single dataset selector if (this.mode == 'single') { radio_buttons.push({icon: 'fa-file-o', label : 'Single dataset', value : 'single'}); this.select_single = new Ui.Select.View({ + error_text : hda_error, onchange : function() { self.trigger('change'); } @@ -54,6 +73,7 @@ radio_buttons.push({icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }); this.select_multiple = new Ui.Select.View({ multiple : true, + error_text : hda_error, onchange : function() { self.trigger('change'); } @@ -68,6 +88,7 @@ if (this.mode == 'single' || this.mode == 'collection') { radio_buttons.push({icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }); this.select_collection = new Ui.Select.View({ + error_text : hdca_error, onchange : function() { self.trigger('change'); } diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 client/galaxy/scripts/mvc/ui/ui-options.js --- a/client/galaxy/scripts/mvc/ui/ui-options.js +++ b/client/galaxy/scripts/mvc/ui/ui-options.js @@ -10,8 +10,8 @@ visible : true, data : [], id : Utils.uuid(), - errorText : 'No data available.', - waitText : 'Please wait...' + error_text : 'No data available.', + wait_text : 'Please wait...' }; // configure options @@ -153,7 +153,7 @@ */ wait: function() { if (this._size() == 0) { - this._messageShow(this.options.waitText, 'info'); + this._messageShow(this.options.wait_text, 'info'); this.$options.hide(); } }, @@ -177,7 +177,7 @@ */ _refresh: function() { if (this._size() == 0) { - this._messageShow(this.options.errorText, 'danger'); + this._messageShow(this.options.error_text, 'danger'); this.$options.hide(); } else { this._messageHide(); diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -9,7 +9,7 @@ optionsDefault : { id : '', cls : '', - empty : 'No data available', + error_text : 'No data available', visible : true, wait : false, multiple : false, @@ -247,7 +247,7 @@ this.disable(); // append placeholder - this.$select.append(this._templateOption({value : 'null', label : this.options.empty})); + this.$select.append(this._templateOption({value : 'null', label : this.options.error_text})); } else { // enable select field this.enable(); diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -340,7 +340,7 @@ buttons: { execute : new Ui.Button({ icon : 'fa-check', - tooltip : 'Execute the tool', + tooltip : 'Execute: ' + self.model.name, title : 'Execute', cls : 'btn btn-primary', floating : 'clear', diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -314,6 +314,7 @@ // data column case 'data_column': + input_def.error_text = 'Referenced dataset contains no suitable columns'; field = this._fieldSelect(input_def); break; @@ -425,6 +426,7 @@ return new SelectClass.View({ id : 'field-' + input_def.id, data : options, + error_text : input_def.error_text || 'No options available', multiple : input_def.multiple, searchable : input_def.searchable, onchange : function() { diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -35,10 +35,29 @@ this.current = this.mode; this.list = {}; + // error messages + var extensions = options.extensions.toString(); + if (extensions) { + extensions = extensions.replace(',', ', '); + var pos = extensions.lastIndexOf(', '); + if (pos != -1) { + extensions = extensions.substr(0, pos) + " or " + extensions.substr(pos+1); + } + } + var hda_error = 'No dataset available'; + if (extensions) { + hda_error = 'No dataset of type ' + extensions + ' available.'; + } + var hdca_error = 'No dataset list available'; + if (extensions) { + hdca_error = 'No dataset list of type ' + extensions + ' available.'; + } + // add single dataset selector if (this.mode == 'single') { radio_buttons.push({icon: 'fa-file-o', label : 'Single dataset', value : 'single'}); this.select_single = new Ui.Select.View({ + error_text : hda_error, onchange : function() { self.trigger('change'); } @@ -54,6 +73,7 @@ radio_buttons.push({icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }); this.select_multiple = new Ui.Select.View({ multiple : true, + error_text : hda_error, onchange : function() { self.trigger('change'); } @@ -68,6 +88,7 @@ if (this.mode == 'single' || this.mode == 'collection') { radio_buttons.push({icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }); this.select_collection = new Ui.Select.View({ + error_text : hdca_error, onchange : function() { self.trigger('change'); } diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 static/scripts/mvc/ui/ui-options.js --- a/static/scripts/mvc/ui/ui-options.js +++ b/static/scripts/mvc/ui/ui-options.js @@ -10,8 +10,8 @@ visible : true, data : [], id : Utils.uuid(), - errorText : 'No data available.', - waitText : 'Please wait...' + error_text : 'No data available.', + wait_text : 'Please wait...' }; // configure options @@ -153,7 +153,7 @@ */ wait: function() { if (this._size() == 0) { - this._messageShow(this.options.waitText, 'info'); + this._messageShow(this.options.wait_text, 'info'); this.$options.hide(); } }, @@ -177,7 +177,7 @@ */ _refresh: function() { if (this._size() == 0) { - this._messageShow(this.options.errorText, 'danger'); + this._messageShow(this.options.error_text, 'danger'); this.$options.hide(); } else { this._messageHide(); diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -9,7 +9,7 @@ optionsDefault : { id : '', cls : '', - empty : 'No data available', + error_text : 'No data available', visible : true, wait : false, multiple : false, @@ -247,7 +247,7 @@ this.disable(); // append placeholder - this.$select.append(this._templateOption({value : 'null', label : this.options.empty})); + this.$select.append(this._templateOption({value : 'null', label : this.options.error_text})); } else { // enable select field this.enable(); diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(this.is_dynamic){var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(!_.isEqual(p.options,u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;case"drill_down":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,cls:"ui-portlet-slim",operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,j,h,m,k,a,e,d,f,l,c,g){var b=Backbone.View.extend({container:"body",initialize:function(o){console.debug(o);var n=this;var p=parent.Galaxy;if(p&&p.modal){this.modal=p.modal}else{this.modal=new m.Modal.View()}if(p&&p.currUser){this.is_admin=p.currUser.get("is_admin")}else{this.is_admin=false}this.options=o;this.deferred=new j();this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f(this);this._buildForm(o)},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},rebuild:function(){this.tree.refresh();console.debug("tools-form::rebuild() - Rebuilding data structures.")},refresh:function(){if(this.is_dynamic){var n=this;this.deferred.reset();this.deferred.execute(function(){n._updateModel()})}},_buildModel:function(){var n=this;var o=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){o+="job_id="+this.options.job_id}else{if(this.options.dataset_id){o+="dataset_id="+this.options.dataset_id}else{var p=top.location.href;var q=p.indexOf("?");if(p.indexOf("tool_id=")!=-1&&q!==-1){o+=p.slice(q+1)}}}i.request({type:"GET",url:o,success:function(r){n.options=$.extend(n.options,r);n.model=r;n.inputs=r.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(r);n._buildForm()},error:function(r){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(r)}})},_updateModel:function(){var n=this;var o=this.tree.finalize({data:function(r){if(r.values.length>0&&r.values[0]&&r.values[0].src==="hda"){return n.content.get({id:r.values[0].id,src:"hda"}).id_uncoded}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(o);function q(u){for(var s in n.input_list){var t=n.field_list[s];var r=n.input_list[s];if(r.is_dynamic&&t.wait&&t.unwait){if(u){t.wait()}else{t.unwait()}}}}q(true);var p=this.deferred.register();i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:o,success:function(r){n._updateForm(r);q(false);n.deferred.done(p);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(r)},error:function(r){n.deferred.done(p);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(r)}})},_updateForm:function(n){var o=this;this.tree.matchModel(n,function(q,u){var p=o.input_list[q];if(p&&p.options){if(!_.isEqual(p.options,u.options)){p.options=u.options;var v=o.field_list[q];if(v.update){var t=[];switch(p.type){case"data":t=p.options;break;case"drill_down":t=p.options;break;default:for(var s in u.options){var r=u.options[s];if(r.length>2){t.push({label:r[0],value:r[1]})}}}v.update(t);v.trigger("change");console.debug("Updating options for "+q)}}}})},_buildForm:function(p){var o=this;this.field_list={};this.input_list={};this.element_list={};this.model=p;this.inputs=p.inputs;var s=new m.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(p.biostar_url){s.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/p/new/post/")}});s.