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commit/galaxy-central: guerler: Trackster: Fix cell content if metadata is inconsistent
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a1c04a1b716a/ Changeset: a1c04a1b716a User: guerler Date: 2013-10-03 19:11:43 Summary: Trackster: Fix cell content if metadata is inconsistent Affected #: 1 file diff -r e55c7a4a88e076f163949381937d38d11e48c74a -r a1c04a1b716a2c83f821b08f5ca18ace27fcfe21 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -179,17 +179,17 @@ // -- Helper functions. -- _renderCell: function(cell_contents, index, colspan) { + var $cell = $('<td>').text(cell_contents); var column_types = this.model.get_metadata('column_types'); if (colspan !== undefined) { - return $('<td>').attr('colspan', colspan).addClass('stringalign').text(cell_contents); + $cell.attr('colspan', colspan).addClass('stringalign'); + } else if (index < column_types.length) { + if (column_types[index] === 'str' || column_types === 'list') { + /* Left align all str columns, right align the rest */ + $cell.addClass('stringalign'); + } } - else if (column_types[index] === 'str' || column_types === 'list') { - /* Left align all str columns, right align the rest */ - return $('<td>').addClass('stringalign').text(cell_contents); - } - else { - return $('<td>').text(cell_contents); - } + return $cell; }, _renderRow: function(line) { 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: dannon: Update universe sample with new inactivity box content default text
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e55c7a4a88e0/ Changeset: e55c7a4a88e0 User: dannon Date: 2013-10-03 18:18:50 Summary: Update universe sample with new inactivity box content default text Affected #: 1 file diff -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd -r e55c7a4a88e076f163949381937d38d11e48c74a universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -299,7 +299,7 @@ # Used for warning box for inactive accounts (unable to run jobs). # In use only if activation_grace_period is set. -#inactivity_box_content = Your account has not been activated yet. Please activate your account by verifying your email address. For now you can access everything at Galaxy but your jobs won't run. +#inactivity_box_content = Your account has not been activated yet. Feel free to browse around and see what's available, but you won't be able to upload data or run jobs until you have verified your email address. # -- Display sites 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: Fix grid_base.mako url_base parameters (grids need to be refactored), continue integration of new modal
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2fed7f7b23fd/ Changeset: 2fed7f7b23fd User: guerler Date: 2013-10-03 18:09:35 Summary: Fix grid_base.mako url_base parameters (grids need to be refactored), continue integration of new modal Affected #: 4 files diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -255,7 +255,8 @@ }); // Initialize ratings. - $('.community_rating_star').rating({}); + if ($('.community_rating_star').length !== 0) + $('.community_rating_star').rating({}); // Initialize item menu operations. make_popup_menus(); diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -20,47 +20,7 @@ data: filters, error: function() { alert( "Grid failed" ); }, success: function(table_html) { - show_modal( - "Select datasets for new tracks", - table_html, - { - "Cancel": function() { - hide_modal(); - }, - "Add": function() { - var requests = []; - $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { - var data = { - data_type: 'track_config', - 'hda_ldda': 'hda' - }, - id = $(this).val(); - if ($(this).attr("name") !== "id") { - data.hda_ldda = 'ldda'; - } - requests[requests.length] = $.ajax({ - url: add_track_async_url + "/" + id, - data: data, - dataType: "json" - }); - }); - // To preserve order, wait until there are definitions for all tracks and then add - // them sequentially. - $.when.apply($, requests).then(function() { - // jQuery always returns an Array for arguments, so need to look at first element - // to determine whether multiple requests were made and consequently how to - // map arguments to track definitions. - var track_defs = (arguments[0] instanceof Array ? - $.map(arguments, function(arg) { return arg[0]; }) : - [ arguments[0] ] - ); - success_fn(track_defs); - }); - hide_modal(); - } - } - ); - /*Galaxy.modal.show({ + Galaxy.modal.show({ title : "Select datasets for new tracks", body : table_html, buttons : @@ -100,7 +60,7 @@ Galaxy.modal.hide(); } } - });*/ + }); } }); }; diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -86,7 +86,7 @@ // Create grid. var grid = new Grid({ - url_base: location.pathname, + url_base: '${trans.request.path_url}', async: is_true('${grid.use_async}'), async_ops: async_ops, categorical_filters: categorical_filters, @@ -102,6 +102,12 @@ // Initialize grid objects on load. // FIXME: use a grid view object eventually. $(document).ready(function() { + + // strip protocol and domain + var url = grid.get('url_base'); + url = url.replace(/^.