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[hg] galaxy 2989: Grid bug fix.
by Nate Coraor 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1612a5f4ed62 changeset: 2989:1612a5f4ed62 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 09 15:50:12 2009 -0500 description: Grid bug fix. diffstat: lib/galaxy/web/framework/helpers/grids.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 62adea4325d7 -r 1612a5f4ed62 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Nov 09 15:33:38 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Nov 09 15:50:12 2009 -0500 @@ -21,7 +21,7 @@ columns = [] operations = [] standard_filters = [] - default_filter = None + default_filter = {} default_sort_key = None preserve_state = False

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[hg] galaxy 2988: Fix error message displayed when setting metad...
by Nate Coraor 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/62adea4325d7 changeset: 2988:62adea4325d7 user: dan date: Mon Nov 09 15:33:38 2009 -0500 description: Fix error message displayed when setting metadata_externally. e.g: Exception exceptions.TypeError: TypeError('<galaxy.datatypes.metadata.MetadataTempFile object at 0x40d9a10> is not JSON serializable',) in <bound method MutableAttrInstanceState._cleanup of <sqlalchemy.orm.state.MutableAttrInstanceState object at 0x40d99d0>> ignored diffstat: scripts/set_metadata.py | 3 +++ 1 files changed, 3 insertions(+), 0 deletions(-) diffs (26 lines): diff -r ef0b9956f7d7 -r 62adea4325d7 scripts/set_metadata.py --- a/scripts/set_metadata.py Mon Nov 09 14:56:21 2009 -0500 +++ b/scripts/set_metadata.py Mon Nov 09 15:33:38 2009 -0500 @@ -8,6 +8,7 @@ import logging logging.basicConfig() +log = logging.getLogger( __name__ ) import os, sys, cPickle assert sys.version_info[:2] >= ( 2, 4 ) @@ -24,6 +25,7 @@ galaxy.model.Job() #this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here galaxy.datatypes.metadata.DATABASE_CONNECTION_AVAILABLE = False #Let metadata know that there is no database connection, and to just assume object ids are valid from galaxy.util import stringify_dictionary_keys +from sqlalchemy.orm import clear_mappers def __main__(): file_path = sys.argv.pop( 1 ) @@ -48,5 +50,6 @@ simplejson.dump( ( True, 'Metadata has been set successfully' ), open( filename_results_code, 'wb+' ) ) #setting metadata has suceeded except Exception, e: simplejson.dump( ( False, str( e ) ), open( filename_results_code, 'wb+' ) ) #setting metadata has failed somehow + clear_mappers() __main__()

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[hg] galaxy 2986: Removing unused files.
by Nate Coraor 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4576ebdab5c9 changeset: 2986:4576ebdab5c9 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 09 14:49:44 2009 -0500 description: Removing unused files. diffstat: templates/grid.mako | 232 ---------------------------------------------- templates/my_data.mako | 13 -- 2 files changed, 0 insertions(+), 245 deletions(-) diffs (253 lines): diff -r cc3e5d4538db -r 4576ebdab5c9 templates/grid.mako --- a/templates/grid.mako Mon Nov 09 14:07:16 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,232 +0,0 @@ -<%! -def inherit(context): - if context.get('use_panels'): - return '/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="title()">${grid.title}</%def> - -%if message: - <p> - <div class="${message_type}message transient-message">${message}</div> - <div style="clear: both"></div> - </p> -%endif - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - ## TODO: generalize and move into galaxy.base.js - $(document).ready(function() { - $(".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 = $(checkboxes).filter("[checked]").size(); - update.text( n ); - }); - }) - }); - }); - ## Can this be moved into base.mako? - %if refresh_frames: - %if 'masthead' in refresh_frames: - ## Refresh masthead == user changes (backward compatibility) - if ( parent.user_changed ) { - %if trans.user: - parent.user_changed( "${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="${h.url_for( controller='root', action='tool_menu')}"; - if ( parent.force_left_panel ) { - parent.force_left_panel( 'show' ); - } - } - %endif - %endif - </script> -</%def> - -<%def name="stylesheets()"> - <link href="${h.url_for('/static/style/base.css')}" rel="stylesheet" type="text/css" /> - <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; - } - </style> -</%def> - -<div