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(o.options.biostar_url+"/t/"+o.options.id+"/")}})}s.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+o.options.id)}});if(this.is_admin){s.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+o.options.id+"/download"}})}this.section=new l.View(o,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,cls:"ui-portlet-slim",operations:{menu:s},buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute: "+o.model.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){o.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(p.help!=""){this.$el.append(d.help(p.help))}if(p.citations){var r=$("<div/>");var n=new k.ToolCitationCollection();n.tool_id=p.id;var q=new a.CitationListView({el:r,collection:n});q.render();n.fetch();this.$el.append(r)}this.portlet.append(this.section.$el);this.rebuild()}});return{View:b}}); \ No newline at end of file diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,type:h.type,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.error_text="Referenced dataset contains no suitable columns";i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,type:h.type,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,error_text:h.error_text||"No options available",multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(g.type=="data_collection"){this.mode="collection"}else{if(g.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};if(this.mode=="single"){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());if(_.size(this.list)>1){this.$el.append(c.wrap(this.button_type.$el))}for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(f,o){this.app=f;this.options=o;var n=this;this.setElement("<div/>");this.list={};var m=[];if(o.type=="data_collection"){this.mode="collection"}else{if(o.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var j=o.extensions.toString();if(j){j=j.replace(",",", ");var k=j.lastIndexOf(", ");if(k!=-1){j=j.substr(0,k)+" or "+j.substr(k+1)}}var h="No dataset available";if(j){h="No dataset of type "+j+" available."}var l="No dataset list available";if(j){l="No dataset list of type "+j+" available."}if(this.mode=="single"){m.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({error_text:h,onchange:function(){n.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,error_text:h,onchange:function(){n.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){m.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({error_text:l,onchange:function(){n.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){n.current=i;n.refresh();n.trigger("change")}});this.$batch=$(a.batchMode());if(_.size(this.list)>1){this.$el.append(c.wrap(this.button_type.$el))}for(var g in this.list){this.$el.append(this.list[g].field.$el)}this.$el.append(this.$batch);this.update(o.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(o.onchange){o.onchange(n.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 static/scripts/packed/mvc/ui/ui-options.js --- a/static/scripts/packed/mvc/ui/ui-options.js +++ b/static/scripts/packed/mvc/ui/ui-options.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={visible:true,data:[],id:b.uuid(),errorText:"No data available.",waitText:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.waitText,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.errorText,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file +define(["utils/utils"],function(b){var a=Backbone.View.extend({initialize:function(g){this.optionsDefault={visible:true,data:[],id:b.uuid(),error_text:"No data available.",wait_text:"Please wait..."};this.options=b.merge(g,this.optionsDefault);this.setElement("<div/>");this.$message=$("<div/>");this.$options=$(this._template(g));this.$el.append(this.$message);this.$el.append(this.$options);if(!this.options.visible){this.$el.hide()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}var f=this;this.on("change",function(){f._change()})},update:function(g){var j=this._getValue();this.$options.empty();if(this._templateOptions){this.$options.append(this._templateOptions(g))}else{for(var h in g){var i=$(this._templateOption(g[h]));i.addClass("ui-option");this.$options.append(i)}}var f=this;this.$el.find("input").on("change",function(){f.value(f._getValue());f._change()});this._refresh();this.value(j)},value:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}this.$el.find("input").prop("checked",false);for(var f in g){this.$el.find('input[value="'+g[f]+'"]').first().prop("checked",true)}}return this._getValue()},exists:function(g){if(g!==undefined){if(!(g instanceof Array)){g=[g]}for(var f in g){if(this.$el.find('input[value="'+g[f]+'"]').length>0){return true}}}return false},first:function(){var f=this.$el.find("input");if(f.length>0){return f.val()}else{return undefined}},validate:function(){var g=this.value();if(!(g instanceof Array)){g=[g]}for(var f in g){if([null,"null",undefined].indexOf(g[f])>-1){return false}}return true},wait:function(){if(this._size()==0){this._messageShow(this.options.wait_text,"info");this.$options.hide()}},unwait:function(){this._messageHide();this._refresh()},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_refresh:function(){if(this._size()==0){this._messageShow(this.options.error_text,"danger");this.$options.hide()}else{this._messageHide();this.$options.css("display","inline-block")}},_getValue:function(){var g=this.$el.find(":checked");if(g.length==0){return"null"}if(this.options.multiple){var f=[];g.each(function(){f.push($(this).val())});return f}else{return g.val()}},_size:function(){return this.$el.find(".ui-option").length},_messageShow:function(g,f){this.$message.show();this.$message.removeClass();this.$message.addClass("ui-message alert alert-"+f);this.$message.html(g)},_messageHide:function(){this.$message.hide()},_template:function(){return'<div class="ui-options"/>'}});var d={};d.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="radio" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var c={};c.View=a.extend({initialize:function(f){f.multiple=true;a.prototype.initialize.call(this,f)},_templateOption:function(f){return'<div><input type="checkbox" name="'+this.options.id+'" value="'+f.value+'"/>'+f.label+"<br></div>"}});var e={};e.View=a.extend({initialize:function(f){a.prototype.initialize.call(this,f)},value:function(f){if(f!==undefined){this.$el.find("input").prop("checked",false);this.$el.find("label").removeClass("active");this.$el.find('[value="'+f+'"]').prop("checked",true).closest("label").addClass("active")}return this._getValue()},_templateOption:function(g){var f='<label class="btn btn-default">';if(g.icon){f+='<i class="fa '+g.icon+'"/>'}f+='<input type="radio" name="'+this.options.id+'" value="'+g.value+'">'+g.label+"</label>";return f},_template:function(){return'<div class="btn-group ui-radiobutton" data-toggle="buttons"/>'}});return{Base:a,Radio:d,RadioButton:e,Checkbox:c}}); \ No newline at end of file diff -r b8dea58ea20ef71e4b30beae636042ffc44d348e -r 6b397d3623e9de8f375f4ce52f501548530a4ef9 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.empty}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"",error_text:"No data available",visible:true,wait:false,multiple:false,searchable:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$select.prop("multiple",true);this.$select.addClass("ui-select-multiple");this.$icon.remove()}else{this.$el.addClass("ui-select")}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}return this.$select.val()},first:function(){var c=this.$select.find("option");if(c.length>0){return c.val()}else{return undefined}},validate:function(){var d=this.value();if(!(d instanceof Array)){d=[d]}for(var c in d){if([null,"null",undefined].indexOf(d[c])>-1){return false}}return true},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this.$select.val();this.$select.find("option").remove();for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();this.$select.val(e);if(!this.$select.val()){this.$select.val(this.first())}if(this.options.searchable){this.$button.hide();this.$select.select2("destroy");this.$select.select2()}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this.$select.val())}},_refresh:function(){this.