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[hg] galaxy 3125: Fix for request_events table migration script ...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/a8234f4d7012 changeset: 3125:a8234f4d7012 user: rc date: Mon Nov 30 09:35:21 2009 -0500 description: Fix for request_events table migration script for MySQL & sqlite diffstat: lib/galaxy/model/migrate/versions/0027_request_events.py | 5 +++-- 1 files changed, 3 insertions(+), 2 deletions(-) diffs (16 lines): diff -r 341d7c1c5c9a -r a8234f4d7012 lib/galaxy/model/migrate/versions/0027_request_events.py --- a/lib/galaxy/model/migrate/versions/0027_request_events.py Mon Nov 30 09:05:28 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0027_request_events.py Mon Nov 30 09:35:21 2009 -0500 @@ -73,9 +73,10 @@ "%s AS create_time," + \ "%s AS update_time," + \ "request.id AS request_id," + \ - "request.state AS state " + \ + "request.state AS state," + \ + "'%s' AS comment " + \ "FROM request;" - cmd = cmd % ( nextval('request_event'), localtimestamp(), localtimestamp() ) + cmd = cmd % ( nextval('request_event'), localtimestamp(), localtimestamp(), 'Imported from request table') db_session.execute( cmd ) # Delete the state column

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[hg] galaxy 3127: Fixed a bug in 'fetch closest features' tool.
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9f7a2a3be0e7 changeset: 3127:9f7a2a3be0e7 user: guru date: Mon Nov 30 11:59:54 2009 -0500 description: Fixed a bug in 'fetch closest features' tool. diffstat: tools/new_operations/flanking_features.py | 5 ++--- 1 files changed, 2 insertions(+), 3 deletions(-) diffs (22 lines): diff -r 71b779fde315 -r 9f7a2a3be0e7 tools/new_operations/flanking_features.py --- a/tools/new_operations/flanking_features.py Mon Nov 30 11:56:58 2009 -0500 +++ b/tools/new_operations/flanking_features.py Mon Nov 30 11:59:54 2009 -0500 @@ -121,7 +121,7 @@ map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval yield outfields - if either: + if either and (result_up or result_down): if result_up and result_down: if abs(start - int(result_up[res_ind].end)) <= abs(end - int(result_down[-1].start)): map(outfields.append, result_up[res_ind].other) @@ -131,8 +131,7 @@ map(outfields.append, result_up[res_ind].other) elif result_down: map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval - yield outfields - + yield outfields def main(): options, args = doc_optparse.parse( __doc__ )

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[hg] galaxy 3126: Added 'N' to the list of mask characters, as p...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/71b779fde315 changeset: 3126:71b779fde315 user: guru date: Mon Nov 30 11:56:58 2009 -0500 description: Added 'N' to the list of mask characters, as per Melissa's request. diffstat: tools/regVariation/maf_cpg_filter.py | 2 +- tools/regVariation/maf_cpg_filter.xml | 1 + tools/regVariation/quality_filter.py | 2 +- tools/regVariation/quality_filter.xml | 1 + 4 files changed, 4 insertions(+), 2 deletions(-) diffs (46 lines): diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/maf_cpg_filter.py --- a/tools/regVariation/maf_cpg_filter.py Mon Nov 30 09:35:21 2009 -0500 +++ b/tools/regVariation/maf_cpg_filter.py Mon Nov 30 11:56:58 2009 -0500 @@ -39,7 +39,7 @@ reader = bx.align.maf.Reader( open(inp_file, 'r') ) writer = bx.align.maf.Writer( open(out_file,'w') ) - mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?'} + mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?', 5:'N'} mask = mask_chr_dict[mask] if sitetype == "CpG": diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/maf_cpg_filter.xml --- a/tools/regVariation/maf_cpg_filter.xml Mon Nov 30 09:35:21 2009 -0500 +++ b/tools/regVariation/maf_cpg_filter.xml Mon Nov 30 11:56:58 2009 -0500 @@ -21,6 +21,7 @@ <option value="2">^</option> <option value="3">*</option> <option value="4">?</option> + <option value="5">N</option> </param> <conditional name="masksite"> <param name="type" size="5" type="select" label="Sites to be masked"> diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/quality_filter.py --- a/tools/regVariation/quality_filter.py Mon Nov 30 09:35:21 2009 -0500 +++ b/tools/regVariation/quality_filter.py Mon Nov 30 11:56:58 2009 -0500 @@ -100,7 +100,7 @@ stop_err( "No mask species selected, try again by selecting at least one species to mask." ) mask_chr_count = 0 - mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?'} + mask_chr_dict = {0:'#', 1:'$', 2:'^', 3:'*', 4:'?', 5:'N'} mask_reg_dict = {0:'Current pos', 1:'Current+Downstream', 2:'Current+Upstream', 3:'Current+Both sides'} #ensure dbkey is present in the twobit loc file diff -r a8234f4d7012 -r 71b779fde315 tools/regVariation/quality_filter.xml --- a/tools/regVariation/quality_filter.xml Mon Nov 30 09:35:21 2009 -0500 +++ b/tools/regVariation/quality_filter.xml Mon Nov 30 11:56:58 2009 -0500 @@ -37,6 +37,7 @@ <option value="2">^</option> <option value="3">*</option> <option value="4">?</option> + <option value="5">N</option> </param> <conditional name="mask_region"> <param name="region" type="select" label="Mask region">

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[hg] galaxy 3118: Remove metadata_source from quality_filter too...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0d750f3f9b94 changeset: 3118:0d750f3f9b94 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Fri Nov 20 16:22:04 2009 -0500 description: Remove metadata_source from quality_filter tool output. This will allow this tool to work on the cluster with external metadata and a readonly database/files filesystem. A better overall fix for setting external metadata files is in the works. diffstat: tools/regVariation/quality_filter.xml | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 82b63d47a0d8 -r 0d750f3f9b94 tools/regVariation/quality_filter.xml --- a/tools/regVariation/quality_filter.xml Fri Nov 20 15:35:30 2009 -0500 +++ b/tools/regVariation/quality_filter.xml Fri Nov 20 16:22:04 2009 -0500 @@ -60,7 +60,7 @@ </conditional> </inputs> <outputs> - <data format="maf" name="out_file1" metadata_source="input"/> + <data format="maf" name="out_file1"/> </outputs> <requirements> <requirement type="python-module">numpy</requirement>

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[hg] galaxy 3119: Remove old tools from runner config in univers...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3fc2db645c80 changeset: 3119:3fc2db645c80 user: Nate Coraor <nate(a)bx.psu.edu> date: Mon Nov 23 09:21:22 2009 -0500 description: Remove old tools from runner config in universe config diffstat: universe_wsgi.ini.sample | 6 ------ 1 files changed, 0 insertions(+), 6 deletions(-) diffs (16 lines): diff -r 0d750f3f9b94 -r 3fc2db645c80 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Fri Nov 20 16:22:04 2009 -0500 +++ b/universe_wsgi.ini.sample Mon Nov 23 09:21:22 2009 -0500 @@ -261,12 +261,6 @@ biomart = local:/// encode_db1 = local:/// -encode_import_all_latest_datasets1 = local:/// -encode_import_chromatin_and_chromosomes1 = local:/// -encode_import_gencode1 = local:/// -encode_import_genes_and_transcripts1 = local:/// -encode_import_multi-species_sequence_analysis1 = local:/// -encode_import_transcription_regulation1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = local:///

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[hg] galaxy 3120: Fix run.sh --reload by requiring Paste before ...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/07c1b4bc14af changeset: 3120:07c1b4bc14af user: Kanwei Li <kanwei(a)gmail.com> date: Mon Nov 23 17:20:01 2009 -0500 description: Fix run.sh --reload by requiring Paste before PasteScript diffstat: scripts/paster.py | 1 + 1 files changed, 1 insertions(+), 0 deletions(-) diffs (11 lines): diff -r 3fc2db645c80 -r 07c1b4bc14af scripts/paster.py --- a/scripts/paster.py Mon Nov 23 09:21:22 2009 -0500 +++ b/scripts/paster.py Mon Nov 23 17:20:01 2009 -0500 @@ -26,6 +26,7 @@ _log_tempfile = TempFile() import tempfile +pkg_resources.require( "Paste" ) pkg_resources.require( "PasteScript" ) from paste.script import command

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[hg] galaxy 3121: Added AJAX functionality to main grid framewor...
by Greg Von Kuster 02 Dec '09