*\/\/[^\/]+/, ''); + grid.set('url_base', url); + init_grid_elements(); init_grid_controls(); // Initialize text filters to select text on click and use normal font when user is typing. diff -r b714089d888cad2942ba3edcd968532f07b56143 -r 2fed7f7b23fd5dbc3f25a8f783b55a4f81e014cd templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -152,38 +152,6 @@ </script></%def> -<%def name="overlay( title='', content='', visible=False )"> - <%def name="title()"></%def> - <%def name="content()"></%def> - - <% - if visible: - display = "style='display: block;'" - overlay_class = "in" - else: - display = "style='display: none;'" - overlay_class = "" - %> - - <div id="top-modal" class="modal fade ${overlay_class}" ${display}> - <div id="top-modal-backdrop" class="modal-backdrop fade ${overlay_class}" style="z-index: -1"></div> - <div id="top-modal-dialog" class="modal-dialog"> - <div class="modal-content"> - <div class="modal-header"> - <button type='button' class='close' style="display: none;">×</button> - <h4 class='title'>${title}</h4> - </div> - <div class="modal-body">${content}</div> - <div class="modal-footer"> - <div class="buttons" style="float: right;"></div> - <div class="extra_buttons" style=""></div> - <div style="clear: both;"></div> - </div> - </div> - </div> - </div> -</%def> - ## document <html><head> @@ -214,7 +182,6 @@ %if self.galaxy_config['message_box']: <div id="messagebox" class="panel-message"></div> %endif - ${self.overlay()} ## left panel %if self.galaxy_config['left_panel']: <div id="left"> 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: martenson: activation feature tweaks
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b714089d888c/ Changeset: b714089d888c User: martenson Date: 2013-10-03 17:18:59 Summary: activation feature tweaks Affected #: 2 files diff -r becb2b5d2d0690fa5217a8101c6d0b5f8c6dc99d -r b714089d888cad2942ba3edcd968532f07b56143 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -133,7 +133,7 @@ self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.activation_email = kwargs.get( 'activation_email', None ) - self.user_activation_on = kwargs.get( 'user_activation_on', None ) + self.user_activation_on = string_as_bool( kwargs.get( 'user_activation_on', False ) ) self.activation_grace_period = kwargs.get( 'activation_grace_period', None ) self.inactivity_box_content = kwargs.get( 'inactivity_box_content', None ) self.registration_warning_message = kwargs.get( 'registration_warning_message', None ) diff -r becb2b5d2d0690fa5217a8101c6d0b5f8c6dc99d -r b714089d888cad2942ba3edcd968532f07b56143 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -670,8 +670,10 @@ user = trans.app.model.User( email=email ) user.set_password_cleartext( password ) user.username = username - if trans.app.config.user_activation_on: # Do not set the active flag in case activation is OFF. + if trans.app.config.user_activation_on: user.active = False + else: + user.active = True # Activation is off, every new user is active by default. trans.sa_session.add( user ) trans.sa_session.flush() trans.app.security_agent.create_private_user_role( user ) 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: Dave Bouvier: Remove reference to removed select field in the repository write permission form.
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/becb2b5d2d06/ Changeset: becb2b5d2d06 User: Dave Bouvier Date: 2013-10-03 16:45:39 Summary: Remove reference to removed select field in the repository write permission form. Affected #: 1 file diff -r 54673424aa68129d1bae517db268d571feb73fae -r becb2b5d2d0690fa5217a8101c6d0b5f8c6dc99d test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -723,7 +723,6 @@ post_submit_strings_not_displayed=[] ): self.display_manage_repository_page( repository ) self.check_for_strings( strings_displayed, strings_not_displayed ) - tc.fv( "user_access", "allow_push", '-Select one' ) for username in usernames: tc.fv( "user_access", "allow_push", '+%s' % username ) tc.submit( 'user_access_button' ) 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: Dave Bouvier: Clean up migration stage functional test script, add check strings for stage 8.