$select.find("option[value=null]").remove();var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.append(this._templateOption({value:"null",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'"><select id="select" class="select '+c.cls+" "+c.id+'"></select><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8ed933747f9a/ Changeset: 8ed933747f9a Branch: next-stable User: dannon Date: 2014-12-04 15:27:08+00:00 Summary: changeset: 15487:c8791bdcbdde user: Dannon Baker <dannonbaker(a)me.com> date: Tue Dec 02 09:40:10 2014 -0500 files: lib/galaxy/webapps/galaxy/controllers/user.py description: Remove never-used success vars. Affected #: 1 file diff -r 0cfba5087d81c4bd0add051cf1d0ab48d8a33cce -r 8ed933747f9acebc51de16939cca3e48533c3305 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1022,12 +1022,10 @@ is_activation_sent = self.send_verification_email( trans, user.email, user.username ) if is_activation_sent: message = 'The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.' - success = True else: message = 'Unable to send activation email, please contact your local Galaxy administrator.' if trans.app.config.error_email_to is not None: message += ' Contact: %s' % trans.app.config.error_email_to - success = False if ( user.username != username ): user.username = username trans.sa_session.add( user ) https://bitbucket.org/galaxy/galaxy-central/commits/4dd689ca4e4f/ Changeset: 4dd689ca4e4f Branch: next-stable User: dannon Date: 2014-12-04 15:56:33+00:00 Summary: Fix indentation to a multiple of 4. Affected #: 1 file diff -r 8ed933747f9acebc51de16939cca3e48533c3305 -r 4dd689ca4e4f1f2148abd67639fba2e48466716f lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1539,7 +1539,7 @@ @web.require_login( "to undelete addresses" ) @web.expose def undelete_address( self, trans, cntrller, address_id=None, **kwd ): - return self.__delete_undelete_address( trans, cntrller, 'undelete', address_id=address_id, **kwd ) + return self.__delete_undelete_address( trans, cntrller, 'undelete', address_id=address_id, **kwd ) def __delete_undelete_address( self, trans, cntrller, op, address_id=None, **kwd ): is_admin = cntrller == 'admin' and trans.user_is_admin() https://bitbucket.org/galaxy/galaxy-central/commits/52bca602fda1/ Changeset: 52bca602fda1 Branch: next-stable User: dannon Date: 2014-12-04 16:00:36+00:00 Summary: Remove another unused variable in the redirect code. Affected #: 1 file diff -r 4dd689ca4e4f1f2148abd67639fba2e48466716f -r 52bca602fda1f49cdd686607cc4b4c3b4943f59d lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1739,7 +1739,6 @@ def __get_redirect_url( self, redirect ): root_url = url_for( '/', qualified=True ) - redirect_url = '' # always start with redirect_url being empty # compare urls, to prevent a redirect from pointing (directly) outside of galaxy # or to enter a logout/login loop if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): https://bitbucket.org/galaxy/galaxy-central/commits/29b2c328b89b/ Changeset: 29b2c328b89b Branch: next-stable User: dannon Date: 2014-12-04 16:09:30+00:00 Summary: Import cleanup in user controller prior to merging password work. Affected #: 1 file diff -r 52bca602fda1f49cdd686607cc4b4c3b4943f59d -r 29b2c328b89b6634c9a3f9a21c2349105a7e485a lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -5,32 +5,30 @@ import glob import logging import os +import random import socket import string -import random import urllib + +from datetime import datetime, timedelta + +from galaxy import model +from galaxy import util from galaxy import web -from galaxy import util -from galaxy import model from galaxy.model.orm import and_ -from galaxy.security.validate_user_input import validate_email -from galaxy.security.validate_user_input import validate_publicname -from galaxy.security.validate_user_input import validate_password -from galaxy.security.validate_user_input import transform_publicname -from galaxy.util.json import loads -from galaxy.util.json import dumps -from galaxy.util import listify -from galaxy.util import docstring_trim +from galaxy.security.validate_user_input import (transform_publicname, + validate_email, + validate_password, + validate_publicname) +from galaxy.util import biostar, hash_util, docstring_trim, listify +from galaxy.util.json import dumps, loads from galaxy.web import url_for -from galaxy.web.base.controller import BaseUIController -from galaxy.web.base.controller import UsesFormDefinitionsMixin -from galaxy.web.base.controller import CreatesUsersMixin -from galaxy.web.base.controller import CreatesApiKeysMixin -from galaxy.web.form_builder import CheckboxField -from galaxy.web.form_builder import build_select_field -from galaxy.web.framework.helpers import time_ago, grids, escape -from datetime import datetime, timedelta -from galaxy.util import hash_util, biostar +from galaxy.web.base.controller import (BaseUIController, + CreatesApiKeysMixin, + CreatesUsersMixin, + UsesFormDefinitionsMixin) +from galaxy.web.form_builder import build_select_field, CheckboxField +from galaxy.web.framework.helpers import escape, grids, time_ago log = logging.getLogger( __name__ ) https://bitbucket.org/galaxy/galaxy-central/commits/b8dea58ea20e/ Changeset: b8dea58ea20e User: dannon Date: 2014-12-04 16:10:26+00:00 Summary: Merge next-stable to default. Affected #: 1 file diff -r 2cdf98534410d48b1a10c03eec30901979955aca -r b8dea58ea20ef71e4b30beae636042ffc44d348e lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -5,32 +5,30 @@ import glob import logging import os +import random import socket import string -import random import urllib + +from datetime import datetime, timedelta + +from galaxy import model +from galaxy import util from galaxy import web -from galaxy import util -from galaxy import model from galaxy.model.orm import and_ -from galaxy.security.validate_user_input import validate_email -from galaxy.security.validate_user_input import validate_publicname -from galaxy.security.validate_user_input import validate_password -from galaxy.security.validate_user_input import transform_publicname -from galaxy.util.json import loads -from galaxy.util.json import dumps -from galaxy.util import listify -from galaxy.util import docstring_trim +from galaxy.security.validate_user_input import (transform_publicname, + validate_email, + validate_password, + validate_publicname) +from galaxy.util import biostar, hash_util, docstring_trim, listify +from galaxy.util.json import dumps, loads from galaxy.web import url_for -from galaxy.web.base.controller import BaseUIController -from galaxy.web.base.controller import UsesFormDefinitionsMixin -from galaxy.web.base.controller import CreatesUsersMixin -from galaxy.web.base.controller import CreatesApiKeysMixin -from galaxy.web.form_builder import CheckboxField -from galaxy.web.form_builder import build_select_field -from galaxy.web.framework.helpers import time_ago, grids, escape -from datetime import datetime, timedelta -from galaxy.util import hash_util, biostar +from galaxy.web.base.controller import (BaseUIController, + CreatesApiKeysMixin, + CreatesUsersMixin, + UsesFormDefinitionsMixin) +from galaxy.web.form_builder import build_select_field, CheckboxField +from galaxy.web.framework.helpers import escape, grids, time_ago log = logging.getLogger( __name__ ) @@ -1022,12 +1020,10 @@ is_activation_sent = self.send_verification_email( trans, user.email, user.username ) if is_activation_sent: message = 'The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.' - success = True else: message = 'Unable to send activation email, please contact your local Galaxy administrator.' if trans.app.config.error_email_to is not None: message += ' Contact: %s' % trans.app.config.error_email_to - success = False if ( user.username != username ): user.username = username trans.sa_session.add( user ) @@ -1542,7 +1538,7 @@ @web.require_login( "to undelete addresses" ) @web.expose def undelete_address( self, trans, cntrller, address_id=None, **kwd ): - return self.__delete_undelete_address( trans, cntrller, 'undelete', address_id=address_id, **kwd ) + return self.__delete_undelete_address( trans, cntrller, 'undelete', address_id=address_id, **kwd ) def __delete_undelete_address( self, trans, cntrller, op, address_id=None, **kwd ): is_admin = cntrller == 'admin' and trans.user_is_admin() @@ -1742,7 +1738,6 @@ def __get_redirect_url( self, redirect ): root_url = url_for( '/', qualified=True ) - redirect_url = '' # always start with redirect_url being empty # compare urls, to prevent a redirect from pointing (directly) outside of galaxy # or to enter a logout/login loop if not util.compare_urls( root_url, redirect, compare_path=False ) or util.compare_urls( url_for( controller='user', action='logout', qualified=True ), redirect ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset 9c482e1d9b3c
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/295fd99b1d57/ Changeset: 295fd99b1d57 Branch: stable User: natefoo Date: 2014-12-04 16:00:22+00:00 Summary: Update tag latest_2014.10.06 for changeset 9c482e1d9b3c Affected #: 1 file diff -r 9c482e1d9b3cfdb2936b3f230d434c1f27898eff -r 295fd99b1d578e4d58af673259b95e703750f757 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -0e663285c74326737d4ff3c637d4c8aba8847755 latest_2014.10.06 +9c482e1d9b3cfdb2936b3f230d434c1f27898eff latest_2014.10.06 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 DynamicOptions AdditionalValueFilter when columns have not been assigned and to give value preference over name.