02 Dec '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5761948422a8 changeset: 3121:5761948422a8 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Nov 24 14:53:19 2009 -0500 description: Added AJAX functionality to main grid framework. Use the use_async flag to turn on AJAXing in a grid; see the history grid for an example of a grid that uses AJAX. Small changes that are needed to fully employ AJAX for a grid are: (a) using the async_compatible flag to indicate which operations can be AJAXed and which cannot; and (b) ensuring that controller code for grid handles operation names in a case-insensitive manner. Also, there are bug fixes for inserting a history link into a page. diffstat: lib/galaxy/web/controllers/history.py | 7 +- lib/galaxy/web/controllers/page.py | 12 +- lib/galaxy/web/framework/helpers/grids.py | 16 +- templates/grid_base.mako | 1162 ++++++++++++++++++++++++--------- templates/grid_base_async.mako | 709 +-------------------- templates/grid_body_async.mako | 5 - templates/grid_common.mako | 63 +- templates/grid_common_async.mako | 155 ---- templates/history/grid.mako | 2 +- templates/page/select_histories_grid.mako | 11 +- 10 files changed, 930 insertions(+), 1212 deletions(-) diffs (2379 lines): diff -r 07c1b4bc14af -r 5761948422a8 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Nov 23 17:20:01 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Tue Nov 24 14:53:19 2009 -0500 @@ -87,11 +87,11 @@ # Grid definition title = "Saved Histories" model_class = model.History - template='/grid_base.mako' + template='/history/grid.mako' default_sort_key = "-create_time" columns = [ NameColumn( "Name", key="name", model_class=model.History, - link=( lambda history: iff( history.deleted, None, dict( operation="switch", id=history.id ) ) ), + link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ), attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), @@ -110,7 +110,7 @@ ) operations = [ - grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=True ), + grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Share", condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Unshare", condition=( lambda item: not item.deleted ), async_compatible=False ), grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ), async_compatible=False ), @@ -127,6 +127,7 @@ default_filter = dict( name="All", deleted="False", tags="All", shared="All" ) num_rows_per_page = 50 preserve_state = False + use_async = True use_paging = True def get_current_item( self, trans ): return trans.get_history() diff -r 07c1b4bc14af -r 5761948422a8 lib/galaxy/web/controllers/page.py --- a/lib/galaxy/web/controllers/page.py Mon Nov 23 17:20:01 2009 -0500 +++ b/lib/galaxy/web/controllers/page.py Tue Nov 24 14:53:19 2009 -0500 @@ -116,11 +116,11 @@ # Grid definition. title = "Saved Histories" - template = "/page/select_histories_grid.mako" - async_template = "grid_body_async.mako" + template = "/page/select_histories_grid.mako" model_class = model.History default_filter = { "deleted" : "False" , "shared" : "All" } default_sort_key = "-update_time" + use_async = True use_paging = True num_rows_per_page = 10 columns = [ @@ -152,15 +152,15 @@ # Handle operation if 'operation' in kwargs and 'id' in kwargs: session = trans.sa_session - operation = kwargs['operation'] + operation = kwargs['operation'].lower() ids = util.listify( kwargs['id'] ) for id in ids: item = session.query( model.Page ).get( trans.security.decode_id( id ) ) - if operation == "Delete": + if operation == "delete": item.deleted = True - elif operation == "Publish": + elif operation == "publish": item.published = True - elif operation == "Unpublish": + elif operation == "unpublish": item.published = False session.flush() # Build grid diff -r 07c1b4bc14af -r 5761948422a8 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Nov 23 17:20:01 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Tue Nov 24 14:53:19 2009 -0500 @@ -17,9 +17,11 @@ title = "" exposed = True model_class = None - # To use grid's async features, set template="grid_base_async.mako" template = "grid_base.mako" - async_template = "grid_body_async.mako" + async_template = "grid_base_async.mako" + + use_async = False + global_actions = [] columns = [] operations = [] @@ -174,6 +176,7 @@ if page_num == 0: # Show all rows in page. total_num_rows = query.count() + page_num = 1 num_pages = 1 else: # Show a limited number of rows. Before modifying query, get the total number of rows that query @@ -218,8 +221,8 @@ new_kwargs[ 'id' ] = trans.security.encode_id( id ) return url_for( **new_kwargs ) - - return trans.fill_template( iff( 'async' not in kwargs, self.template, self.async_template), + async_request = ( ( self.use_async ) and ( 'async' in kwargs ) and ( kwargs['async'] in [ 'True', 'true'] ) ) + return trans.fill_template( iff( async_request, self.async_template, self.template), grid=self, query=query, cur_page_num = page_num, @@ -233,7 +236,10 @@ ids = kwargs.get( 'id', [] ), url = url, message_type = status, - message = message ) + message = message, + # Pass back kwargs so that grid template can set and use args without grid explicitly having to pass them. + kwargs=kwargs + ) def get_ids( self, **kwargs ): id = [] if 'id' in kwargs: diff -r 07c1b4bc14af -r 5761948422a8 templates/grid_base.mako --- a/templates/grid_base.mako Mon Nov 23 17:20:01 2009 -0500 +++ b/templates/grid_base.mako Tue Nov 24 14:53:19 2009 -0500 @@ -1,4 +1,5 @@ <%! + from galaxy.web.framework.helpers.grids import TextColumn from galaxy.model import History, HistoryDatasetAssociation, User, Role, Group import galaxy.util def inherit(context): @@ -10,208 +11,727 @@ <%inherit file="${inherit(context)}"/> ## Render the grid's basic elements. Each of these elements can be subclassed. -%if message: - <p> - <div class="${message_type}message transient-message">${util.restore_text( message )}</div> - <div style="clear: both"></div> - </p> -%endif +<table> + <tr> + <td width="75%">${self.render_grid_header()}</td> + <td></td> + <td width="25%" id="grid-message" valign="top">${self.render_grid_message()}</td> + </tr> +</table> -${self.grid_header()} -${self.grid_table()} +${self.render_grid_table()} + ## Function definitions. <%def name="title()">${grid.title}</%def> <%def name="javascripts()"> - ${parent.javascripts()} - ${h.js("jquery.autocomplete", "autocomplete_tagging" )} - <script type="text/javascript"> - ## TODO: generalize and move into galaxy.base.js - $(document).ready(function() { - // Initialize grid elements. - $(".grid").each( function() { - var grid = this; - var checkboxes = $(this).find("input.grid-row-select-checkbox"); - var update = $(this).find( "span.grid-selected-count" ); - $(checkboxes).each( function() { - $(this).change( function() { - var n = $(checkboxes).filter("[checked]").size(); - update.text( n ); - }); - }) - }); - - // Initialize autocomplete for text inputs in search UI. - var t = $("#input-tags-filter"); - if (t.length) - { - - var autocomplete_options = - { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; + ${parent.javascripts()} + ${h.js("jquery.autocomplete", "autocomplete_tagging" )} + <script type="text/javascript"> + ## TODO: generalize and move into galaxy.base.js + $(document).ready(function() { + init_grid_elements(); + init_grid_controls(); + }); + ## Can this be moved into base.mako? + %if refresh_frames: + %if 'masthead' in refresh_frames: + ## Refresh masthead == user changes (backward compatibility) + if ( parent.user_changed ) { + %if trans.user: + parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); + %else: + parent.user_changed( null, false ); + %endif + } + %endif + %if 'history' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_history ) { + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; + if ( parent.force_right_panel ) { + parent.force_right_panel( 'show' ); + } + } + %endif + %if 'tools' in refresh_frames: + if ( parent.frames && parent.frames.galaxy_tools ) { + parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; + if ( parent.force_left_panel ) { + parent.force_left_panel( 'show' ); + } + } + %endif + %endif + + // + // Code to handle grid operations: filtering, sorting, paging, and operations. + // + + // Operations that are not async (AJAX) compatible. + var no_async_ops = new Object(); + %for operation in grid.operations: + %if not operation.async_compatible: + no_async_ops['${operation.label.lower()}'] = "True"; + %endif + %endfor + + // Initialize grid controls + function init_grid_controls() + { + + // Initialize operation buttons. + $('input[name=operation]:submit').each(function() { + $(this).click( function() { + // Get operation name. + var operation_name = $(this).attr("value"); - t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='History' )}", autocomplete_options); - } - - var t2 = $("#input-name-filter"); - if (t2.length) - { - var autocomplete_options = - { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; + // For some reason, $('input[name=id]:checked').val() does not return all ids for checked boxes. + // The code below performs this function. + var item_ids = new Array() + $('input[name=id]:checked').each(function() { + item_ids[item_ids.length] = $(this).val(); + }); + do_operation(operation_name, item_ids); + }); + }); + + // Initialize submit image elements. + $('.submit-image').each( function() + { + // On mousedown, add class to simulate click. + $(this).mousedown( function() { + $(this).addClass('gray-background'); + }); + + // On mouseup, add class to simulate click. + $(this).mouseup( function() { + $(this).removeClass('gray-background'); + }); + + }); + + // Initialize sort links. + $('.sort-link').each( function() + { + var sort_key = $(this).attr('sort_key'); + $(this).click( function() { + set_sort_condition(sort_key); + return false; + }); + + }); + + // Initialize page links. + $('.page-link > a').each( function() + { + var page_num = $(this).attr('page_num'); + $(this).click( function() { + set_page(page_num); + return false; + }); + + }); + $('#show-all-link').click( function() { + set_page('all'); + return false; + }); + + // Initialize categorical filters. + $('.categorical-filter > a').each( function() + { + $(this).click( function() { + var filter_key = $(this).attr('filter_key'); + var filter_val = $(this).attr('filter_val'); + set_categorical_filter(filter_key, filter_val); + return false; + }); + }); + + // Initialize text filters. + $('.text-filter-form').each( function() + { + $(this).submit( function() { + var column_key = $(this).attr('column_key'); + var text_input_obj = $('#input-' + column_key + '-filter'); + var text_input = text_input_obj.val(); + text_input_obj.val(''); + add_filter_condition(column_key, text_input, true); + return false; + }); + }); + + // Initialize autocomplete for text inputs in