class="grid-header"> - <h2>${grid.title}</h2> - - %if grid.global_actions: - <ul class="manage-table-actions"> - %for action in grid.global_actions: - <li> - <a class="action-button" href="${h.url_for( **action.url_args )}">${action.label}</a> - </li> - %endfor - </ul> - %endif - - %if grid.standard_filters: - <span class="title">Filter:</span> - %for i, filter in enumerate( grid.standard_filters ): - %if i > 0: - <span>|</span> - %endif - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endfor - %endif -</div> - -<form action="${url()}" method="post" > - <table class="grid"> - <thead> - <tr> - %if grid.has_multiple_item_operations: - <th></th> - %endif - %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\ - %if column.ncells > 1: - colspan="${column.ncells}" - %endif - > - %if href: - <a href="${href}">${column.label}</a> - %else: - ${column.label} - %endif - <span>${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 - %if grid.has_multiple_item_operations: - <td style="width: 1.5em;"> - <input type="checkbox" name="id" value=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> - </td> - %endif - ## Data columns - %for column in grid.columns: - %if column.visible: - <% - # Link - link = column.get_link( trans, grid, item ) - if link: - href = url( **link ) - else: - href = None - # Value (coerced to list so we can loop) - value = column.get_value( trans, grid, item ) - if column.ncells == 1: - value = [ value ] - %> - %for cellnum, v in enumerate( value ): - <% - # Attach popup menu? - if column.attach_popup and cellnum == 0: - extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>▼</span></a>' % i - else: - extra = "" - # Button class - if href and extra: - cls = "menubutton split" - elif extra: - cls = "menubutton" - else: - cls = "" - %> - %if href: - <td><div class="${cls}"><a class="label" href="${href}">${v|h}${extra}</a></div></td> - %else: - <td><div class="${cls}">${v}${extra}</div></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 ) )}">${operation.label}</a> - %endif - %endfor - </div> - </td> - </tr> - %endfor - </tbody> - %if grid.has_multiple_item_operations: - <tfoot> - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected items: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> - %endif - %endfor - </td> - </tr> - </tfoot> - %endif - </table> -</form> diff -r cc3e5d4538db -r 4576ebdab5c9 templates/my_data.mako --- a/templates/my_data.mako Mon Nov 09 14:07:16 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -<%inherit file="/base.mako"/> - -<%def name="stylesheets()"> - ${h.css( "base" )} -</%def> - -<h2>Available Galaxy Data</h2> - -<ul> - <li><a href='${h.url_for( controller='history', action='list' )}'>Histories</li> - <li><a href='${h.url_for( controller='dataset', action='list' )}'>Datasets</li> -</ul> -

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[hg] galaxy 2987: Bug fix.
by Nate Coraor 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ef0b9956f7d7 changeset: 2987:ef0b9956f7d7 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 09 14:56:21 2009 -0500 description: Bug fix. diffstat: templates/grid_base.mako | 20 ++++++++++---------- 1 files changed, 10 insertions(+), 10 deletions(-) diffs (44 lines): diff -r 4576ebdab5c9 -r ef0b9956f7d7 templates/grid_base.mako --- a/templates/grid_base.mako Mon Nov 09 14:49:44 2009 -0500 +++ b/templates/grid_base.mako Mon Nov 09 14:56:21 2009 -0500 @@ -296,6 +296,14 @@ </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" + %> %if num_pages > 1: <tr> <td></td> @@ -328,7 +336,7 @@ </select> ## Show all link. <% args = { "page" : "all" } %> - <span>| <a href="${url( args )}">Show all histories on one page</a></span> + <span>| <a href="${url( args )}">Show all ${items_plural} on one page</a></span> </td> </tr> %endif @@ -336,15 +344,7 @@ ## Grid operations. <td></td> <td colspan="100"> - <% - # Mapping between item class and plural term for item. - plural = "items" - if grid.model_class == History: - plural = "histories" - elif grid.model_class == HistoryDatasetAssociation: - plural = "datasets" - %> - For <span class="grid-selected-count"></span> selected ${plural}: + 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">

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[hg] galaxy 2985: Refactoring and bug fixes for grid templates.