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9c482e1d9b3c/ Changeset: 9c482e1d9b3c Branch: stable User: dan Date: 2014-12-03 21:52:56+00:00 Summary: Fix for DynamicOptions AdditionalValueFilter when columns have not been assigned and to give value preference over name. Affected #: 1 file diff -r caade2c602d65a005d54997e95fcb1a9eab6ea17 -r 9c482e1d9b3cfdb2936b3f230d434c1f27898eff lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -301,8 +301,11 @@ add_value = [] for i in range( self.dynamic_option.largest_index + 1 ): add_value.append( "" ) - add_value[self.dynamic_option.columns['value']] = self.value - add_value[self.dynamic_option.columns['name']] = self.name + value_col = self.dynamic_option.columns.get( 'value', 0 ) + name_col = self.dynamic_option.columns.get( 'name', value_col ) + # Set name first, then value, in case they are the same column + add_value[ name_col ] = self.name + add_value[ value_col ] = self.value if self.index is not None: rval.insert( self.index, add_value ) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Merged in lance_parsons/galaxy-central-pull-requests/admin_cleanup_datasets_fix (pull request #586)
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2cdf98534410/ Changeset: 2cdf98534410 User: natefoo Date: 2014-12-04 15:33:52+00:00 Summary: Merged in lance_parsons/galaxy-central-pull-requests/admin_cleanup_datasets_fix (pull request #586) Added pkg_resources to load required Mako package Affected #: 1 file diff -r 171511af9fcf2689e2761cf79e2cf02ff8324acc -r 2cdf98534410d48b1a10c03eec30901979955aca scripts/cleanup_datasets/admin_cleanup_datasets.py --- a/scripts/cleanup_datasets/admin_cleanup_datasets.py +++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py @@ -47,10 +47,10 @@ log.addHandler(logging.StreamHandler(sys.stdout)) from cleanup_datasets import CleanupDatasetsApplication -#import pkg_resources +import pkg_resources #pkg_resources.require("SQLAlchemy >= 0.4") -#pkg_resources.require("Mako") +pkg_resources.require("Mako") from mako.template import Template import time 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 commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/aa75079bf2cb/ Changeset: aa75079bf2cb Branch: admin_cleanup_datasets_fix User: lance_parsons Date: 2014-12-03 19:50:56+00:00 Summary: Added pkg_resources to load required Mako package Affected #: 1 file diff -r 25d6c1903eceb8a2ed47459d1fefcfaed57e8995 -r aa75079bf2cb6e5a03774442aed99e2c16e540f5 scripts/cleanup_datasets/admin_cleanup_datasets.py --- a/scripts/cleanup_datasets/admin_cleanup_datasets.py +++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py @@ -47,10 +47,10 @@ log.addHandler(logging.StreamHandler(sys.stdout)) from cleanup_datasets import CleanupDatasetsApplication -#import pkg_resources +import pkg_resources #pkg_resources.require("SQLAlchemy >= 0.4") -#pkg_resources.require("Mako") +pkg_resources.require("Mako") from mako.template import Template import time https://bitbucket.org/galaxy/galaxy-central/commits/2cdf98534410/ Changeset: 2cdf98534410 User: natefoo Date: 2014-12-04 15:33:52+00:00 Summary: Merged in lance_parsons/galaxy-central-pull-requests/admin_cleanup_datasets_fix (pull request #586) Added pkg_resources to load required Mako package Affected #: 1 file diff -r 171511af9fcf2689e2761cf79e2cf02ff8324acc -r 2cdf98534410d48b1a10c03eec30901979955aca scripts/cleanup_datasets/admin_cleanup_datasets.py --- a/scripts/cleanup_datasets/admin_cleanup_datasets.py +++ b/scripts/cleanup_datasets/admin_cleanup_datasets.py @@ -47,10 +47,10 @@ log.addHandler(logging.StreamHandler(sys.stdout)) from cleanup_datasets import CleanupDatasetsApplication -#import pkg_resources +import pkg_resources #pkg_resources.require("SQLAlchemy >= 0.4") -#pkg_resources.require("Mako") +pkg_resources.require("Mako") from mako.template import Template import time 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: jmchilton: Merged in jmchilton/galaxy-central-fork-1 (pull request #575)
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/171511af9fcf/ Changeset: 171511af9fcf User: jmchilton Date: 2014-12-04 14:50:45+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #575) Allow using attribute 'optional' for data column parameters. Affected #: 2 files diff -r 100a7353b7faf9815783ec7f1245bb539a1b2717 -r 171511af9fcf2689e2761cf79e2cf02ff8324acc lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1130,7 +1130,13 @@ SelectToolParameter.__init__( self, tool, elem ) self.tool = tool self.numerical = string_as_bool( elem.get( "numerical", False )) - self.force_select = string_as_bool( elem.get( "force_select", True )) + # Allow specifing force_select for backward compat., but probably + # should use optional going forward for consistency with other + # parameters. + if "force_select" in elem.attrib: + self.force_select = string_as_bool( elem.get( "force_select" ) ) + else: + self.force_select = not string_as_bool( elem.get( "optional", False ) ) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None diff -r 100a7353b7faf9815783ec7f1245bb539a1b2717 -r 171511af9fcf2689e2761cf79e2cf02ff8324acc test/unit/tools/test_column_parameters.py --- a/test/unit/tools/test_column_parameters.py +++ b/test/unit/tools/test_column_parameters.py @@ -13,6 +13,21 @@ class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + def test_not_optional_by_default(self): + assert not self.__param_optional() + + def test_force_select_disable(self): + self.other_attributes = 'force_select="false"' + assert self.__param_optional() + + def test_optional_override(self): + self.other_attributes = 'optional="true"' + assert self.__param_optional() + + def __param_optional(self): + # TODO: don't break abstraction, try setting null value instead + return not self.param.force_select + def test_from_html(self): value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) assert value == "3" 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 commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/df52b3de192d/ Changeset: df52b3de192d User: jmchilton Date: 2014-11-25 15:57:49+00:00 Summary: Allow using attribute 'optional' for data column parameters. For consistency with other parameters, has the opposite effect of 'force_select'. Affected #: 2 files diff -r 69a6f901230540012d38f17adb1995d96f6a5dba -r df52b3de192d2edeffedd6fe325ecce6c3c33ddc lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1125,7 +1125,13 @@ SelectToolParameter.__init__( self, tool, elem ) self.tool = tool self.numerical = string_as_bool( elem.get( "numerical", False )) - self.force_select = string_as_bool( elem.get( "force_select", True )) + # Allow specifing force_select for backward compat., but probably + # should use optional going forward for consistency with other + # parameters. + if "force_select" in elem.attrib: + self.force_select = string_as_bool( elem.get( "force_select" ) ) + else: + self.force_select = not string_as_bool( elem.get( "optional", False ) ) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None diff -r 69a6f901230540012d38f17adb1995d96f6a5dba -r df52b3de192d2edeffedd6fe325ecce6c3c33ddc test/unit/tools/test_column_parameters.py --- a/test/unit/tools/test_column_parameters.py +++ b/test/unit/tools/test_column_parameters.py @@ -13,6 +13,21 @@ class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + def test_not_optional_by_default(self): + assert not self.__param_optional() + + def test_force_select_disable(self): + self.other_attributes = 'force_select="false"' + assert self.__param_optional() + + def test_optional_override(self): + self.other_attributes = 'optional="true"' + assert self.__param_optional() + + def __param_optional(self): + # TODO: don't break abstraction, try setting null value instead + return not self.param.force_select + def test_from_html(self): value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) assert value == "3" https://bitbucket.org/galaxy/galaxy-central/commits/171511af9fcf/ Changeset: 171511af9fcf User: jmchilton Date: 2014-12-04 14:50:45+00:00 Summary: Merged in jmchilton/galaxy-central-fork-1 (pull request #575) Allow using attribute 'optional' for data column parameters. Affected #: 2 files diff -r 100a7353b7faf9815783ec7f1245bb539a1b2717 -r 171511af9fcf2689e2761cf79e2cf02ff8324acc lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1130,7 +1130,13 @@ SelectToolParameter.__init__( self, tool, elem ) self.tool = tool self.numerical = string_as_bool( elem.get( "numerical", False )) - self.force_select = string_as_bool( elem.get( "force_select", True )) + # Allow specifing force_select for backward compat., but probably + # should use optional going forward for consistency with other + # parameters. + if "force_select" in elem.attrib: + self.force_select = string_as_bool( elem.get( "force_select" ) ) + else: + self.force_select = not string_as_bool( elem.get( "optional", False ) ) self.accept_default = string_as_bool( elem.get( "accept_default", False )) self.data_ref = elem.get( "data_ref", None ) self.ref_input = None diff -r 100a7353b7faf9815783ec7f1245bb539a1b2717 -r 171511af9fcf2689e2761cf79e2cf02ff8324acc test/unit/tools/test_column_parameters.py --- a/test/unit/tools/test_column_parameters.py +++ b/test/unit/tools/test_column_parameters.py @@ -13,6 +13,21 @@ class DataColumnParameterTestCase( TestCase, tools_support.UsesApp ): + def test_not_optional_by_default(self): + assert not self.__param_optional() + + def test_force_select_disable(self): + self.other_attributes = 'force_select="false"' + assert self.__param_optional() + + def test_optional_override(self): + self.other_attributes = 'optional="true"' + assert self.__param_optional() + + def __param_optional(self): + # TODO: don't break abstraction, try setting null value instead + return not self.param.force_select + def test_from_html(self): value = self.param.from_html("3", self.trans, { "input_tsv": self.build_ready_hda() } ) assert value == "3" 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: natefoo: Merged in dan/galaxy-central-prs/stable (pull request #584)