search UI. + var t = $("#input-tags-filter"); + if (t.length) + { + + var autocomplete_options = + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; - t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); - } - - // Initialize submit image elements. - $('.submit-image').each( function() - { - // On mousedown, add class to simulate click. - $(this).mousedown( function() { - $(this).addClass('gray-background'); - }); - - // On mouseup, add class to simulate click. - $(this).mouseup( function() { - $(this).removeClass('gray-background'); - }); - - }); - }); - ## Can this be moved into base.mako? - %if refresh_frames: - %if 'masthead' in refresh_frames: - ## Refresh masthead == user changes (backward compatibility) - if ( parent.user_changed ) { - %if trans.user: - parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); - %else: - parent.user_changed( null, false ); - %endif - } - %endif - %if 'history' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; - if ( parent.force_right_panel ) { - parent.force_right_panel( 'show' ); - } - } - %endif - %if 'tools' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_tools ) { - parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; - if ( parent.force_left_panel ) { - parent.force_left_panel( 'show' ); - } - } - %endif - %endif - - // Filter and sort args for grid. - var filter_args = ${h.to_json_string(cur_filter_dict)}; - var sort_key = "${sort_key}"; - - // - // Add tag to grid filter. - // - function add_tag_to_grid_filter(tag_name, tag_value) - { - // Put tag name and value together. - var tag = tag_name + (tag_value != null && tag_value != "" ? ":" + tag_value : ""); - add_condition_to_grid_filter("tags", tag, true); - } - - // - // Add a filter to the current grid filter; this adds the filter and then issues a request to refresh the grid. - // - function add_condition_to_grid_filter(name, value, append) - { - // Update filter arg with new condition. - if (append) - { - // Append value. - var cur_val = filter_args[name]; - if (cur_val != "All") - cur_val = cur_val + ", " + value; - else - cur_val = value; - filter_args[name] = cur_val; - } - else - { - // Replace value. - filter_args[name] = value; - } - - // Build URL with filter args, sort key. - var filter_arg_value_strs = new Array(); - var i = 0; - for (arg in filter_args) - { - filter_arg_value_strs[i++] = "f-" + arg + "=" + filter_args[arg]; - } - var filter_str = filter_arg_value_strs.join("&"); - var url_base = "${h.url_for( action='list')}"; - var url = url_base + "?" + filter_str + "&sort=" + sort_key; - self.location = url; - } - - // - // Initiate navigation when user selects a page to view. - // - function navigate_to_page(page_select) - { - page_num = $(page_select).val(); - <% url_args = {"page" : "PAGE"} %> - var url_base = "${url( url_args )}"; - var url = url_base.replace("PAGE", page_num); - self.location = url; - } + t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='History' )}", autocomplete_options); + } + + var t2 = $("#input-name-filter"); + if (t2.length) + { + var autocomplete_options = + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; + + t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); + } + + // Initialize advanced search toggles. + $('.advanced-search-toggle').each( function() + { + $(this).click( function() { + $('#more-search-options').slideToggle('fast'); + return false; + }); + }); + } + + // Overrides function in galaxy.base.js so that click does operation. + function make_popup_menus() + { + jQuery( "div[popupmenu]" ).each( function() { + var options = {}; + $(this).find( "a" ).each( function() { + var confirmtext = $(this).attr( "confirm" ), + href = $(this).attr( "href" ), + target = $(this).attr( "target" ); + options[ $(this).text() ] = function() { + if ( !confirmtext || confirm( confirmtext ) ) { + do_operation_from_href(href); + } + }; + }); + var b = $( "#" + $(this).attr( 'popupmenu' ) ); + make_popupmenu( b, options ); + $(this).remove(); + b.show(); + }); + } + + // Initialize grid elements. + function init_grid_elements() + { + // Initialize grid selection checkboxes. + $(".grid").each( function() { + var grid = this; + var checkboxes = $(this).find("input.grid-row-select-checkbox"); + var update = $(this).find( "span.grid-selected-count" ); + $(checkboxes).each( function() { + $(this).change( function() { + var n = $(checkboxes).filter("[checked]").size(); + update.text( n ); + }); + }) + }); + + // Initialize item labels. + $(".label").each( function() { + // If href has an operation in it, do operation when clicked. Otherwise do nothing. + var href = $(this).attr('href'); + if ( href.indexOf('operation=') != -1 ) + { + $(this).click( function() { + do_operation_from_href( $(this).attr('href') ); + return false; + }); + } + }); + + // Initialize item menu operations. + make_popup_menus(); + } + + // Filter values for categorical filters. + var categorical_filters = new Object(); + %for column in grid.columns: + %if column.filterable is not None and not isinstance( column, TextColumn ): + var ${column.key}_filters = + { + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + , + %endif + ${filter.label} : ${h.to_json_string( filter.args )} + %endfor + }; + categorical_filters['${column.key}'] = ${column.key}_filters; + %endif + %endfor + + // Initialize URL args with filter arguments. + var url_args = ${h.to_json_string( cur_filter_dict )}; + + // Place "f-" in front of all filter arguments. + var arg; + for (arg in url_args) + { + value = url_args[arg]; + delete url_args[arg]; + url_args["f-" + arg] = value; + } + + // Add sort argument to URL args. + url_args['sort'] = "${encoded_sort_key}"; + + // Add async keyword to URL args. + url_args['async'] = true; + + // Add page to URL args. + url_args['page'] = ${cur_page_num}; + + var num_pages = ${num_pages}; + + // Go back to page one; this is useful when a filter is applied. + function go_page_one() + { + // Need to go back to page 1 if not showing all. + var cur_page = url_args['page']; + if (cur_page != null && cur_page != undefined && cur_page != 'all') + url_args['page'] = 1; + } + + // Add tag to grid filter. + function add_tag_to_grid_filter(tag_name, tag_value) + { + // Put tag name and value together. + var tag = tag_name + (tag_value != null && tag_value != "" ? ":" + tag_value : ""); + $('#more-search-options').show('fast'); + add_filter_condition("tags", tag, true); + } + + // Add a condition to the grid filter; this adds the condition and refreshes the grid. + function add_filter_condition(name, value, append) + { + // Do nothing is value is empty. + if (value == "") + return false; + + // Update URL arg with new condition. + if (append) + { + // Update or append value. + var cur_val = url_args["f-" + name]; + var new_val; + if (cur_val == null || cur_val == undefined) + { + new_val = value; + } + else if (typeof(cur_val) == "string") + { + if (cur_val == "All") + new_val = value; + else + { + // Replace string with array. + var values = new Array(); + values[0] = cur_val; + values[1] = value; + new_val = values; + } + } + else { + // Current value is an array. + new_val = cur_val; + new_val[new_val.length] = value; + } + url_args["f-" + name] = new_val; + } + else + { + // Replace value. + url_args["f-" + name] = value; + } + + // Add button that displays filter and provides a button to delete it. + var t = $("<span>" + value + + " <a href='#'><img src='${h.url_for('/static/images/delete_tag_icon_gray.png')}'/></a></span>"); + t.addClass('text-filter-val'); + t.click(function() { + // Remove filter condition. + + // Remove visible element. + $(this).remove(); + + // Remove condition from URL args. + var cur_val = url_args["f-" + name]; + if (cur_val == null || cur_val == undefined) + { + // Unexpected. Throw error? + } + else if (typeof(cur_val) == "string") + { + if (cur_val == "All") + { + // Unexpected. Throw error? + } + else + // Remove condition. + delete url_args["f-" + name]; + } + else { + // Current value is an array. + var conditions = cur_val; + var index; + for (index = 0; index < conditions.length; index++) + if (conditions[index] == value) + { + conditions.splice(index, 1); + break; + } + } + + go_page_one(); + update_grid(); + }); + + var container = $('#' + name + "-filtering-criteria"); + container.append(t); + + go_page_one(); + update_grid(); + } + + // Set sort condition for grid. + function set_sort_condition(col_key) + { + // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on + // currently sorted column, sort is reversed. + var cur_sort = url_args['sort']; + var new_sort = col_key; + if ( cur_sort.indexOf( col_key ) != -1) + { + // Reverse sort. + if ( cur_sort.substring(0,1) != '-' ) + new_sort = '-' + col_key; + else + { + // Sort reversed by using just col_key. + } + } + + // Remove sort arrows elements. + $('.sort-arrow').remove() + + // Add sort arrow element to new sort column. + var sort_arrow = "↑"; + if (new_sort.substring(0,1) != '-') + sort_arrow = "↓"; + var t = $("<span>" + sort_arrow + "</span>").addClass('sort-arrow'); + var th = $("#" + col_key + '-header'); + th.append(t); + + // Need to go back to page 1 if not showing all. + var cur_page = url_args['page']; + if (cur_page != null && cur_page != undefined && cur_page != 'all') + url_args['page'] = 1; + + // Update grid. + url_args['sort'] = new_sort; + go_page_one(); + update_grid(); + } + + // Set new value for categorical filter. + function set_categorical_filter(name, new_value) + { + // Update filter hyperlinks to reflect new filter value. + var category_filter = categorical_filters[name]; + var cur_value = url_args["f-" + name]; + $("." + name + "-filter").each( function() { + var text = $.trim( $(this).text() ); + var filter = category_filter[text]; + var filter_value = filter[name]; + if (filter_value == new_value) + { + // Remove filter link since grid will be using this filter. It is assumed that + // this element has a single child, a hyperlink/anchor with text. + $(this).empty(); + $(this).addClass("current-filter"); + $(this).append(text); + } + else if (filter_value == cur_value) + { + // Add hyperlink for this filter since grid will no longer be using this filter. It is assumed that + // this element has a single child, a hyperlink/anchor. + $(this).empty(); + var t = $("<a href='#'>" + text + "</a>"); + t.click(function() { + set_categorical_filter( name, filter_value ); + }); + $(this).removeClass("current-filter"); + $(this).append(t); + } + }); + + // Update grid. + url_args["f-" + name] = new_value; + go_page_one(); + update_grid(); + } + + // Set page to view. + function set_page(new_page) + { + // Update page hyperlink to reflect new page. + $(".page-link").each( function() { + var id = $(this).attr('id'); + var page_num = parseInt( id.split("-")[2] ); // Id has form 