by commits-noreply＠bitbucket.org 03 Oct '13

03 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/54673424aa68/ Changeset: 54673424aa68 User: Dave Bouvier Date: 2013-10-03 16:15:42 Summary: Clean up migration stage functional test script, add check strings for stage 8. Affected #: 1 file diff -r a3c0180445385eb708e03304769599a8c9cc2760 -r 54673424aa68129d1bae517db268d571feb73fae test/tool_shed/functional/test_1400_review_migration_stages.py --- a/test/tool_shed/functional/test_1400_review_migration_stages.py +++ b/test/tool_shed/functional/test_1400_review_migration_stages.py @@ -20,14 +20,26 @@ def test_0005_load_migration_stages_page( self ): '''Load the migration page and check for the appropriate migration stages.''' - stages = [ - 'emboss_5', 'emboss_datatypes', 'emboss', '5.0.0', '0002_tools.sh', - 'freebayes', '0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8', 'samtools', '0.1.18', 'FreeBayes requires g++', - 'ncurses', 'zlib', '0003_tools.sh', - 'ncbi_blast_plus', 'blast_datatypes', 'blast+', '2.2.26+', 'blast.ncbi.nlm.nih.gov', 'NCBI BLAST+ tools', '0004_tools.sh', - 'bwa_wrappers', '0.5.9', 'zlib and libpthread', 'Map with BWA for Illumina', '0005_tools.sh', - 'picard', '1.56.0', 'FASTQ to BAM', '0006_tools.sh', - 'lastz', '1.02.00', 'bowtie', '0.12.7', 'Map with Bowtie for Illumina', 'Bowtie requires libpthread', '0007_tools.sh' - ] + stages = [] + migration_message_strings = [ 'The Emboss 5.0.0 tools have been eliminated', + 'The freebayes tool has been eliminated', + 'The NCBI BLAST+ tools', + 'The tools "Map with BWA for Illumina"', + 'FASTQ to BAM, SAM to FASTQ, BAM ', + 'Map with Bowtie for Illumina, ', + 'BAM-to-SAM converts BAM format' ] + migrated_repository_names = [ 'emboss_5', 'emboss_datatypes', 'freebayes', 'ncbi_blast_plus', + 'blast_datatypes', 'bwa_wrappers', 'picard', 'lastz', + 'lastz_paired_reads', 'bowtie_color_wrappers', 'bowtie_wrappers', + 'xy_plot', 'bam_to_sam' ] + migrated_tool_dependencies = [ 'emboss', '5.0.0', 'freebayes', '0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8', + 'samtools', '0.1.18', 'blast+', '2.2.26+', 'bwa', '0.5.9', 'picard', '1.56.0', + 'lastz', '1.02.00', 'bowtie', '0.12.7', 'FreeBayes requires g++', 'ncurses', 'zlib', + 'zlib and libpthread', 'blast.ncbi.nlm.nih.gov', 'fastx_toolkit', '0.0.13', + 'samtools', '0.1.16', 'cufflinks', '2.1.1', 'R', '2.11.0' ] + migration_scripts = [ '0002_tools.sh', '0003_tools.sh', '0004_tools.sh', '0005_tools.sh', '0006_tools.sh', + '0007_tools.sh', '0008_tools.sh' ] + stages.extend( migration_scripts + migrated_tool_dependencies + migrated_repository_names ) + stages.extend( migration_message_strings ) self.load_galaxy_tool_migrations_page( strings_displayed=stages ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Eliminate the problematic "Select one" option from select fields.