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/caade2c602d6/ Changeset: caade2c602d6 Branch: stable User: natefoo Date: 2014-12-04 14:20:19+00:00 Summary: Merged in dan/galaxy-central-prs/stable (pull request #584) [STABLE] DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format). Affected #: 1 file diff -r cfdd5c45c63eee193cdefa7767e9b43217238e88 -r caade2c602d65a005d54997e95fcb1a9eab6ea17 lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -39,26 +39,30 @@ return state_valid and ( not check_security or self.__can_access_dataset( dataset ) ) def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ): - """ Return False of this parameter can not be matched to a the supplied + """ Return False of this parameter can not be matched to the supplied HDA, otherwise return a description of the match (either a HdaDirectMatch describing a direct match or a HdaImplicitMatch describing an implicit conversion.) """ + rval = False + formats = self.param.formats + if hda.datatype.matches_any( formats ): + rval = HdaDirectMatch( hda ) + else: + if not check_implicit_conversions: + return False + target_ext, converted_dataset = hda.find_conversion_destination( formats ) + if target_ext: + if converted_dataset: + hda = converted_dataset + if check_security and not self.__can_access_dataset( hda.dataset ): + return False + rval = HdaImplicitMatch( hda, target_ext ) + else: + return False if self.filter( hda ): return False - formats = self.param.formats - if hda.datatype.matches_any( formats ): - return HdaDirectMatch( hda ) - if not check_implicit_conversions: - return False - target_ext, converted_dataset = hda.find_conversion_destination( formats ) - if target_ext: - if converted_dataset: - hda = converted_dataset - if check_security and not self.__can_access_dataset( hda.dataset ): - return False - return HdaImplicitMatch( hda, target_ext ) - return False + return rval def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ): """ If HDA is accessible, return information about whether it could 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 commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f6914532d844/ Changeset: f6914532d844 Branch: stable User: dan Date: 2014-12-03 16:35:35+00:00 Summary: DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format). Affected #: 1 file diff -r 26aab19109ce7956f29bfc4f5877e6950c0fae56 -r f6914532d8440041ee6741815355d36dac0c1b10 lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -39,26 +39,30 @@ return state_valid and ( not check_security or self.__can_access_dataset( dataset ) ) def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ): - """ Return False of this parameter can not be matched to a the supplied + """ Return False of this parameter can not be matched to the supplied HDA, otherwise return a description of the match (either a HdaDirectMatch describing a direct match or a HdaImplicitMatch describing an implicit conversion.) """ + rval = False + formats = self.param.formats + if hda.datatype.matches_any( formats ): + rval = HdaDirectMatch( hda ) + else: + if not check_implicit_conversions: + return False + target_ext, converted_dataset = hda.find_conversion_destination( formats ) + if target_ext: + if converted_dataset: + hda = converted_dataset + if check_security and not self.__can_access_dataset( hda.dataset ): + return False + rval = HdaImplicitMatch( hda, target_ext ) + else: + return False if self.filter( hda ): return False - formats = self.param.formats - if hda.datatype.matches_any( formats ): - return HdaDirectMatch( hda ) - if not check_implicit_conversions: - return False - target_ext, converted_dataset = hda.find_conversion_destination( formats ) - if target_ext: - if converted_dataset: - hda = converted_dataset - if check_security and not self.__can_access_dataset( hda.dataset ): - return False - return HdaImplicitMatch( hda, target_ext ) - return False + return rval def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ): """ If HDA is accessible, return information about whether it could https://bitbucket.org/galaxy/galaxy-central/commits/caade2c602d6/ Changeset: caade2c602d6 Branch: stable User: natefoo Date: 2014-12-04 14:20:19+00:00 Summary: Merged in dan/galaxy-central-prs/stable (pull request #584) [STABLE] DatasetMatcher should check to see if hda is of the correct format before attempting to filter on e.g. metadata attributes (that may not exist for a non-expected format). Affected #: 1 file diff -r cfdd5c45c63eee193cdefa7767e9b43217238e88 -r caade2c602d65a005d54997e95fcb1a9eab6ea17 lib/galaxy/tools/parameters/dataset_matcher.py --- a/lib/galaxy/tools/parameters/dataset_matcher.py +++ b/lib/galaxy/tools/parameters/dataset_matcher.py @@ -39,26 +39,30 @@ return state_valid and ( not check_security or self.__can_access_dataset( dataset ) ) def valid_hda_match( self, hda, check_implicit_conversions=True, check_security=False ): - """ Return False of this parameter can not be matched to a the supplied + """ Return False of this parameter can not be matched to the supplied HDA, otherwise return a description of the match (either a HdaDirectMatch describing a direct match or a HdaImplicitMatch describing an implicit conversion.) """ + rval = False + formats = self.param.formats + if hda.datatype.matches_any( formats ): + rval = HdaDirectMatch( hda ) + else: + if not check_implicit_conversions: + return False + target_ext, converted_dataset = hda.find_conversion_destination( formats ) + if target_ext: + if converted_dataset: + hda = converted_dataset + if check_security and not self.__can_access_dataset( hda.dataset ): + return False + rval = HdaImplicitMatch( hda, target_ext ) + else: + return False if self.filter( hda ): return False - formats = self.param.formats - if hda.datatype.matches_any( formats ): - return HdaDirectMatch( hda ) - if not check_implicit_conversions: - return False - target_ext, converted_dataset = hda.find_conversion_destination( formats ) - if target_ext: - if converted_dataset: - hda = converted_dataset - if check_security and not self.__can_access_dataset( hda.dataset ): - return False - return HdaImplicitMatch( hda, target_ext ) - return False + return rval def hda_match( self, hda, check_implicit_conversions=True, ensure_visible=True ): """ If HDA is accessible, return information about whether it could 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 commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ef86eb163f3f/ Changeset: ef86eb163f3f User: jmchilton Date: 2014-12-04 14:16:01+00:00 Summary: Easier debugging of API test problems. Affected #: 1 file diff -r 50fe8f57c2fbe71ec3ee7b7dd2b489a0d7c32d78 -r ef86eb163f3f66c046f7ca4ff0d829b38b0728d4 test/api/helpers.py --- a/test/api/helpers.py +++ b/test/api/helpers.py @@ -76,7 +76,11 @@ return run_response.json()["outputs"][0] def wait_for_history( self, history_id, assert_ok=False, timeout=DEFAULT_HISTORY_TIMEOUT ): - return wait_on_state( lambda: self.galaxy_interactor.get( "histories/%s" % history_id ), assert_ok=assert_ok, timeout=timeout ) + try: + return wait_on_state( lambda: self.galaxy_interactor.get( "histories/%s" % history_id ), assert_ok=assert_ok, timeout=timeout ) + except AssertionError: + self.galaxy_interactor._summarize_history_errors( history_id ) + raise def wait_for_job( self, job_id, assert_ok=False, timeout=DEFAULT_HISTORY_TIMEOUT ): return wait_on_state( lambda: self.galaxy_interactor.get( "jobs/%s" % job_id ), assert_ok=assert_ok, timeout=timeout ) https://bitbucket.org/galaxy/galaxy-central/commits/100a7353b7fa/ Changeset: 100a7353b7fa User: jmchilton Date: 2014-12-04 14:16:01+00:00 Summary: Remove seemingly unlinked to workflow action and template. Please let me know if I missed something. Affected #: 2 files diff -r