'page-link-<page_num> + var cur_page = url_args['page']; + if (page_num == new_page) + { + // Remove link to page since grid will be on this page. It is assumed that + // this element has a single child, a hyperlink/anchor with text. + var text = $(this).children().text(); + $(this).empty(); + $(this).addClass("inactive-link"); + $(this).text(text); + } + else if (page_num == cur_page) + { + // Add hyperlink to this page since grid will no longer be on this page. It is assumed that + // this element has a single child, a hyperlink/anchor. + var text = $(this).text(); + $(this).empty(); + $(this).removeClass("inactive-link"); + var t = $("<a href='#'>" + text + "</a>"); + t.click(function() { + set_page(page_num); + }); + $(this).append(t); + } + }); + + var maintain_page_links = true; + if (new_page == "all") + { + url_args['page'] = new_page; + maintain_page_links = false; + } + else + url_args['page'] = parseInt(new_page); + update_grid(maintain_page_links); + } + + // Perform a grid operation. + function do_operation(operation, item_ids) + { + operation = operation.toLowerCase(); + + // Update URL args. + url_args['operation'] = operation; + url_args['id'] = item_ids; + + // If operation cannot be performed asynchronously, redirect to location. Otherwise do operation. + var no_async = ( no_async_ops[operation] != undefined && no_async_ops[operation] != null); + if (no_async) + { + go_to_URL(); + } + else + { + update_grid(true); + delete url_args['operation']; + delete url_args['id']; + } + } + + // Perform a hyperlink click that initiates an operation. If there is no operation, ignore click. + function do_operation_from_href(href) + { + // Get operation, id in hyperlink's href. + var href_parts = href.split("?"); + if (href_parts.length > 1) + { + var href_parms_str = href_parts[1]; + var href_parms = href_parms_str.split("&"); + var operation = null; + var id = -1; + for (var index = 0; index < href_parms.length; index++) + { + if (href_parms[index].indexOf('operation') != -1) + { + // Found operation parm; get operation value. + operation = href_parms[index].split('=')[1]; + } + else if (href_parms[index].indexOf('id') != -1) + { + // Found operation parm; get operation value. + id = href_parms[index].split('=')[1]; + } + } + + // Do operation. + do_operation(operation, id); + return false; + } + + } + + // Navigate window to the URL defined by url_args. This method should be used to short-circuit grid AJAXing. + function go_to_URL() + { + // Not async request. + url_args['async'] = false; + + // Build argument string. + var arg_str = ""; + var arg; + for (arg in url_args) + arg_str = arg_str + arg + "=" + url_args[arg] + "&"; + + // Go. + window.location = encodeURI( "${h.url_for()}?" + arg_str ); + } + + // Update grid. + function update_grid(maintain_page_links) + { + ## If grid is not using async, then go to URL. + %if not grid.use_async: + go_to_URL(); + return; + %endif + + // If there's an operation in the args, do POST; otherwise, do GET. + var operation = url_args['operation']; + var method = (operation != null && operation != undefined ? "POST" : "GET" ); + $.ajax({ + type: method, + url: "${h.url_for()}", + data: url_args, + error: function() { alert( "Grid refresh failed" ) }, + success: function(response_text) { + // HACK: use a simple string to separate the elements in the + // response: (1) table body; (2) number of pages in table; and (3) message. + var parsed_response_text = response_text.split("*****"); + + // Update grid body. + var table_body = parsed_response_text[0]; + $('#grid-table-body').html(table_body); + + // Process grid body. + init_grid_elements(); + make_popup_menus(); + + // Update number of pages. + var num_pages = parseInt( parsed_response_text[1] ); + + // Rebuild page links. + if (!maintain_page_links) + { + // Remove page links. + var page_link_container = $('#page-link-container'); + page_link_container.children().remove(); + + // First page is the current page. + var t = $("<span>1</span>"); + t.addClass('page-link'); + t.addClass('inactive-link'); + t.attr('id', 'page-link-1'); + page_link_container.append(t); + + // Show all link is visible only if there are multiple pages. + var elt = $('#show-all-link-span'); + if (num_pages > 1) + elt.show(); + else + elt.hide(); + + // Subsequent pages are navigable. + for (var i = 2; i <= num_pages; i++) + { + var span = $("<span></span>"); + span.addClass('page-link'); + span.attr('id', 'page-link-' + i); + var t = $("<a href='#'>" + i + "</a>"); + t.attr('page', i); + t.click(function() { + var page = $(this).attr('page'); + set_page(page); + }); + span.append(t) + page_link_container.append(span); + } + } + + // Show message if there is one. + var message = $.trim( parsed_response_text[2] ); + if (message != "") + { + $('#grid-message').html( message ); + setTimeout("$('#grid-message').hide()", 5000); + } + } + }); + } </script> </%def> <%def name="stylesheets()"> ${h.css( "base", "autocomplete_tagging" )} <style> - ## Not generic to all grids -- move to base? - .count-box { - min-width: 1.1em; - padding: 5px; - border-width: 1px; - border-style: solid; - text-align: center; - display: inline-block; - } - .submit-image { - vertical-align: text-bottom; - margin: 0; - padding: 0; - } - .no-padding-or-margin { - margin: 0; - padding: 0; - } - .gray-background { - background-color: #DDDDDD; - } - .text-filter-val { - border: solid 1px #AAAAAA; - padding: 1px 3px 1px 3px; - margin-right: 5px; - -moz-border-radius: .5em; - -webkit-border-radius: .5em; - font-style: italic; - } + ## Not generic to all grids -- move to base? + .count-box { + min-width: 1.1em; + padding: 5px; + border-width: 1px; + border-style: solid; + text-align: center; + display: inline-block; + } + .text-filter-val { + border: solid 1px #AAAAAA; + padding: 1px 3px 1px 3px; + margin-right: 5px; + -moz-border-radius: .5em; + -webkit-border-radius: .5em; + font-style: italic; + } + .page-link a, .inactive-link { + padding: 0px 7px 0px 7px; + } + .inactive-link, .current-filter { + font-style: italic; + } + .submit-image { + vertical-align: text-bottom; + margin: 0; + padding: 0; + } + .no-padding-or-margin { + margin: 0; + padding: 0; + } + .gray-background { + background-color: #DDDDDD; + } </style> </%def> <%namespace file="./grid_common.mako" import="*" /> -## Print grid header. -<%def name="grid_header()"> +## Render grid message. +<%def name="render_grid_message()"> + %if message: + <p> + <div class="${message_type}message transient-message">${util.restore_text( message )}</div> + <div style="clear: both"></div> + </p> + %endif +</%def> + +## Render grid header. +<%def name="render_grid_header(render_title=True)"> <div class="grid-header"> - <h2>${grid.title}</h2> + %if render_title: + <h2>${grid.title}</h2> + %endif %if grid.global_actions: <ul class="manage-table-actions"> @@ -227,11 +747,11 @@ </div> </%def> -## Print grid. -<%def name="grid_table()"> - <form action="${url()}" method="post" > +## Render grid. +<%def name="render_grid_table()"> + <form action="${url()}" method="post" onsubmit="return false;"> <table class="grid"> - <thead> + <thead id="grid-table-header"> <tr> <th></th> %for column in grid.columns: @@ -251,152 +771,164 @@ href = url( sort=column.key ) %> <th\ + id="${column.key}-header" %if column.ncells > 1: colspan="${column.ncells}" %endif > %if href: - <a href="${href}">${column.label}</a> + <a href="${href}" class="sort-link" sort_key='${column.key}'>${column.label}</a> %else: ${column.label} %endif - <span>${extra}</span> + <span class="sort-arrow">${extra}</span> </th> %endif %endfor <th></th> </tr> </thead> - <tbody> - %for i, item in enumerate( query ): - <tr \ - %if current_item == item: - class="current" \ - %endif - > - ## Item selection column - <td style="width: 1.5em;"> - <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> - </td> - ## Data columns - %for column in grid.columns: - %if column.visible: - <% - # Link - link = column.get_link( trans, grid, item ) - if link: - href = url( **link ) - else: - href = None - # Value (coerced to list so we can loop) - value = column.get_value( trans, grid, item ) - if column.ncells == 1: - value = [ value ] - %> - %for cellnum, v in enumerate( value ): - <% - # Handle non-ascii chars. - if isinstance(v, str): - v = unicode(v, 'utf-8') - # Attach popup menu? - if column.attach_popup and cellnum == 0: - extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>▼</span></a>' % i - else: - extra = "" - %> - %if href: - <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}</a>${extra}</td> - %else: - <td >${v}${extra}</td> - %endif - %endfor - %endif - %endfor - ## Actions column - <td> - <div popupmenu="grid-${i}-popup"> - %for operation in grid.operations: - %if operation.allowed( item ): - <% - target = "" - if operation.target: - target = "target='" + operation.target + "'" - %> - <a class="action-button" ${target} href="${ url( **operation.get_url_args( item ) ) }">${operation.label}</a> - %endif - %endfor - </div> - </td> - </tr> - %endfor + <tbody id="grid-table-body"> + ${render_grid_table_body_contents()} </tbody> <tfoot> - ## Row for navigating among pages. - <% - # Mapping between item class and plural term for item. - items_plural = "items" - if grid.model_class == History: - items_plural = "histories" - elif grid.model_class == HistoryDatasetAssociation: - items_plural = "datasets" - elif grid.model_class == User: - items_plural = "users" - elif grid.model_class == Role: - items_plural = "roles" - elif grid.model_class == Group: - items_plural = "groups" - %> - %if num_pages > 1: - <tr> - <td></td> - <td colspan="100"> - Page ${cur_page_num} of ${num_pages} -     Go to: - ## Next page link. - %if cur_page_num != num_pages: - <% args = { "page" : cur_page_num+1 } %> - <span><a href="${url( args )}">Next</a></span> - %endif - ## Previous page link. - %if cur_page_num != 1: - <span>|</span> - <% args = { "page" : cur_page_num-1 } %> - <span><a href="${url( args )}">Previous</a></span> - %endif - ## Go to page select box. - <span>| Select:</span> - <select id="page-select" onchange="navigate_to_page(this)"> - <option value=""></option> - %for page_index in range(1, num_pages + 1): - %if page_index == cur_page_num: - continue - %else: - <% args = { "page" : page_index } %> - <option value='${page_index}'>Page ${page_index}</option> - %endif - %endfor - </select> - ## Show all link. - <% args = { "page" : "all" } %> - <span>| <a href="${url( args )}">Show all ${items_plural} on one page</a></span> - </td> - </tr> - %endif - ## Grid operations. - %if grid.operations: - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected ${items_plural}: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> - %endif - %endfor - </td> - </tr> - %endif + ${render_grid_table_footer_contents()} </tfoot> </table> </form> -</%def> \ No newline at end of file +</%def> + +## Render grid table body contents. +<%def name="render_grid_table_body_contents()"> + <% num_rows_rendered = 0 %> + %if query.count() == 0: + ## No results. + <tr><td></td><td><em>No Items</em></td></tr> + <% num_rows_rendered = 1 %> + %endif + %for i, item in enumerate( query ): + <tr \ + %if current_item == item: + class="current" \ + %endif + > + ## Item selection column + <td style="width: 1.5em;"> + <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> + </td> + ## Data columns + %for column in grid.columns: + %if column.visible: + <% + # Link + link = column.get_link( trans, grid, item ) + if link: + href = url( **link ) + else: + href = None + # Value (coerced to list so we can loop) + value = column.get_value( trans, grid, item ) + if column.ncells == 1: + value = [ value ] + %> + %for cellnum, v in enumerate( value ): + <% + # Handle non-ascii chars. + if isinstance(v, str): + v = unicode(v, 'utf-8') + # Attach popup menu? + if column.attach_popup and cellnum == 0: + extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>▼</span></a>' % i + else: + extra = "" + %> + %if href: + <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}</a>${extra}</td> + %else: + <td >${v}${extra}</td> + %endif + %endfor + %endif + %endfor + ## Actions column + <td> + <div popupmenu="grid-${i}-popup"> + %for operation in grid.operations: + %if operation.allowed( item ): + <% + target = "" + if operation.target: + target = "target='" + operation.target + "'" + %> + <a class="action-button" ${target} href="${ url( **operation.get_url_args( item ) ) }">${operation.label}</a> + %endif + %endfor + </div> + </td> + </tr> + <% num_rows_rendered += 1 %> + %endfor + ## Dummy rows to prevent table for moving too much. + ##%if grid.use_paging: + ## %for i in range( num_rows_rendered , grid.num_rows_per_page ): + ## <tr><td colspan="1000"> </td></tr> + ## %endfor + ##%endif +</%def> + +## Render grid table footer contents. +<%def name="render_grid_table_footer_contents()"> + ## Row for navigating among pages. + <% + # Mapping between item class and plural term for item. + items_plural = "items" + if grid.model_class == History: + items_plural = "histories" + elif grid.model_class == HistoryDatasetAssociation: + items_plural = "datasets" + elif grid.model_class == User: + items_plural = "users" + elif grid.model_class == Role: + items_plural = "roles" + elif grid.model_class == Group: + items_plural = "groups" + %> + %if grid.use_paging and num_pages > 1: + <tr id="page-links-row"> + <td></td> + <td colspan="100"> + <span id='page-link-container'> + ## Page links. + Page: + %for page_index in range(1, num_pages + 1): + %if page_index == cur_page_num: + <span class='page-link inactive-link' id="page-link-${page_index}">${page_index}</span> + %else: + <% args = { 'page' : page_index } %> + <span class='page-link' id="page-link-${page_index}"><a href="${url( args )}" page_num='${page_index}'>${page_index}</a></span> + %endif + %endfor + </span> + + ## Show all link. + <% args = { "page" : "all" } %> + <span id='show-all-link-span'>| <a href="${url( args )}" id="show-all-link">Show all ${items_plural} on one page</a></span> + </td> + </tr> + %endif + ## Grid operations. + %if grid.operations: + <tr> + <td></td> + <td colspan="100"> + For <span class="grid-selected-count"></span> selected ${items_plural}: + %for operation in grid.operations: + %if operation.allow_multiple: + <input type="submit" name="operation" value="${operation.label}" class="action-button"> + %endif + %endfor + </td> + </tr> + %endif +</%def> + diff -r 07c1b4bc14af -r 5761948422a8 templates/grid_base_async.mako --- a/templates/grid_base_async.mako Mon Nov 23 17:20:01 2009 -0500 +++ b/templates/grid_base_async.mako Tue Nov 24 14:53:19 2009 -0500 @@ -1,704 +1,7 @@ -<%! - from galaxy.web.framework.helpers.grids import TextColumn - from galaxy.model import History, HistoryDatasetAssociation, User, Role, Group - import galaxy.util - def inherit(context): - if context.get('use_panels'): - return '/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> +<%namespace file="./grid_base.mako" import="*" /> -## Render the grid's basic elements. Each of these elements can be subclassed. -%if message: - <p> - <div class="${message_type}message transient-message">${util.restore_text( message )}</div> - <div style="clear: both"></div> - </p> -%endif - -${self.render_grid_header()} -${self.render_grid_table()} - -## Function definitions. - -<%def name="title()">${grid.title}</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js("jquery.autocomplete", "autocomplete_tagging" )} - <script type="text/javascript"> - ## TODO: generalize and move into galaxy.base.js - $(document).ready(function() { - // Initialize grid elements. - init_grid_elements(); - - // Operations that are not async (AJAX) compatible. - var no_async_ops = new Object(); - %for operation in grid.operations: - %if not operation.async_compatible: - no_async_ops['${operation.label}'] = "True"; - %endif - %endfor - - // Initialize each operation button to do operation when clicked. - $('input[name=operation]:submit').each(function() { - $(this).click( function() { - var this_value = $(this).attr("value"); - var no_async = ( no_async_ops[this_value] != undefined && no_async_ops[this_value] != null); - do_operation(this_value, no_async); - }); - }); - - // Initialize autocomplete for text inputs in search UI. - var t = $("#input-tags-filter"); - if (t.length) - { - - var autocomplete_options = - { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; - - t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='History' )}", autocomplete_options); - } - - var t2 = $("#input-name-filter"); - if (t2.length) - { - var autocomplete_options = - { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; - - t2.autocomplete("${h.url_for( controller='history', action='name_autocomplete_data' )}", autocomplete_options); - } - }); - ## Can this be moved into base.mako? - %if refresh_frames: - %if 'masthead' in refresh_frames: - ## Refresh masthead == user changes (backward compatibility) - if ( parent.user_changed ) { - %if trans.user: - parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); - %else: - parent.user_changed( null, false ); - %endif - } - %endif - %if 'history' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history')}"; - if ( parent.force_right_panel ) { - parent.force_right_panel( 'show' ); - } - } - %endif - %if 'tools' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_tools ) { - parent.frames.galaxy_tools.location.href="${h.url_for( controller='root', action='tool_menu')}"; - if ( parent.force_left_panel ) { - parent.force_left_panel( 'show' ); - } - } - %endif - %endif - - // - // Code to handle grid operations: filtering, sorting, paging, and operations. - // - - // Initialize grid elements. - function init_grid_elements() - { - $(".grid").each( function() { - var grid = this; - var checkboxes = $(this).find("input.grid-row-select-checkbox"); - var update = $(this).find( "span.grid-selected-count" ); - $(checkboxes).each( function() { - $(this).change( function() { - var n = $(checkboxes).filter("[checked]").size(); - update.text( n ); - }); - }) - }); - } - - // Filter values for categorical filters. - var categorical_filters = new Object(); - %for column in grid.columns: - %if column.filterable is not None and not isinstance( column, TextColumn ): - var ${column.key}_filters = - { - %for i, filter in enumerate( column.get_accepted_filters() ): - %if i > 0: - , - %endif - ${filter.label} : ${h.to_json_string( filter.args )} - %endfor - }; - categorical_filters['${column.key}'] = ${column.key}_filters; - %endif - %endfor - - // Initialize URL args with filter arguments. - var url_args = ${h.to_json_string( cur_filter_dict )}; - - // Place "f-" in front of all filter arguments. - var arg; - for (arg in url_args) - { - value = url_args[arg]; - delete url_args[arg]; - url_args["f-" + arg] = value; - } - - // Add sort argument to URL args. - url_args['sort'] = "${encoded_sort_key}"; - - // Add async keyword to URL args. - url_args['async'] = true; - - // Add tag to grid filter. - function add_tag_to_grid_filter(tag_name, tag_value) - { - // Put tag name and value together. - var tag = tag_name + (tag_value != null && tag_value != "" ? ":" + tag_value : ""); - add_filter_condition("tags", tag, true); - } - - // Add a condition to the grid filter; this adds the condition and refreshes the grid. - function add_filter_condition(name, value, append) - { - // Update URL arg with new condition. - if (append) - { - // Update or append value. - var cur_val = url_args["f-" + name]; - var new_val; - if (cur_val == null || cur_val == undefined) - { - new_val = value; - } - else if (typeof(cur_val) == "string") - { - if (cur_val == "All") - new_val = value; - else - { - // Replace string with array. - var values = new Array(); - values[0] = cur_val; - values[1] = value; - new_val = values; - } - } - else { - // Current value is an array. - new_val = cur_val; - new_val[new_val.length] = value; - } - url_args["f-" + name] = new_val; - } - else - { - // Replace value. - url_args["f-" + name] = value; - } - - // Add button that displays filter and provides a button to delete it. - var t = $("<span>" + value + - " <a href='#'><img src='${h.url_for('/static/images/delete_tag_icon_gray.png')}'/></a></span>"); - t.addClass('text-filter-val'); - t.click(function() { - // - // Remove filter condition. - // - - // TODO: remove element. - //var tag_button = $(this).parent(); - $(this).remove(); - - // Remove condition from URL args. - var cur_val = url_args["f-" + name]; - if (cur_val == null || cur_val == undefined) - { - // Unexpected. Throw error? - } - else if (typeof(cur_val) == "string") - { - if (cur_val == "All") - { - // Unexpected. Throw error? - } - else - // Remove condition. - delete url_args["f-" + name]; - } - else { - // Current value is an array. - var conditions = cur_val; - var index; - for (index = 0; index < conditions.length; index++) - if (conditions[index] == value) - { - conditions.splice(index, 1); - break; - } - } - - update_grid(); - }); - - var container = $('#' + name + "-filtering-criteria"); - container.append(t); - - update_grid(); - } - - // Set sort condition for grid. - function set_sort_condition(col_key) - { - // Set new sort condition. New sort is col_key if sorting new column; if reversing sort on - // currently sorted column, sort is reversed. - var cur_sort = url_args['sort']; - var new_sort = col_key; - if ( cur_sort.indexOf( col_key ) != -1) - { - // Reverse sort. - if ( cur_sort.substring(0,1) != '-' ) - new_sort = '-' + col_key; - else - { - // Sort reversed by using just col_key. - } - } - - // Remove sort arrows elements. - $('.sort-arrow').remove() - - // Add