by Nate Coraor 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cc3e5d4538db changeset: 2985:cc3e5d4538db user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 09 14:07:16 2009 -0500 description: Refactoring and bug fixes for grid templates. diffstat: lib/galaxy/web/controllers/dataset.py | 2 +- lib/galaxy/web/framework/helpers/grids.py | 6 +- templates/dataset/grid.mako | 299 +----------------------------- templates/grid_base.mako | 358 +++++++++++++++++++++++++++++++++++ templates/grid_common.mako | 95 ++++----- templates/history/grid.mako | 312 +------------------------------- 6 files changed, 409 insertions(+), 663 deletions(-) diffs (1126 lines): diff -r 736b4ebcd9db -r cc3e5d4538db lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Mon Nov 09 12:21:32 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Mon Nov 09 14:07:16 2009 -0500 @@ -83,7 +83,7 @@ grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[2] ], - key="free-text-search", visible=False, filterable="default" ) + key="free-text-search", visible=False, filterable="standard" ) ) operations = [] standard_filters = [] diff -r 736b4ebcd9db -r cc3e5d4538db lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Mon Nov 09 12:21:32 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Mon Nov 09 14:07:16 2009 -0500 @@ -16,7 +16,7 @@ title = "" exposed = True model_class = None - template = "grid.mako" + template = "grid_base.mako" global_actions = [] columns = [] operations = [] @@ -99,9 +99,9 @@ if isinstance( decoded_item, list): decoded_list = from_json_string_recurse( decoded_item ) else: - decoded_list = [ str( decoded_item ) ] + decoded_list = [ unicode( decoded_item ) ] except ValueError: - decoded_list = [ str( item ) ] + decoded_list = [ unicode ( item ) ] elif isinstance( item, list): return_val = [] for element in item: diff -r 736b4ebcd9db -r cc3e5d4538db templates/dataset/grid.mako --- a/templates/dataset/grid.mako Mon Nov 09 12:21:32 2009 -0500 +++ b/templates/dataset/grid.mako Mon Nov 09 14:07:16 2009 -0500 @@ -1,298 +1,1 @@ -<%! from galaxy.web.framework.helpers.grids import GridColumnFilter %> - -<%inherit file="/base.mako"/> -<%def name="title()">${grid.title}</%def> - -%if message: - <p> - <div class="${message_type}message transient-message">${message}</div> - <div style="clear: both"></div> - </p> -%endif - -<%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() { - $(".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 ); - }); - }) - }); - - // Set up autocomplete for tag filter input. - var t = $("#input-tag-filter"); - t.keyup( function( e ) - { - if ( e.keyCode == 27 ) - { - // Escape key - $(this).trigger( "blur" ); - } else if ( - ( e.keyCode == 13 ) || // Return Key - ( e.keyCode == 188 ) || // Comma - ( e.keyCode == 32 ) // Space - ) - { - // - // Check input. - // - - new_value = this.value; - - // Do nothing if return key was used to autocomplete. - if (return_key_pressed_for_autocomplete == true) - { - return_key_pressed_for_autocomplete = false; - return false; - } - - // Suppress space after a ":" - if ( new_value.indexOf(": ", new_value.length - 2) != -1) - { - this.value = new_value.substring(0, new_value.length-1); - return false; - } - - // Remove trigger keys from input. - if ( (e.keyCode == 188) || (e.keyCode == 32) ) - new_value = new_value.substring( 0 , new_value.length - 1 ); - - // Trim whitespace. - new_value = new_value.replace(/^\s+|\s+$/g,""); - - // Too short? - if (new_value.length < 3) - return false; - - // - // New tag OK. - // - } - }); - - // Add autocomplete to input. - var format_item_func = function(key, row_position, num_rows, value, search_term) - { - tag_name_and_value = value.split(":"); - return (tag_name_and_value.length == 1 ? tag_name_and_value[0] :tag_name_and_value[1]); - //var array = new Array(key, value, row_position, num_rows, - //search_term ); return "\"" + array.join("*") + "\""; - } - var autocomplete_options = - { selectFirst: false, formatItem : format_item_func, autoFill: false, highlight: false, mustMatch: true }; - - t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='HistoryDatasetAssociation' )}", autocomplete_options); - - return t; - }); - ## Can this be moved into base.mako? - %if refresh_frames: - %if 'masthead' in refresh_frames: - ## Refresh masthead == user changes (backward compatibility) - if ( parent.user_changed ) { - %if trans.user: - parent.user_changed( "${trans.user.email}", ${int( app.config.is_admin_user( trans.user ) )} ); - %else: - parent.user_changed( null, false ); - %endif - } - %endif - %if 'history' in refresh_frames: - if ( parent.frames && parent.frames.galaxy_history ) { - ## If available, include HDA ids to seek to in history request. - <% - hda_id = None - if seek_hda_ids: - hda_id = str( seek_hda_ids[0] ) # Use only the first id. - print hda_id - %> - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history', hda_id=hda_id )}"; - 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="${h.url_for( controller='root', action='tool_menu')}"; - if ( parent.force_left_panel ) { - parent.force_left_panel( 'show' ); - } - } - %endif - %endif - - // - // Add a tag to the current grid filter; this adds the tag to the filter and then issues a request to refresh the grid. - // - function add_tag_to_grid_filter(tag_name, tag_value) - { - // Use tag as a filter: replace TAGNAME with tag_name and issue query. - <% - url_args = {} - if "tags" in cur_filter_dict and cur_filter_dict["tags"] != "All": - url_args["f-tags"] = cur_filter_dict["tags"].encode("utf-8") + ", TAGNAME" - else: - url_args["f-tags"] = "TAGNAME" - %> - var url_base = "${url( url_args )}"; - var url = url_base.replace("TAGNAME", tag_name); - self.location = url; - } - - </script> -</%def> - -<%def name="stylesheets()"> - ${h.css( "base", "autocomplete_tagging" )} - <style> - ## Not generic to all grids -- move to base? - .count-box { - min-width: 1.1em; - padding: 5px; - border-width: 1px; - border-style: solid; - text-align: center; - display: inline-block; - } - </style> -</%def> - -<%namespace file="../grid_common.mako" import="*" /> - -## Print grid header. -${render_grid_filters()} - -## Print grid. -<form name="dataset_actions" action="${url()}" method="post" > - <table class="grid"> - <thead> - <tr> - %for column in grid.columns: - %if column.visible: - <% - href = "" - extra = "" - if column.sortable: - if sort_key == column.key: - if sort_order == "asc": - href = url( sort=( "-" + column.key ) ) - extra = "↓" - else: - href = url( sort=( column.key ) ) - extra = "↑" - else: - href = url( sort=column.key ) - %> - <th\ - %if column.ncells > 1: - colspan="${column.ncells}" - %endif - > - %if href: - <a href="${href}">${column.label}</a> - %else: - ${column.label} - %endif - <span>${extra}</span> - </th> - %endif - %endfor - <th></th> - </tr> - </thead> - <tbody> - %for i, item in enumerate( query ): - <tr \ - %if current_item == item: - class="current" \ - %endif - > - ## 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 ): - <% - 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}${extra}</a> </td> - %else: - <td >${v}${extra}</td> - %endif - %endfor - %endif - %endfor - ## Actions column - <td> - <div popupmenu="grid-${i}-popup"> - %for operation in grid.operations: - %if operation.allowed( item ): - <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a> - %endif - %endfor - </div> - </td> - </tr> - %endfor - </tbody> - <tfoot> - %if num_pages > 1: - <tr> - <td></td> - <td colspan="100" style="text-align: right"> - Page: - %for page_index in range(1, num_pages + 1): - %if page_index == cur_page_num: - <span style="font-style: italic">${page_index}</span> - %else: - <% args = { "page" : page_index } %> - <span><a href="${url( args )}">${page_index}</a></span> - %endif - %endfor - </td> - </tr> - %endif - %if grid.operations: - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected histories: - %for operation in grid.operations: - %if operation.allow_multiple: - <input type="submit" name="operation" value="${operation.label}" class="action-button"> - %endif - %endfor - </td> - </tr> - %endif - </tfoot> - </table> -</form> +<%inherit file="/grid_base.mako"/> \ No newline at end of file diff -r 736b4ebcd9db -r cc3e5d4538db templates/grid_base.