ef86eb163f3f66c046f7ca4ff0d829b38b0728d4 -r 100a7353b7faf9815783ec7f1245bb539a1b2717 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -407,27 +407,6 @@ @web.expose @web.require_login( "use Galaxy workflows" ) - def edit_attributes( self, trans, id, **kwargs ): - # Get workflow and do error checking. - stored = self.get_stored_workflow( trans, id ) - if not stored: - error( "You do not own this workflow or workflow ID is invalid." ) - # Update workflow attributes if new values submitted. - if 'name' in kwargs: - # Rename workflow. - stored.name = sanitize_html( kwargs['name'] ) - if 'annotation' in kwargs: - # Set workflow annotation; sanitize annotation before adding it. - annotation = sanitize_html( kwargs[ 'annotation' ], 'utf-8', 'text/html' ) - self.add_item_annotation( trans.sa_session, trans.get_user(), stored, annotation ) - trans.sa_session.flush() - return trans.fill_template( 'workflow/edit_attributes.mako', - stored=stored, - annotation=self.get_item_annotation_str( trans.sa_session, trans.user, stored ) - ) - - @web.expose - @web.require_login( "use Galaxy workflows" ) def rename( self, trans, id, new_name=None, **kwargs ): stored = self.get_stored_workflow( trans, id ) if new_name is not None: diff -r ef86eb163f3f66c046f7ca4ff0d829b38b0728d4 -r 100a7353b7faf9815783ec7f1245bb539a1b2717 templates/webapps/galaxy/workflow/edit_attributes.mako --- a/templates/webapps/galaxy/workflow/edit_attributes.mako +++ /dev/null @@ -1,66 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> - -<%def name="title()">${_('Edit Workflow Attributes')}</%def> - -<%def name="stylesheets()"> - ${h.css( "base", "autocomplete_tagging" )} -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} -</%def> - -%if msg: - ${render_msg( msg, messagetype )} -%endif - -<%def name="body()"> - <div class="toolForm"> - <div class="toolFormTitle">${_('Edit Workflow Attributes')}</div> - <div class="toolFormBody"> - <form name="edit_attributes" action="${h.url_for(controller='workflow', action='edit_attributes' )}" method="post"> - <input type="hidden" name="id" value="${trans.security.encode_id( stored.id )}"/> - <div class="form-row"> - <label> - Name: - </label> - <div style="float: left; width: 225px; margin-right: 10px;"> - <input type="text" name="name" value="${stored.name}" size="30"/> - </div> - <div style="clear: both"></div> - </div> - <%namespace file="/tagging_common.mako" import="render_individual_tagging_element" /> - <div class="form-row"> - <label> - Tags: - </label> - <div style="float: left; width: 265px; margin-right: 10px; border-style: inset; border-width: 1px; margin-left: 2px"> - <style> - .tag-area { - border: none; - } - </style> - ${render_individual_tagging_element(user=trans.get_user(), tagged_item=stored, elt_context="edit_attributes.mako", use_toggle_link=False, in_form=True, input_size="25")} - </div> - <div style="clear: both"></div> - <div class="toolParamHelp">Apply tags to make it easy to search for and find items with the same tag.</div> - </div> - <div class="form-row"> - <label> - Annotation / Notes: - </label> - <div style="float: left; width: 225px; margin-right: 10px;"> - <textarea name="annotation" cols="30" rows="2">${annotation}</textarea> - </div> - <div style="clear: both"></div> - <div class="toolParamHelp">Add an annotation notes to a workflow; annotations are available when a workflow is viewed.</div> - </div> - <div class="form-row"> - <input type="submit" name="save" value="${_('Save')}"/> - </div> - </form> - </div> - </div> -</%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset 0e663285c743
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cfdd5c45c63e/ Changeset: cfdd5c45c63e Branch: stable User: natefoo Date: 2014-12-04 14:00:18+00:00 Summary: Update tag latest_2014.10.06 for changeset 0e663285c743 Affected #: 1 file diff -r 0e663285c74326737d4ff3c637d4c8aba8847755 -r cfdd5c45c63eee193cdefa7767e9b43217238e88 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -546ff6ef27b4b83e26ae228c292fd981173ac550 latest_2014.10.06 +0e663285c74326737d4ff3c637d4c8aba8847755 latest_2014.10.06 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 commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0cfba5087d81/ Changeset: 0cfba5087d81 Branch: next-stable User: guerler Date: 2014-12-04 05:42:39+00:00 Summary: ToolForm: Fix error mapping Affected #: 3 files diff -r 97fdb9c106886f9f768b35b2cbe5fd164e95f3c7 -r 0cfba5087d81c4bd0add051cf1d0ab48d8a33cce client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -234,7 +234,11 @@ for (var i in head) { var new_id = i; if (id !== '') { - new_id = id + '|' + new_id; + var separator = '|'; + if (head instanceof Array) { + separator = '_'; + } + new_id = id + separator + new_id; } search (new_id, head[i]); } diff -r 97fdb9c106886f9f768b35b2cbe5fd164e95f3c7 -r 0cfba5087d81c4bd0add051cf1d0ab48d8a33cce static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -234,7 +234,11 @@ for (var i in head) { var new_id = i; if (id !== '') { - new_id = id + '|' + new_id; + var separator = '|'; + if (head instanceof Array) { + separator = '_'; + } + new_id = id + separator + new_id; } search (new_id, head[i]); } diff -r 97fdb9c106886f9f768b35b2cbe5fd164e95f3c7 -r 0cfba5087d81c4bd0add051cf1d0ab48d8a33cce static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/50fe8f57c2fb/ Changeset: 50fe8f57c2fb User: guerler Date: 2014-12-04 05:43:07+00:00 Summary: Merge Affected #: 3 files diff -r 7591b8c658b50d484cacfa5aca61df0babfdaca2 -r 50fe8f57c2fbe71ec3ee7b7dd2b489a0d7c32d78 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -234,7 +234,11 @@ for (var i in head) { var new_id = i; if (id !== '') { - new_id = id + '|' + new_id; + var separator = '|'; + if (head instanceof Array) { + separator = '_'; + } + new_id = id + separator + new_id; } search (new_id, head[i]); } diff -r 7591b8c658b50d484cacfa5aca61df0babfdaca2 -r 50fe8f57c2fbe71ec3ee7b7dd2b489a0d7c32d78 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -234,7 +234,11 @@ for (var i in head) { var new_id = i; if (id !== '') { - new_id = id + '|' + new_id; + var separator = '|'; + if (head instanceof Array) { + separator = '_'; + } + new_id = id + separator + new_id; } search (new_id, head[i]); } diff -r 7591b8c658b50d484cacfa5aca61df0babfdaca2 -r 50fe8f57c2fbe71ec3ee7b7dd2b489a0d7c32d78 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(l,o){for(var j in o){var g=o[j];if(g.input){var q=g.input;var k=l;if(l!=""){k+="|"}k+=q.name;switch(q.type){case"repeat":var f="section-";var t=[];var n=null;for(var s in g){var m=s.indexOf(f);if(m!=-1){m+=f.length;t.push(parseInt(s.substr(m)));if(!n){n=s.substr(0,m)}}}t.sort(function(u,i){return u-i});var j=0;for(var h in t){b(k+"_"+j++,g[n+t[h]])}break;case"conditional":var r=a.app.field_list[q.id].value();if(d[q.test_param.type]){r=d[q.test_param.type](r)}c(k+"|"+q.test_param.name,q.id,r);var e=a.matchCase(q,r);if(e!=-1){b(k,o[q.id+"-section-"+e])}break;default:var p=a.app.field_list[q.id];var r=p.value();if(d[q.type]){r=d[q.type](r)}if(!p.skip){c(k,q.id,r)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchCase:function(a,c){if(a.test_param.type=="boolean"){if(c=="true"){c=a.test_param.truevalue||"true"}else{c=a.test_param.falsevalue||"false"}}for(var b in a.cases){if(a.cases[b].value==c){return b}}return -1},matchModel:function(c,e){var a={};var b=this;function d(f,o){for(var l in o){var h=o[l];var m=h.name;if(f!=""){m=f+"|"+m}switch(h.type){case"repeat":for(var k in h.cache){d(m+"_"+k,h.cache[k])}break;case"conditional":var p=h.test_param&&h.test_param.value;var g=b.matchCase(h,p);if(g!=-1){d(m,h.cases[g].inputs)}break;default:var n=b.app.tree.job_ids[m];if(n){e(n,h)}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(k,h){if(typeof h==="string"){var f=b.app.tree.job_ids[k];if(f){a[f]=h}}else{for(var g in h){var e=g;if(k!==""){var j="|";if(h instanceof Array){j="_"}e=k+j+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/97fdb9c10688/ Changeset: 97fdb9c10688 Branch: next-stable User: guerler Date: 2014-12-04 04:49:15+00:00 Summary: Fix inf swapping for json Affected #: 1 file diff -r 06d53d20887d55bf27f412c2248741e940d5424f -r 97fdb9c106886f9f768b35b2cbe5fd164e95f3c7 lib/galaxy/util/json.py --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -48,6 +48,8 @@ return "__Infinity__" elif val == float("-inf"): return "__-Infinity__" + else: + return val else: return val https://bitbucket.org/galaxy/galaxy-central/commits/7591b8c658b5/ Changeset: 7591b8c658b5 User: guerler Date: 2014-12-04 04:49:43+00:00 Summary: Merge Affected #: 1 file diff -r 1deca66fc876e855e8f286b6f0cd610227276e48 -r 7591b8c658b50d484cacfa5aca61df0babfdaca2 lib/galaxy/util/json.py --- a/lib/galaxy/util/json.py +++ b/lib/galaxy/util/json.py @@ -48,6 +48,8 @@ return "__Infinity__" elif val == float("-inf"): return "__-Infinity__" + else: + return val else: return val 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.