sort arrow element to new sort column. - var sort_arrow = "↑"; - if (new_sort.substring(0,1) != '-') - sort_arrow = "↓"; - var t = $("<span>" + sort_arrow + "</span>").addClass('sort-arrow'); - var th = $("#" + col_key + '-header'); - th.append(t); - - // Update grid. - url_args['sort'] = new_sort; - update_grid(); - } - - // Set new value for categorical filter. - function set_categorical_filter(this_obj, name, new_value) - { - // Update filter hyperlinks to reflect new filter value. - var category_filter = categorical_filters[name]; - var cur_value = url_args["f-" + name]; - $("." + name + "-filter").each( function() { - var text = $(this).text().trim(); - var filter = category_filter[text]; - var filter_value = filter[name]; - if (filter_value == new_value) - { - // Remove filter link since grid will be using this filter. It is assumed that - // this element has a single child, a hyperlink/anchor with text. - $(this).empty(); - $(this).append("<span style='font-style: italic'>" + text + "</span>"); - } - else if (filter_value == cur_value) - { - // Add hyperlink for this filter since grid will no longer be using this filter. It is assumed that - // this element has a single child, a hyperlink/anchor. - $(this).empty(); - var t = $("<a href='#'>" + text + "</a>"); - t.click(function() { - set_categorical_filter( $(this), name, filter_value ); - }); - $(this).append(t); - } - }); - - // Need to go back to page 1 if not showing all. - var cur_page = url_args['page']; - if (cur_page != null && cur_page != undefined && cur_page != 'all') - url_args['page'] = 1; - - // Update grid. - url_args["f-" + name] = new_value; - update_grid(); - } - - var num_pages = ${num_pages}; - url_args['page'] = 1; - // Set page to view. - function set_page(new_page) - { - // Update page hyperlink to reflect new page. - $(".page-link").each( function() { - var id = $(this).attr('id'); - var page_num = parseInt( id.split("-")[2] ); // Id has form 'page-link-<page_num> - var cur_page = url_args['page']; - if (page_num == new_page) - { - // Remove link to page since grid will be on this page. It is assumed that - // this element has a single child, a hyperlink/anchor with text. - var text = $(this).children().text(); - $(this).empty(); - $(this).addClass("inactive-link"); - $(this).text(text); - } - else if (page_num == cur_page) - { - // Add hyperlink to this page since grid will no longer be on this page. It is assumed that - // this element has a single child, a hyperlink/anchor. - var text = $(this).text(); - $(this).empty(); - $(this).removeClass("inactive-link"); - var t = $("<a href='#'>" + text + "</a>"); - t.click(function() { - set_page(page_num); - }); - $(this).append(t); - } - }); - - - if (new_page == "all") - { - url_args['page'] = new_page; - $('#page-links-row').hide('slow'); - } - else - { - url_args['page'] = parseInt(new_page); - } - update_grid(true); - } - - // Perform a grid operation. TODO: this is not complete. - function do_operation(operation, no_async) - { - // For some reason, $('input[name=id]:checked').val() does not return all ids for checked boxes. - // The code below performs this function. - var item_ids = new Array() - $('input[name=id]:checked').each(function() { - item_ids[item_ids.length] = $(this).val(); - }); - - // Update URL args. - url_args['operation'] = operation; - url_args['id'] = item_ids; - - // If operation cannot be performed asynchronously, redirect to location. Otherwise do operation. - if (no_async) - { - var arg_str = ""; - var arg; - - for (arg in url_args) - arg_str = arg_str + arg + "=" + url_args[arg] + "&"; - - self.location = encodeURI( "${h.url_for()}?" + arg_str ); - } - else - update_grid(); - - } - - // Update grid. - function update_grid(maintain_page_links) - { - // If there's an operation in the args, do POST; otherwise, do GET. - var operation = url_args['operation']; - var method = (operation != null && operation != undefined ? "POST" : "GET" ); - $.ajax({ - type: method, - url: "${h.url_for()}", - data: url_args, - error: function() { alert( "Grid refresh failed" ) }, - success: function(response_text) { - // HACK: use a simple string to separate the two elements in the - // response: (1) table body and (2) number of pages in table. - var parsed_response_text = response_text.split("*****"); - - // Update grid body. - var table_body = parsed_response_text[0]; - $('#grid-table-body').html(table_body); - - // Process grid body. - init_grid_elements(); - make_popup_menus(); - - // Update pages. - var num_pages = parseInt( parsed_response_text[1] ); - - // Rebuild page links. - if (!maintain_page_links) - { - var page_link_container = $('#page-link-container'); - page_link_container.children().remove(); - if (num_pages > 1) - { - // Show page link row. - $('#page-links-row').show(); - - // First page is the current page. - var t = $("<span>1</span>"); - t.addClass('page-link'); - t.addClass('inactive-link'); - t.attr('id', 'page-link-1'); - page_link_container.append(t); - - // Subsequent pages are navigable. - for (var i = 2; i <= num_pages; i++) - { - var span = $("<span></span>"); - span.addClass('page-link'); - span.attr('id', 'page-link-' + i); - var t = $("<a href='#'>" + i + "</a>"); - var page_num = i - t.click(function() { - set_page(page_num); - }); - span.append(t) - page_link_container.append(span); - } - } - else - { - // Hide page link row. - $('#page-links-row').hide('slow'); - } - } - } - }); - } - - </script> -</%def> - -<%def name="stylesheets()"> - ${h.css( "base", "autocomplete_tagging" )} - <style> - ## Not generic to all grids -- move to base? - .count-box { - min-width: 1.1em; - padding: 5px; - border-width: 1px; - border-style: solid; - text-align: center; - display: inline-block; - } - .text-filter-val { - border: solid 1px #AAAAAA; - padding: 1px 3px 1px 3px; - margin-right: 5px; - -moz-border-radius: .5em; - -webkit-border-radius: .5em; - font-style: italic; - } - .page-link a, .inactive-link { - padding: 0px 7px 0px 7px; - } - .inactive-link { - font-style: italic; - } - </style> -</%def> - -<%namespace file="./grid_common_async.mako" import="*" /> - -## Print grid header. -<%def name="render_grid_header(include_title)"> - <div class="grid-header"> - %if include_title: - <h2>${grid.title}</h2> - %endif - - %if grid.global_actions: - <ul class="manage-table-actions"> - %for action in grid.global_actions: - <li> - <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label}</a> - </li> - %endfor - </ul> - %endif - - ${render_grid_filters()} - </div> -</%def> - -## Print grid. -<%def name="render_grid_table()"> - <form action="${url()}" method="post" onsubmit="return false;"> - <table class="grid"> - <thead id="grid-table-header"> - <tr> - <th></th> - %for column in grid.columns: - %if column.visible: - <% - href = "" - extra = "" - if column.sortable: - if sort_key == column.key: - if sort_order == "asc": - href = url( sort=( "-" + column.key ) ) - extra = "↓" - else: - href = url( sort=( column.key ) ) - extra = "↑" - else: - href = url( sort=column.key ) - %> - <th\ - id="${column.key}-header" - %if column.ncells > 1: - colspan="${column.ncells}" - %endif - > - %if href: - <a href="${href}" onclick="set_sort_condition('${column.key}');return false;">${column.label}</a> - %else: - ${column.label} - %endif - <span class="sort-arrow">${extra}</span> - </th> - %endif - %endfor - <th></th> - </tr> - </thead> - <tbody id="grid-table-body"> - ${render_grid_table_body_contents()} - </tbody> - <tfoot id="grid-table-footer"> - ${render_grid_table_footer_contents()} - </tfoot> - </table> - </form> -</%def> - -<%def name="render_grid_table_body_contents()"> - %if query.count() == 0: - ## No results. - <tr><td></td><td><em>No Items</em></td></tr> - %endif - %for i, item in enumerate( query ): - <tr \ - %if current_item == item: - class="current" \ - %endif - > - ## Item selection column - <td style="width: 1.5em;"> - <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> - </td> - ## Data columns - %for column in grid.columns: - %if column.visible: - <% - # Link - link = column.get_link( trans, grid, item ) - if link: - href = url( **link ) - else: - href = None - # Value (coerced to list so we can loop) - value = column.get_value( trans, grid, item ) - if column.ncells == 1: - value = [ value ] - %> - %for cellnum, v in enumerate( value ): - <% - # Handle non-ascii chars. - if isinstance(v, str): - v = unicode(v, 'utf-8') - # Attach popup menu? - if column.attach_popup and cellnum == 0: - extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>▼</span></a>' % i - else: - extra = "" - %> - %if href: - <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}</a>${extra}</td> - %else: - <td >${v}${extra}</td> - %endif - %endfor - %endif - %endfor - ## Actions column - <td> - <div popupmenu="grid-${i}-popup"> - %for operation in grid.operations: - %if operation.allowed( item ): - <% - target = "" - if operation.target: - target = "target='" + operation.target + "'" - %> - <a class="action-button" ${target} href="${ url( **operation.get_url_args( item ) ) }">${operation.label}</a> - %endif - %endfor - </div> - </td> - </tr> - %endfor -</%def> - -<%def name="render_grid_table_footer_contents()"> - ## Row for navigating among pages. - <% - # Mapping between item class and plural term for item. - items_plural = "items" - if grid.model_class == History: - items_plural = "histories" - elif grid.model_class == HistoryDatasetAssociation: - items_plural = "datasets" - elif grid.model_class == User: - items_plural = "users" - elif grid.model_class == Role: - items_plural = "roles" - elif grid.model_class == Group: - items_plural = "groups" - %> - %if num_pages > 1: - <tr id="page-links-row"> - <td></td> - <td colspan="100"> - <span id='page-link-container'> - ## Page links. - Page: - %for page_index in range(1, num_pages + 1): - %if page_index == cur_page_num: - <span class='page-link inactive-link' id="page-link-${page_index}">${page_index}</span> - %else: - <% args = { 'page' : page_index } %> - <span class='page-link' id="page-link-${page_index}"><a href="${url( args )}" onclick="set_page('${page_index}'); return false;">${page_index}</a></span> - %endif - %endfor - </span> - - ## Show all link. - <% args = { "page" : "all" } %> - <span id='show-all-link'>| <a href="${url( args )}" onclick="set_page('all');return false;">Show all ${items_plural} on one page</a></span> - </td> - </tr> - %endif - ## Grid operations. - %if grid.operations: - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected ${items_plural}: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> - %endif - %endfor - </td> - </tr> - %endif -</%def> - +${render_grid_table_body_contents()} +***** +${num_pages} +***** +${render_grid_message()} \ No newline at end of file diff -r 07c1b4bc14af -r 5761948422a8 