by commits-noreply＠bitbucket.org 02 Oct '13

02 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3c018044538/ Changeset: a3c018044538 User: greg Date: 2013-10-02 22:44:48 Summary: Eliminate the problematic "Select one" option from select fields. Affected #: 1 file diff -r e262ddfe44c34200bac86dfab64c7acbdc5c54a3 -r a3c0180445385eb708e03304769599a8c9cc2760 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -756,13 +756,6 @@ refresh_on_change=refresh_on_change, refresh_on_change_values=refresh_on_change_values, size=size ) - if display is None and initial_value == 'none': - # Only insert an initial "Select one" option if we are not displaying check boxes - # or radio buttons and we have not received an initial_value other than 'none'. - if selected_value == initial_value: - select_field.add_option( 'Select one', initial_value, selected=True ) - else: - select_field.add_option( 'Select one', initial_value ) for obj in objs: if label_attr == 'self': # Each obj is a string 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: Fix links in masterhead
by commits-noreply＠bitbucket.org 02 Oct '13

02 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e262ddfe44c3/ Changeset: e262ddfe44c3 User: guerler Date: 2013-10-02 19:34:52 Summary: Fix links in masterhead Affected #: 1 file diff -r 99e18f8868470f48a6a5d91070019d9bfc801f7e -r e262ddfe44c34200bac86dfab64c7acbdc5c54a3 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -51,7 +51,7 @@ <ul class="nav navbar-nav" border="0" cellspacing="0"> - <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='', menu_options=None )"> + <%def name="tab( id, display, href, onclick=False, target='_parent', visible=True, extra_class='', menu_options=None )"> ## Create a tab at the top of the panels. menu_options is a list of 2-elements lists of [name, link] ## that are options in the menu. @@ -61,8 +61,6 @@ extra = "" if extra_class: cls += " " + extra_class - ##if self.active_view == id: - ## cls += " active" if menu_options: cls += " dropdown" a_cls += " dropdown-toggle" @@ -88,7 +86,11 @@ ${menu_item[0]} %elif len ( menu_item ) == 2: <% name, link = menu_item %> - <a href="${link}">${name}</a> + %if onclick: + <a href="${link}" onclick="Galaxy.frame_manager.frame_new({title: '${name}', type: 'url', content: '${link}'}); return false;">${name}</a> + %else: + <a href="${link}">${name}</a> + %endif %else: <% name, link, target = menu_item %><a target="${target}" href="${link}">${name}</a> @@ -105,7 +107,7 @@ ${tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) )} ## Workflow tab. - ${tab( "workflow", _("Workflow"), "javascript:Galaxy.frame_manager.frame_new({title: 'Workflow', type: 'url', content: '" + h.url_for( controller='/workflow', action='index' ) + "'});")} + ${tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) )} ## 'Shared Items' or Libraries tab. <% @@ -135,10 +137,10 @@ ## Visualization menu. <% menu_options = [ - [_('New Track Browser'), "javascript:Galaxy.frame_manager.frame_new({title: 'Trackster', type: 'url', content: '" + h.url_for( controller='/visualization', action='trackster' ) + "'});"], - [_('Saved Visualizations'), "javascript:Galaxy.frame_manager.frame_new({ type: 'url', content : '" + h.url_for( controller='/visualization', action='list' ) + "'});" ] + [_('New Track Browser'), h.url_for( controller='/visualization', action='trackster' )], + [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' )] ] - tab( "visualization", _("Visualization"), "javascript:Galaxy.frame_manager.frame_new({title: 'Trackster', type: 'url', content: '" + h.url_for( controller='/visualization', action='list' ) + "'});", menu_options=menu_options ) + tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list' ), menu_options=menu_options, onclick=True ) %> ## Cloud menu. 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: Fix links in masterhead, continue integration of new modal
by commits-noreply＠bitbucket.org 02 Oct '13