1 0

commit/galaxy-central: jmchilton: Re-attempt fix in 37cf9cd.
by commits-noreply＠bitbucket.org 04 Dec '14

04 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1deca66fc876/ Changeset: 1deca66fc876 User: jmchilton Date: 2014-12-04 03:38:37+00:00 Summary: Re-attempt fix in 37cf9cd. Affected #: 2 files diff -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 -r 1deca66fc876e855e8f286b6f0cd610227276e48 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2222,10 +2222,6 @@ raise ValueError( "History does not include a dataset collection of the correct type or containing the correct types of datasets" ) if value in [None, "None"]: return None - # would really like to not need to handle lists in here but - # doing it for uniformity with DataToolParameters for now. - if isinstance( value, list ): - value = value[ 0 ] if isinstance( value, str ) and value.find( "," ) > 0: value = [ int( value_part ) for value_part in value.split( "," ) ] elif isinstance( value, trans.app.model.HistoryDatasetCollectionAssociation ): diff -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 -r 1deca66fc876e855e8f286b6f0cd610227276e48 lib/galaxy/tools/parameters/meta.py --- a/lib/galaxy/tools/parameters/meta.py +++ b/lib/galaxy/tools/parameters/meta.py @@ -123,6 +123,10 @@ def __collection_multirun_parameter( value ): + is_batch = value.get( 'batch', False ) + if not is_batch: + return False + batch_values = util.listify( value[ 'values' ] ) if len( batch_values ) == 1: batch_over = batch_values[ 0 ] 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.

1 0

commit/galaxy-central: guerler: ToolForm: Add data collection parameter
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f2e8f6fdeb72/ Changeset: f2e8f6fdeb72 User: guerler Date: 2014-12-03 22:29:34+00:00 Summary: ToolForm: Add data collection parameter Affected #: 7 files diff -r caf0f2bf161d9cd6e8fe6a205c6c967d5495c0fe -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -307,6 +307,11 @@ field = this._fieldData(input_def); break; + // collection selector + //case 'data_collection': + // field = this._fieldData(input_def); + // break; + // data column case 'data_column': field = this._fieldSelect(input_def); @@ -383,6 +388,7 @@ id : 'field-' + input_def.id, extensions : input_def.extensions, multiple : input_def.multiple, + type : input_def.type, data : input_def.options, onchange : function() { self.app.refresh(); diff -r caf0f2bf161d9cd6e8fe6a205c6c967d5495c0fe -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -20,15 +20,23 @@ // radio button options var radio_buttons = []; + // identify selector type + if (options.type == 'data_collection') { + this.mode = 'collection'; + } else { + if (options.multiple) { + this.mode = 'multiple'; + } else { + this.mode = 'single'; + } + } + // set initial state - if (!options.multiple) { - this.current = 'single'; - } else { - this.current = 'multiple'; - } - + this.current = this.mode; + this.list = {}; + // add single dataset selector - if (!options.multiple) { + if (this.mode == 'single') { radio_buttons.push({icon: 'fa-file-o', label : 'Single dataset', value : 'single'}); this.select_single = new Ui.Select.View({ onchange : function() { @@ -42,29 +50,33 @@ } // add multiple dataset selector - radio_buttons.push({icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }); - this.select_multiple = new Ui.Select.View({ - multiple : true, - onchange : function() { - self.trigger('change'); - } - }); - this.list['multiple'] = { - field: this.select_multiple, - type : 'hda' - }; + if (this.mode == 'single' || this.mode == 'multiple') { + radio_buttons.push({icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }); + this.select_multiple = new Ui.Select.View({ + multiple : true, + onchange : function() { + self.trigger('change'); + } + }); + this.list['multiple'] = { + field: this.select_multiple, + type : 'hda' + }; + } // add collection selector - radio_buttons.push({icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }); - this.select_collection = new Ui.Select.View({ - onchange : function() { - self.trigger('change'); - } - }); - this.list['collection'] = { - field: this.select_collection, - type : 'hdca' - }; + if (this.mode == 'single' || this.mode == 'collection') { + radio_buttons.push({icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }); + this.select_collection = new Ui.Select.View({ + onchange : function() { + self.trigger('change'); + } + }); + this.list['collection'] = { + field: this.select_collection, + type : 'hdca' + }; + } // create button this.button_type = new Ui.RadioButton.View({ @@ -81,7 +93,9 @@ this.$batch = $(ToolTemplate.batchMode()); // add elements to dom - this.$el.append(Utils.wrap(this.button_type.$el)); + if (_.size(this.list) > 1) { + this.$el.append(Utils.wrap(this.button_type.$el)); + } for (var i in this.list) { this.$el.append(this.list[i].field.$el); } @@ -144,8 +158,8 @@ // update selection fields this.select_single && this.select_single.update(dataset_options); - this.select_multiple.update(dataset_options); - this.select_collection.update(collection_options); + this.select_multiple && this.select_multiple.update(dataset_options); + this.select_collection && this.select_collection.update(collection_options); // add to content list this.app.content.add(options); @@ -167,7 +181,7 @@ this.current = 'collection'; this.select_collection.value(list[0]); } else { - if (list.length > 1 || this.options.multiple) { + if (this.mode == 'multiple') { this.current = 'multiple'; this.select_multiple.value(list); } else { @@ -195,7 +209,7 @@ // prepare result dict var result = { - batch : !this.options.multiple && this.current != 'single', + batch : this.mode == 'single' && this.current != 'single', values : [] } @@ -227,7 +241,7 @@ $el.hide(); } } - if (this.current != 'single' && !this.options.multiple) { + if (this.mode == 'single' && this.current != 'single') { this.$batch.show(); } else { this.$batch.hide(); diff -r caf0f2bf161d9cd6e8fe6a205c6c967d5495c0fe -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2314,6 +2314,47 @@ return d + def to_dict( self, trans, view='collection', value_mapper=None, other_values=None ): + # create dictionary and fill default parameters + d = super( DataCollectionToolParameter, self ).to_dict( trans ) + d['multiple'] = self.multiple + d['is_dynamic'] = False + d['options'] = {'hda': [], 'hdca': []} + + # return default content if context is not available + if other_values is None: + return d + + # prepare dataset/collection matching + dataset_matcher = DatasetMatcher( trans, self, None, other_values ) + history = trans.history + + # append directly matched collections + for hdca in self.match_collections( trans, history, dataset_matcher ): + d['options']['hdca'].append({ + 'id' : trans.security.encode_id( hdca.id ), + 'id_uncoded' : hdca.id, + 'hid' : hdca.hid, + 'name' : hdca.name, + 'src' : 'hdca' + }) + + # append matching subcollections + for hdca in self.match_multirun_collections( trans, history, dataset_matcher ): + subcollection_type = self._history_query( trans ).collection_type_description.collection_type + d['options']['hdca'].append({ + 'id' : trans.security.encode_id( hdca.id ), + 'id_uncoded' : hdca.id, + 'hid' : hdca.hid, + 'name' : hdca.name, + 'src' : 'hdca' + }) + + # sort both lists + d['options']['hdca'] = sorted(d['options']['hdca'], key=lambda k: k['hid'], reverse=True) + + # return final dictionary + return d class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ): """ diff -r caf0f2bf161d9cd6e8fe6a205c6c967d5495c0fe -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -307,6 +307,11 @@ field = this._fieldData(input_def); break; + // collection selector + //case 'data_collection': + // field = this._fieldData(input_def); + // break; + // data column case 'data_column': field = this._fieldSelect(input_def); @@ -383,6 +388,7 @@ id : 'field-' + input_def.id, extensions : input_def.extensions, multiple : input_def.multiple, + type : input_def.type, data : input_def.options, onchange : function() { self.app.refresh(); diff -r caf0f2bf161d9cd6e8fe6a205c6c967d5495c0fe -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -20,15 +20,23 @@ // radio button options var radio_buttons = []; + // identify selector type + if (options.type == 'data_collection') { + this.mode = 'collection'; + } else { + if (options.multiple) { + this.mode = 'multiple'; + } else { + this.mode = 'single'; + } + } + // set initial state - if (!options.multiple) { - this.current = 'single'; - } else { - this.current = 'multiple'; - } - + this.current = this.mode; + this.list = {}; + // add single dataset selector - if (!options.multiple) { + if (this.mode == 'single') { radio_buttons.push({icon: 'fa-file-o', label : 'Single dataset', value : 'single'}); this.select_single = new Ui.Select.View({ onchange : function() { @@ -42,29 +50,33 @@ } // add multiple dataset selector - radio_buttons.push({icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }); - this.select_multiple = new Ui.Select.View({ - multiple : true, - onchange : function() { - self.trigger('change'); - } - }); - this.list['multiple'] = { - field: this.select_multiple, - type : 'hda' - }; + if (this.mode == 'single' || this.mode == 'multiple') { + radio_buttons.push({icon: 'fa-files-o', label : 'Multiple datasets', value : 'multiple' }); + this.select_multiple = new Ui.Select.View({ + multiple : true, + onchange : function() { + self.trigger('change'); + } + }); + this.list['multiple'] = { + field: this.select_multiple, + type : 'hda' + }; + } // add collection selector - radio_buttons.push({icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }); - this.select_collection = new Ui.Select.View({ - onchange : function() { - self.trigger('change'); - } - }); - this.list['collection'] = { - field: this.select_collection, - type : 'hdca' - }; + if (this.mode == 'single' || this.mode == 'collection') { + radio_buttons.push({icon: 'fa-folder-o', label : 'List of datasets', value : 'collection' }); + this.select_collection = new Ui.Select.View({ + onchange : function() { + self.trigger('change'); + } + }); + this.list['collection'] = { + field: this.select_collection, + type : 'hdca' + }; + } // create button this.button_type = new Ui.RadioButton.View({ @@ -81,7 +93,9 @@ this.