templates/grid_body_async.mako --- a/templates/grid_body_async.mako Mon Nov 23 17:20:01 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -<%namespace file="./grid_base_async.mako" import="*" /> - -${render_grid_table_body_contents()} -***** -${num_pages} \ No newline at end of file diff -r 07c1b4bc14af -r 5761948422a8 templates/grid_common.mako --- a/templates/grid_common.mako Mon Nov 23 17:20:01 2009 -0500 +++ b/templates/grid_common.mako Tue Nov 24 14:53:19 2009 -0500 @@ -11,8 +11,7 @@ <td align="left" style="padding-left: 10px">${column_label}:</td> <td> %if isinstance(column, TextColumn): - <form name="history_actions" action="${url( dict() )}" - method="get" > + <form class="text-filter-form" column_key="${column.key}" action="${url( dict() )}" method="get" > ## Carry forward filtering criteria with hidden inputs. %for temp_column in grid.columns: %if temp_column.key in cur_filter_dict: @@ -28,6 +27,7 @@ %endfor ## Print current filtering criteria and links to delete. + <span id="${column.key}-filtering-criteria"> %if column.key in cur_filter_dict: <% column_filter = cur_filter_dict[column.key] %> %if isinstance( column_filter, basestring ): @@ -54,21 +54,34 @@ %endif %endif + </span> + ## Print input field for column. <span> - <input class="no-padding-or-margin" id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/> - <input class='submit-image' type='image' src='${h.url_for('/static/images/mag_glass.png')}' alt='Filter'/></span> + <input class="no-padding-or-margin" id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/> + <input class='submit-image' type='image' src='${h.url_for('/static/images/mag_glass.png')}' alt='Filter'/> + </span> </form> %else: + <span id="${column.key}-filtering-criteria"> %for i, filter in enumerate( column.get_accepted_filters() ): + <% + # HACK: we know that each filter will have only a single argument, so get that single argument. + for key, arg in filter.args.items(): + filter_key = key + filter_arg = arg + %> %if i > 0: - <span>|</span> + | %endif %if column.key in cur_filter_dict and column.key in filter.args and cur_filter_dict[column.key] == filter.args[column.key]: - <span class="filter" style="font-style: italic">${filter.label}</span> + <span class="categorical-filter ${column.key}-filter current-filter">${filter.label}</span> %else: - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> + <span class="categorical-filter ${column.key}-filter"> + <a href="${url( filter.get_url_args() )}" filter_key="${filter_key}" filter_val="${filter_arg}">${filter.label}</a> + </span> %endif %endfor + </span> %endif </td> </tr> @@ -96,31 +109,47 @@ ## Only show advanced search if there are filterable columns. <% - show_advanced_search = False + show_advanced_search_link = False for column in grid.columns: if column.filterable == "advanced": - show_advanced_search = True + show_advanced_search_link = True break endif %> - %if show_advanced_search: - | <a href="" onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Advanced Search</a> + %if show_advanced_search_link: + <% args = { "advanced-search" : True } %> + | <a href="${url( args )}" class="advanced-search-toggle">Advanced Search</a> %endif </td> </tr></table> </div> ## Advanced search. - <div id="more-search-options" style="display: none; padding-top: 5px"> + <% + # Show advanced search if flag set or if there are filters for advanced search fields. + advanced_search_display = "none" + if 'advanced-search' in kwargs and kwargs['advanced-search'] in ['True', 'true']: + advanced_search_display = "block" + + for column in grid.columns: + if column.filterable == "advanced": + ## Show div if current filter has value that is different from the default filter. + if column.key in cur_filter_dict and column.key in default_filter_dict and \ + cur_filter_dict[column.key] != default_filter_dict[column.key]: + advanced_search_display = "block" + %> + <div id="more-search-options" style="display: ${advanced_search_display}; padding-top: 5px"> <table style="border: 1px solid gray;"> <tr><td style="text-align: left" colspan="100"> Advanced Search | - <a href=""# onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Close</a> | + <% args = { "advanced-search" : False } %> + <a href="${url( args )}" class="advanced-search-toggle">Close</a> ## Link to clear all filters. - <% - no_filter = GridColumnFilter("Clear All", default_filter_dict) - %> - <a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a> + ##| + ##<% + ## no_filter = GridColumnFilter("Clear All", default_filter_dict) + ##%> + ##<a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a> </td></tr> %for column in grid.columns: %if column.filterable == "advanced": diff -r 07c1b4bc14af -r 5761948422a8 templates/grid_common_async.mako --- a/templates/grid_common_async.mako Mon Nov 23 17:20:01 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,155 +0,0 @@ -<%! from galaxy.web.framework.helpers.grids import TextColumn, GridColumnFilter %> - -## Render an AJAX filter UI for a grid column. Filter is rendered as a table row. -<%def name="render_ajax_grid_column_filter(column)"> - <tr> - <% - column_label = column.label - if column.filterable == "advanced": - column_label = column_label.lower() - %> - <td align="left" style="padding-left: 10px">${column_label}:</td> - <td> - %if isinstance(column, TextColumn): - <form action="${url( dict() )}" id="form-filter-${column.key}" - ## Move this to doc.ready() - ##onsubmit="var text_input=$('#input-${column.key}-filter').val();$('#input-${column.key}-filter').val('');add_filter_condition('${column.key}',text_input,true);return false;" - onsubmit="var text_input=$('#input-${column.key}-filter').val();$('#input-${column.key}-filter').val('');add_filter_condition('${column.key}',text_input,true);return false;" - method="get" > - ## Carry forward filtering criteria with hidden inputs. - %for temp_column in grid.columns: - %if temp_column.key in cur_filter_dict: - <% value = cur_filter_dict[ temp_column.key ] %> - %if value != "All": - <% - if isinstance( temp_column, TextColumn ): - value = h.to_json_string( value ) - %> - <input type="hidden" id="${temp_column.key}" name="f-${temp_column.key}" value='${value}'/> - %endif - %endif - %endfor - - ## Print current filtering criteria and links to delete. - <span id="${column.key}-filtering-criteria"> - %if column.key in cur_filter_dict: - <% column_filter = cur_filter_dict[column.key] %> - %if isinstance( column_filter, basestring ): - %if column_filter != "All": - <span style="font-style: italic">${cur_filter_dict[column.key]}</span> - <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> - | - %endif - %elif isinstance( column_filter, list ): - %for i, filter in enumerate( column_filter ): - %if i > 0: - , - %endif - <span style="font-style: italic">${filter}</span> - <% - new_filter = list( column_filter ) - del new_filter[ i ] - new_column_filter = GridColumnFilter( "", { column.key : h.to_json_string( new_filter ) } ) - %> - <a href="${url( new_column_filter.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> - %endfor - - %endif - %endif - </span> - - ## Print input field for column. - <span><input id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/></span> - </form> - %else: - <span id="${column.key}-filtering-criteria"> - %for i, filter in enumerate( column.get_accepted_filters() ): - <% - # HACK: we know that each filter will have only a single argument, so get that single argument. - for key, arg in filter.args.items(): - filter_key = key - filter_arg = arg - %> - %if i > 0: - | - %endif - %if column.key in cur_filter_dict and column.key in filter.args and cur_filter_dict[column.key] == filter.args[column.key]: - <span class="${column.key}-filter">${filter.label}</span> - %else: - <span class="${column.key}-filter"> - <a href="${url( filter.get_url_args() )}" - onclick="set_categorical_filter($(this), '${column.key}','${filter_arg}'); return false;">${filter.label}</a> - </span> - %endif - %endfor - </span> - %endif - </td> - </tr> -</%def> - -## Print grid search/filtering UI. -<%def name="render_grid_filters()"> - ## Standard search. - <div> - <table><tr> - <td> - <table> - %for column in grid.columns: - %if column.filterable == "standard": - ${render_ajax_grid_column_filter(column)} - %endif - %endfor - </table> - </td> - <td> - ## Clear the standard search. - ##| - ##<% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - ##<a href="${url( filter_all.get_url_args() )}">Clear All</a> - - ## Only show advanced search if there are filterable columns. - <% - show_advanced_search = False - for column in grid.columns: - if column.filterable == "advanced": - show_advanced_search = True - break - endif - %> - %if show_advanced_search: - | <a href="" onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Advanced Search</a> - %endif - </td> - </tr></table> - </div> - - ## Advanced search. - <div id="more-search-options" style="display: none; padding-top: 5px"> - <table style="border: 1px solid gray;"> - <tr><td style="text-align: left" colspan="100"> - Advanced Search | - <a href=""# onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Close</a> | - ## Link to clear all filters. - <% - no_filter = GridColumnFilter("Clear All", default_filter_dict) - %> - <a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a> - </td></tr> - %for column in grid.columns: - %if column.filterable == "advanced": - ## Show div if current filter has value that is different from the default filter. - %if column.key in cur_filter_dict and column.key in default_filter_dict and \ - cur_filter_dict[column.key] != default_filter_dict[column.key]: - <script type="text/javascript"> - $('#more-search-options').css("display", "block"); - </script> - %endif - - ${render_ajax_grid_column_filter(column)} - %endif - %endfor - </table> - </div> -</%def> \ No newline at end of file diff -r 07c1b4bc14af -r 5761948422a8 templates/history/grid.mako --- a/templates/history/grid.mako Mon Nov 23 17:20:01 2009 -0500 +++ b/templates/history/grid.mako Tue Nov 24 14:53:19 2009 -0500 @@ -1,1 +1,1 @@ -<%inherit file="/grid_base.mako"/> +<%inherit file="../grid_base.mako"/> diff -r 07c1b4bc14af -r 5761948422a8 templates/page/select_histories_grid.mako --- a/templates/page/select_histories_grid.mako Mon Nov 23 17:20:01 2009 -0500 +++ b/templates/page/select_histories_grid.mako Tue Nov 24 14:53:19 2009 -0500 @@ -1,6 +1,13 @@ ## Template generates a grid that enables user to select histories. -<%namespace file="../grid_base_async.mako" import="*" /> +<%namespace file="../grid_base.mako" import="*" /> ${javascripts()} +${stylesheets()} ${render_grid_header(False)} -${render_grid_table()} \ No newline at end of file +${render_grid_table()} + +## Initialize the grid. +<script type="text/javascript"> + init_grid_elements(); + init_grid_controls(); +</script>