02 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/99e18f886847/ Changeset: 99e18f886847 User: guerler Date: 2013-10-02 19:23:22 Summary: Fix links in masterhead, continue integration of new modal Affected #: 8 files diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -416,49 +416,54 @@ error: function() { alert( ( "Could not add this dataset to browser" ) + '.' ); }, success: function(table_html) { var parent = window.parent; + parent.Galaxy.modal.show({ + title : "View Data in a New or Saved Visualization", + buttons :{ + "Cancel": function(){ + parent.Galaxy.modal.hide(); + }, + "View in saved visualization": function(){ + // Show new modal with saved visualizations. + parent.Galaxy.modal.show( + { + title: "Add Data to Saved Visualization", + body: table_html, + buttons :{ + "Cancel": function(){ + parent.Galaxy.modal.hide(); + }, + "Add to visualization": function(){ + $(parent.document).find('input[name=id]:checked').each(function(){ + // hide + parent.Galaxy.modal.hide(); + + var vis_id = $(this).val(); + dataset_params.id = vis_id; + + // add widget + parent.Galaxy.frame_manager.frame_new({ + title : "Trackster", + type : "url", + content : vis_url + "/trackster?" + $.param(dataset_params) + }); + }); + } + } + }); + }, + "View in new visualization": function(){ + // hide + parent.Galaxy.modal.hide(); + + var url = vis_url + "/trackster?" + $.param(dataset_params); - parent.show_modal( ( "View Data in a New or Saved Visualization" ), "", { - "Cancel": function() { - parent.hide_modal(); - }, - "View in saved visualization": function() { - // Show new modal with saved visualizations. - parent.show_modal( ( "Add Data to Saved Visualization" ), table_html, { - "Cancel": function() { - parent.hide_modal(); - }, - "Add to visualization": function() { - $(parent.document).find('input[name=id]:checked').each(function() { - var vis_id = $(this).val(); - dataset_params.id = vis_id; - - // add widget - parent.Galaxy.frame_manager.frame_new( - { - title : "Trackster", - type : "url", - content : vis_url + "/trackster?" + $.param(dataset_params) - }); - - // hide - parent.hide_modal(); - }); - } - }); - }, - "View in new visualization": function() { - var url = vis_url + "/trackster?" + $.param(dataset_params); - - // add widget - parent.Galaxy.frame_manager.frame_new( - { - title : "Trackster", - type : "url", - content : url - }); - - // hide - parent.hide_modal(); + // add widget + parent.Galaxy.frame_manager.frame_new({ + title : "Trackster", + type : "url", + content : url + }); + } } }); } diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -635,67 +635,77 @@ * @returns function that displays modal, loads trackster */ //TODO: should be imported from trackster.js -function create_trackster_action_fn(vis_url, dataset_params, dbkey) { - return function() { - var listTracksParams = {}; - if (dbkey){ - // list_tracks seems to use 'f-dbkey' (??) - listTracksParams[ 'f-dbkey' ] = dbkey; - } - $.ajax({ - url: vis_url + '/list_tracks?' + $.param( listTracksParams ), - dataType: "html", - error: function() { alert( _l( "Could not add this dataset to browser" ) + '.' ); }, - success: function(table_html) { - var parent = window.parent; +//TODO: This function is redundant and also exists in data.js + // create action + function create_trackster_action_fn (vis_url, dataset_params, dbkey) { + return function() { + var listTracksParams = {}; + if (dbkey){ + // list_tracks seems to use 'f-dbkey' (??) + listTracksParams[ 'f-dbkey' ] = dbkey; + } + $.ajax({ + url: vis_url + '/list_tracks?' + $.param( listTracksParams ), + dataType: "html", + error: function() { alert( ( "Could not add this dataset to browser" ) + '.' ); }, + success: function(table_html) { + var parent = window.parent; + parent.Galaxy.modal.show({ + title : "View Data in a New or Saved Visualization", + buttons :{ + "Cancel": function(){ + parent.Galaxy.modal.hide(); + }, + "View in saved visualization": function(){ + // Show new modal with saved visualizations. + parent.Galaxy.modal.show( + { + title: "Add Data to Saved Visualization", + body: table_html, + buttons :{ + "Cancel": function(){ + parent.Galaxy.modal.hide(); + }, + "Add to visualization": function(){ + $(parent.document).find('input[name=id]:checked').each(function(){ + // hide + parent.Galaxy.modal.hide(); + + var vis_id = $(this).val(); + dataset_params.id = vis_id; + + // add widget + parent.Galaxy.frame_manager.frame_new({ + title : "Trackster", + type : "url", + content : vis_url + "/trackster?" + $.param(dataset_params) + }); + }); + } + } + }); + }, + "View in new visualization": function(){ + // hide + parent.Galaxy.modal.hide(); + + var url = vis_url + "/trackster?" + $.param(dataset_params); - parent.show_modal( _l( "View Data in a New or Saved Visualization" ), "", { - "Cancel": function() { - parent.hide_modal(); - }, - "View in saved visualization": function() { - // Show new modal with saved visualizations. - parent.show_modal( _l( "Add Data to Saved Visualization" ), table_html, { - "Cancel": function() { - parent.hide_modal(); - }, - "Add to