$batch = $(ToolTemplate.batchMode()); // add elements to dom - this.$el.append(Utils.wrap(this.button_type.$el)); + if (_.size(this.list) > 1) { + this.$el.append(Utils.wrap(this.button_type.$el)); + } for (var i in this.list) { this.$el.append(this.list[i].field.$el); } @@ -144,8 +158,8 @@ // update selection fields this.select_single && this.select_single.update(dataset_options); - this.select_multiple.update(dataset_options); - this.select_collection.update(collection_options); + this.select_multiple && this.select_multiple.update(dataset_options); + this.select_collection && this.select_collection.update(collection_options); // add to content list this.app.content.add(options); @@ -167,7 +181,7 @@ this.current = 'collection'; this.select_collection.value(list[0]); } else { - if (list.length > 1 || this.options.multiple) { + if (this.mode == 'multiple') { this.current = 'multiple'; this.select_multiple.value(list); } else { @@ -195,7 +209,7 @@ // prepare result dict var result = { - batch : !this.options.multiple && this.current != 'single', + batch : this.mode == 'single' && this.current != 'single', values : [] } @@ -227,7 +241,7 @@ $el.hide(); } } - if (this.current != 'single' && !this.options.multiple) { + if (this.mode == 'single' && this.current != 'single') { this.$batch.show(); } else { this.$batch.hide(); diff -r caf0f2bf161d9cd6e8fe6a205c6c967d5495c0fe -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(h)}},_addConditional:function(h){var j=this;h.test_param.id=h.id;var m=this._addRow(h.test_param);m.options.onchange=function(t){var p=j.app.tree.matchCase(h,t);for(var r in h.cases){var w=h.cases[r];var u=h.id+"-section-"+r;var o=j.table.get(u);var v=false;for(var q in w.inputs){var s=w.inputs[q].type;if(s&&s!=="hidden"){v=true;break}}if(r==p&&v){o.fadeIn("fast")}else{o.hide()}}j.app.refresh()};for(var l in h.cases){var k=h.id+"-section-"+l;var n=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});n.$el.addClass("ui-table-form-section");this.table.add(n.$el);this.table.append(k)}m.trigger("change")},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.rebuild();r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.rebuild();r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e(this.app,{label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(h){var k=h.id;var i=this._createField(h);if(h.is_dynamic){this.app.is_dynamic=true}this.app.field_list[k]=i;var j=new e(this.app,{label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[k]=j;this.table.add(j.$el);this.table.append(k);return i},_createField:function(h){var i=null;switch(h.type){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":i=this._fieldSelect(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":h.searchable=true;i=this._fieldSelect(h);break;case"drill_down":i=this._fieldDrilldown(h);break;case"baseurl":i=this._fieldHidden(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+h.type+").")}if(h.value!==undefined){i.value(h.value)}return i},_fieldData:function(h){var i=this;return new a.View(this.app,{id:"field-"+h.id,extensions:h.extensions,multiple:h.multiple,type:h.type,data:h.options,onchange:function(){i.app.refresh()}})},_fieldSelect:function(h){var k=[];for(var l in h.options){var m=h.options[l];k.push({label:m[0],value:m[1]})}var n=g.Select;switch(h.display){case"checkboxes":n=g.Checkbox;break;case"radio":n=g.Radio;break}var j=this;return new n.View({id:"field-"+h.id,data:k,multiple:h.multiple,searchable:h.searchable,onchange:function(){j.app.refresh()}})},_fieldDrilldown:function(h){var i=this;return new g.Drilldown.View({id:"field-"+h.id,data:h.options,display:h.display,onchange:function(){i.app.refresh()}})},_fieldText:function(h){var i=this;return new g.Input({id:"field-"+h.id,area:h.area,onchange:function(){i.app.refresh()}})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r caf0f2bf161d9cd6e8fe6a205c6c967d5495c0fe -r f2e8f6fdeb720a4c1d4643306f45f13bb9fc8924 static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(!g.multiple){this.current="single"}else{this.current="multiple"}if(!g.multiple){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"};j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"};this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());this.$el.append(c.wrap(this.button_type.$el));for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple.update(l);this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(l.length>1||this.options.multiple){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:!this.options.multiple&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.current!="single"&&!this.options.multiple){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(k,g){this.app=k;this.options=g;var f=this;this.setElement("<div/>");this.list={};var j=[];if(g.type=="data_collection"){this.mode="collection"}else{if(g.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};if(this.mode=="single"){j.push({icon:"fa-file-o",label:"Single dataset",value:"single"});this.select_single=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){j.push({icon:"fa-files-o",label:"Multiple datasets",value:"multiple"});this.select_multiple=new e.Select.View({multiple:true,onchange:function(){f.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="collection"){j.push({icon:"fa-folder-o",label:"List of datasets",value:"collection"});this.select_collection=new e.Select.View({onchange:function(){f.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:j,onchange:function(i){f.current=i;f.refresh();f.trigger("change")}});this.$batch=$(a.batchMode());if(_.size(this.list)>1){this.$el.append(c.wrap(this.button_type.$el))}for(var h in this.list){this.$el.append(this.list[h].field.$el)}this.$el.append(this.$batch);this.update(g.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(g.onchange){g.onchange(f.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){var l=[];for(var j in g.hda){var k=g.hda[j];l.push({label:k.hid+": "+k.name,value:k.id})}var f=[];for(var j in g.hdca){var h=g.hdca[j];f.push({label:h.hid+": "+h.name,value:h.id})}this.select_single&&this.select_single.update(l);this.select_multiple&&this.select_multiple.update(l);this.select_collection&&this.select_collection.update(f);this.app.content.add(g)},value:function(m){if(m&&m.values){try{var l=[];for(var h in m.values){l.push(m.values[h].id)}if(m&&m.values.length>0&&m.values[0].src=="hcda"){this.current="collection";this.select_collection.value(l[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(l)}else{this.current="single";this.select_single.value(l[0])}}this.refresh();var g=this._select();if(!g.validate()){g.value(g.first())}}catch(k){console.debug("tools-select-content::value() - Skipped.")}}var j=this._select().value();if(!(j instanceof Array)){j=[j]}var f={batch:this.mode=="single"&&this.current!="single",values:[]};for(var h in j){f.values.push({id:j[h],src:this.list[this.current].type})}return f},validate:function(){return this._select().validate()},refresh:function(){for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this.mode=="single"&&this.current!="single"){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field}});return{View:d}}); \ No newline at end of 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: 2 new changesets
by commits-noreply＠bitbucket.org 03 Dec '14

03 Dec '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/06d53d20887d/ Changeset: 06d53d20887d Branch: next-stable User: dan Date: 2014-12-03 21:52:56+00:00 Summary: Fix for DynamicOptions AdditionalValueFilter when columns have not been assigned and to give value preference over name. Affected #: 1 file diff -r 4b6b1d2d740732a982c922b264d2027ed2c90370 -r 06d53d20887d55bf27f412c2248741e940d5424f lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -301,8 +301,11 @@ add_value = [] for i in range( self.dynamic_option.largest_index + 1 ): add_value.append( "" ) - add_value[self.dynamic_option.columns['value']] = self.value - add_value[self.dynamic_option.columns['name']] = self.name + value_col = self.dynamic_option.columns.get( 'value', 0 ) + name_col = self.dynamic_option.columns.get( 'name', value_col ) + # Set name first, then value, in case they are the same column + add_value[ name_col ] = self.name + add_value[ value_col ] = self.value if self.index is not None: rval.insert( self.index, add_value ) else: https://bitbucket.org/galaxy/galaxy-central/commits/caf0f2bf161d/ Changeset: caf0f2bf161d User: dan Date: 2014-12-03 21:54:10+00:00 Summary: merge Affected #: 0 files 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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