1 0

no reference genome listed for NGS bowtie or bwa
by Dean Snyder 01 Dec '09

01 Dec '09

The "Select a reference genome" popup in the NGS mapping section is empty for the Bowtie and BWA tools on my local Galaxy install (latest release). How can I populate it? Dean A. Snyder Senior Programmer/Analyst Center for Inherited Disease Research (CIDR) Johns Hopkins School of Medicine Bayview Research Campus 333 Cassell Dr, Triad Bldg, Suite 2000 Baltimore, MD 21224 www.cidr.jhmi.edu cell:717 668-3048 office:410-550-4629

2 1

Some NGS tools not available on local Galaxy install
by Dean Snyder 30 Nov '09

30 Nov '09

Some of the NGS tools like fastx_quality_stats and fastq_quality_boxplot_graph.sh are not available on my local Galaxy install, while others, like the fastq groomer, are. An example error message is: "An error occurred running this job: /bin/sh: fastx_quality_stats: command not found" Two questions: 1) Why are these tools not available with the standard install while being listed in the tools list? 2) How do I go about installing them? Thanks, Dean A. Snyder Senior Programmer/Analyst Center for Inherited Disease Research (CIDR) Johns Hopkins School of Medicine Bayview Research Campus 333 Cassell Dr, Triad Bldg, Suite 2000 Baltimore, MD 21224 www.cidr.jhmi.edu cell:717 668-3048 office:410-550-4629

2 1

Saving large files
by Dijk, F van 29 Nov '09

29 Nov '09

Hi, I use Galaxy to do Next-gen sequencing analysis. I do the alignment and such and after the alignment performed by Bowtie I want to save the files to my own harddisk, using the save option. The problem is I can't download large files (probably due to http which can't transfer files larger than 2 gb I think). Is there a way to work around this problem? I tried using the gzip options, but those options crashed Galaxy. I hope to hear from you soon. Sincerely, Freerk van Dijk De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

2 1