visualization": function() { - $(parent.document).find('input[name=id]:checked').each(function() { - var vis_id = $(this).val(); - dataset_params.id = vis_id; - - // hide modal - parent.hide_modal(); - - // add widget - Galaxy.frame_manager.frame_new( - { - title : "Trackster", - type : "url", - content : vis_url + "/trackster?" + $.param(dataset_params) - }); + // add widget + parent.Galaxy.frame_manager.frame_new({ + title : "Trackster", + type : "url", + content : url }); } - }); - }, - "View in new visualization": function() { - // hide modal - parent.hide_modal(); + } + }); + } + }); + return false; + }; + } - // add widget - Galaxy.frame_manager.frame_new( - { - title : "Trackster", - type : "url", - content : vis_url + "/trackster?" + $.param(dataset_params) - }); - } - }); - } - }); - return false; - }; -} //============================================================================== //return { diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e static/scripts/utils/config.js --- a/static/scripts/utils/config.js +++ b/static/scripts/utils/config.js @@ -245,9 +245,13 @@ if (this.$el.children().length === 0) { this.render(); } - show_modal("Configure", drawable.config.build_form(), { - "Cancel": cancel_fn, - "OK": ok_fn + Galaxy.modal.show({ + title: "Configure", + body: drawable.config.build_form(), + buttons: { + "Cancel": cancel_fn, + "OK": ok_fn + } }); }, diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e static/scripts/viz/trackster/filters.js --- a/static/scripts/viz/trackster/filters.js +++ b/static/scripts/viz/trackster/filters.js @@ -596,15 +596,19 @@ $.getJSON(run_tool_url, url_params, function(response) { if (response.error) { // General error. - show_modal("Filter Dataset", - "Error running tool " + tool_id, - { "Close" : hide_modal } ); + Galaxy.modal.show({ + title: "Filter Dataset", + body : "Error running tool " + tool_id, + buttons : { "Close" : Galaxy.modal.hide() } + }); } else if (filters.length === 0) { // No more filters to run. - show_modal("Filtering Dataset", - "Filter(s) are running on the complete dataset. Outputs are in dataset's history.", - { "Close" : hide_modal } ); + Galaxy.modal.show({ + title: "Filtering Dataset", + body: "Filter(s) are running on the complete dataset. Outputs are in dataset's history.", + buttons: { "Close" : Galaxy.modal.hide() } + }); } else { // More filters to run. diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -20,7 +20,47 @@ data: filters, error: function() { alert( "Grid failed" ); }, success: function(table_html) { - Galaxy.modal.show({ + show_modal( + "Select datasets for new tracks", + table_html, + { + "Cancel": function() { + hide_modal(); + }, + "Add": function() { + var requests = []; + $('input[name=id]:checked,input[name=ldda_ids]:checked').each(function() { + var data = { + data_type: 'track_config', + 'hda_ldda': 'hda' + }, + id = $(this).val(); + if ($(this).attr("name") !== "id") { + data.hda_ldda = 'ldda'; + } + requests[requests.length] = $.ajax({ + url: add_track_async_url + "/" + id, + data: data, + dataType: "json" + }); + }); + // To preserve order, wait until there are definitions for all tracks and then add + // them sequentially. + $.when.apply($, requests).then(function() { + // jQuery always returns an Array for arguments, so need to look at first element + // to determine whether multiple requests were made and consequently how to + // map arguments to track definitions. + var track_defs = (arguments[0] instanceof Array ? + $.map(arguments, function(arg) { return arg[0]; }) : + [ arguments[0] ] + ); + success_fn(track_defs); + }); + hide_modal(); + } + } + ); + /*Galaxy.modal.show({ title : "Select datasets for new tracks", body : table_html, buttons : @@ -60,7 +100,7 @@ Galaxy.modal.hide(); } } - }); + });*/ } }); }; diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -102,10 +102,11 @@ }); ## load galaxy js-modules - require(['galaxy.master', 'galaxy.frame', 'galaxy.upload'], function(master, frame, upload) + require(['galaxy.master', 'galaxy.frame', 'galaxy.modal', 'galaxy.upload'], function(master, frame, modal, upload) { Galaxy.master = new master.GalaxyMaster(); Galaxy.frame_manager = new frame.GalaxyFrameManager(); + Galaxy.modal = new modal.GalaxyModal(); ##Galaxy.upload = new upload.GalaxyUpload(); }); </script> diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -63,7 +63,7 @@ <ul class="nav navbar-nav" border="0" cellspacing="0"> - <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='', menu_options=None )"> + <%def name="tab( id, display, href, onclick=False, target='_parent', visible=True, extra_class='', menu_options=None )"> ## Create a tab at the top of the panels. menu_options is a list of 2-elements lists of [name, link] ## that are options in the menu. @@ -100,7 +100,11 @@ ${menu_item[0]} %elif len ( menu_item ) == 2: <% name, link = menu_item %> - <a href="${link}">${name}</a> + %if onclick: + <a href="${link}" onclick="Galaxy.frame_manager.frame_new({title: '${name}', type: 'url', content: '${link}'}); return false;">${name}</a> + %else: + <a href="${link}">${name}</a> + %endif %else: <% name, link, target = menu_item %><a target="${target}" href="${link}">${name}</a> @@ -117,7 +121,7 @@ ${tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) )} ## Workflow tab. - ${tab( "workflow", _("Workflow"), "javascript:Galaxy.frame_manager.frame_new({title: 'Workflow', type: 'url', content: '" + h.url_for( controller='/workflow', action='index' ) + "'});")} + ${tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) )} ## 'Shared Items' or Libraries tab. <% @@ -147,10 +151,10 @@ ## Visualization menu. <% menu_options = [ - [_('New Track Browser'), "javascript:Galaxy.frame_manager.frame_new({title: 'Trackster', type: 'url', content: '" + h.url_for( controller='/visualization', action='trackster' ) + "'});"], - [_('Saved Visualizations'), "javascript:Galaxy.frame_manager.frame_new({ type: 'url', content : '" + h.url_for( controller='/visualization', action='list' ) + "'});" ] + [_('New Track Browser'), h.url_for( controller='/visualization', action='trackster' )], + [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' )] ] - tab( "visualization", _("Visualization"), "javascript:Galaxy.frame_manager.frame_new({title: 'Trackster', type: 'url', content: '" + h.url_for( controller='/visualization', action='list' ) + "'});", menu_options=menu_options ) + tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list' ), menu_options=menu_options, onclick=True ) %> ## Cloud menu. diff -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e -r 99e18f8868470f48a6a5d91070019d9bfc801f7e templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -152,6 +152,38 @@ </script></%def> +<%def name="overlay( title='', content='', visible=False )"> + <%def name="title()"></%def> + <%def name="content()"></%def> + + <% + if visible: + display = "style='display: block;'" + overlay_class = "in" + else: + display = "style='display: none;'" + overlay_class = "" + %> + + <div id="top-modal" class="modal fade ${overlay_class}" ${display}> + <div id="top-modal-backdrop" class="modal-backdrop fade ${overlay_class}" style="z-index: -1"></div> + <div id="top-modal-dialog" class="modal-dialog"> + <div class="modal-content"> + <div class="modal-header"> + <button type='button' class='close' style="display: none;">×</button> + <h4 class='title'>${title}</h4> + </div> + <div class="modal-body">${content}</div> + <div class="modal-footer"> + <div class="buttons" style="float: right;"></div> + <div class="extra_buttons" style=""></div> + <div style="clear: both;"></div> + </div> + </div> + </div> + </div> +</%def> + ## document <html><head> @@ -182,7 +214,7 @@ %if self.galaxy_config['message_box']: <div id="messagebox" class="panel-message"></div> %endif - + ${self.overlay()} ## left panel %if self.galaxy_config['left_panel']: <div id="left"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: activation config settings made better
by commits-noreply＠bitbucket.org 02 Oct '13

02 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0fc6c5554877/ Changeset: 0fc6c5554877 User: martenson Date: 2013-10-02 15:39:40 Summary: activation config settings made better Affected #: 3 files diff -r 0026e8e49df4273dc9bebcf3475e1873e5e808f3 -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -132,7 +132,7 @@ self.admin_users = kwargs.get( "admin_users", "" ) self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join(a)bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) - self.admin_email = kwargs.get( 'admin_email', None ) + self.activation_email = kwargs.get( 'activation_email', None ) self.user_activation_on = kwargs.get( 'user_activation_on', None ) self.activation_grace_period = kwargs.get( 'activation_grace_period', None ) self.inactivity_box_content = kwargs.get( 'inactivity_box_content', None ) @@ -143,10 +143,10 @@ if self.blacklist_location is not None: self.blacklist_file = resolve_path( kwargs.get( 'blacklist_file', None ), self.root ) try: - with open(self.blacklist_file) as blacklist: - self.blacklist_content = [ line.rstrip() for line in blacklist.readlines() ] + with open( self.blacklist_file ) as blacklist: + self.blacklist_content = [ line.rstrip() for line in blacklist.readlines() ] except IOError: - print ( "CONFIGURATION ERROR: Can't open supplied blacklist file from path: " + str( self.blacklist_file ) ) + print ( "CONFIGURATION ERROR: Can't open supplied blacklist file from path: " + str( self.blacklist_file ) ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.smtp_username = kwargs.get( 'smtp_username', None ) self.smtp_password = kwargs.get( 'smtp_password', None ) diff -r 0026e8e49df4273dc9bebcf3475e1873e5e808f3 -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -491,12 +491,12 @@ message = "No such user (please note that login is case sensitive)" elif user.deleted: message = "This account has been marked deleted, contact your local Galaxy administrator to restore the account." - if trans.app.config.admin_email is not None: - message += 'Contact: %s' % trans.app.config.admin_email + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to elif user.external: message = "This account was created for use with an external authentication method, contact your local Galaxy administrator to activate it." - if trans.app.config.admin_email is not None: - message += 'Contact: %s' % trans.app.config.admin_email + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to elif not user.check_password( password ): message = "Invalid password" elif trans.app.config.user_activation_on and not user.active: # activation is ON and the user is INACTIVE @@ -536,8 +536,8 @@ message = 'This account has not been activated yet. The activation link has been sent again. Please check your email address %s.<br>' % email else: message = 'This account has not been activated yet but we are unable to send the activation link. Please contact your local Galaxy administrator.' - if trans.app.config.admin_email is not None: - message += 'Contact: %s' % trans.app.config.admin_email + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to return message def is_outside_grace_period ( self, trans, create_time ): @@ -591,8 +591,8 @@ is_admin = cntrller == 'admin' and trans.user_is_admin if not trans.app.config.allow_user_creation and not trans.user_is_admin(): message = 'User registration is disabled. Please contact your local Galaxy administrator for an account.' - if trans.app.config.admin_email is not None: - message += 'Contact: %s' % trans.app.config.admin_email + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to status = 'error' else: if not refresh_frames: @@ -733,8 +733,8 @@ success = True else: message = 'Unable to send activation email, please contact your local Galaxy administrator.' - if trans.app.config.admin_email is not None: - message += 'Contact: %s' % trans.app.config.admin_email + if trans.app.config.error_email_to is not None: + message += ' Contact: %s' % trans.app.config.error_email_to success = False else: # User activation is OFF, proceed without sending the activation email. message = 'Now logged in as %s.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) ) @@ -752,7 +752,7 @@ "Activation link: %s \n\n" "Your Galaxy Team" % ( email, activation_link )) to = email - frm = trans.app.config.admin_email + frm = trans.app.config.activation_email subject = 'How to activate your Galaxy account' try: util.send_mail( frm, to, subject, body, trans.app.config ) diff -r 0026e8e49df4273dc9bebcf3475e1873e5e808f3 -r 0fc6c5554877c4389fc074cdfac60fdc12ebcb6e universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -269,11 +269,11 @@ # Datasets in an error state include a link to report the error. Those reports # will be sent to this address. Error reports are disabled if no address is set. +# Also this email is shown as a contact to user in case of Galaxy misconfiguration and other events user may encounter. #error_email_to = None -# Administrator's email is shown to user in case of Galaxy misconfiguration or a generic error. -# It is also used as a sender for the account activation mail. -#admin_email = None +# Activation email is used as a sender ('from' field) for the account activation mail. +#activation_email = None # E-mail domains blacklist is used for filtering out users that are using disposable email address # during the registration. If their address domain matches any domain in the BL they are refused the registration. 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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