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/grid_base.mako Mon Nov 09 14:07:16 2009 -0500 @@ -0,0 +1,358 @@ +<%! + from galaxy.model import History, HistoryDatasetAssociation + def inherit(context): + if context.get('use_panels'): + return '/base_panels.mako' + else: + return '/base.mako' +%> +<%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">${message}</div> + <div style="clear: both"></div> + </p> +%endif + +${self.grid_header()} +${self.grid_table()} + +## Function definitions. + +<%def name="title()">${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 = $("#input-tags-filter"); + if (t.length) + { + + var autocomplete_options = + { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; + + t.autocomplete("${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 + + // 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; + } + </script> +</%def> + +<%def name="stylesheets()"> + ${h.css( "base", "autocomplete_tagging" )} + <style> + ## Not generic to all grids -- move to base? + .count-box { + min-width: 1.1em; + padding: 5px; + border-width: 1px; + border-style: solid; + text-align: center; + display: inline-block; + } + </style> +</%def> + +<%namespace file="./grid_common.mako" import="*" /> + +## Print grid header. +<%def name="grid_header()"> + <div class="grid-header"> + <h2>${grid.title}</h2> + + %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 + + ${render_grid_filters()} + </div> +</%def> + +## Print grid. +<%def name="grid_table()"> + <form action="${url()}" method="post" > + <table class="grid"> + <thead> + <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\ + %if column.ncells > 1: + colspan="${column.ncells}" + %endif + > + %if href: + <a href="${href}">${column.label}</a> + %else: + ${column.label} + %endif + <span>${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=operation.label, id=item.id )}">${operation.label}</a> + %endif + %endfor + </div> + </td> + </tr> + %endfor + </tbody> + <tfoot> + ## Row for navigating among pages. + %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 histories on one page</a></span> + </td> + </tr> + %endif + <tr> + ## Grid operations. + <td></td> + <td colspan="100"> + <% + # Mapping between item class and plural term for item. + plural = "items" + if grid.model_class == History: + plural = "histories" + elif grid.model_class == HistoryDatasetAssociation: + plural = "datasets" + %> + For <span class="grid-selected-count"></span> selected ${plural}: + %for operation in grid.operations: + %if operation.allow_multiple: + <input type="submit" name="operation" value="${operation.label}" class="action-button"> + %endif + %endfor + </td> + </tr> + </tfoot> + </table> + </form> +</%def> \ No newline at end of file diff -r 736b4ebcd9db -r cc3e5d4538db templates/grid_common.mako --- a/templates/grid_common.mako Mon Nov 09 12:21:32 2009 -0500 +++ b/templates/grid_common.mako Mon Nov 09 14:07:16 2009 -0500 @@ -73,57 +73,52 @@ ## Print grid search/filtering UI. <%def name="render_grid_filters()"> - <div class="grid-header"> - <h2>${grid.title}</h2> - - ## Default search. - <div> - <table><tr> - <td> - <table> - %for column in grid.columns: - %if column.filterable == "default": - ${render_grid_column_filter(column)} - %endif - %endfor - </table> - </td> - <td> - ##| - ##<% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - ##<a href="${url( filter_all.get_url_args() )}">Clear All</a> - | <a href="" onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Advanced Search</a> - </td> - </tr></table> - </div> - - - ## Advanced search. - <div id="more-search-options" style="display: none; padding-top: 5px"> - <table style="border: 1px solid gray;"> - <tr><td style="text-align: left" colspan="100"> - Advanced Search | - <a href=""# onclick="javascript:$('#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_grid_column_filter(column)} + ## Standard search. + <div> + <table><tr> + <td> + <table> + %for column in grid.columns: + %if column.filterable == "standard": + ${render_grid_column_filter(column)} %endif %endfor - </table> - </div> + </table> + </td> + <td> + ##| + ##<% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + ##<a href="${url( filter_all.get_url_args() )}">Clear All</a> + | <a href="" onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Advanced Search</a> + </td> + </tr></table> + </div> + + ## Advanced search. + <div id="more-search-options" style="display: none; padding-top: 5px"> + <table style="border: 1px solid gray;"> + <tr><td style="text-align: left" colspan="100"> + Advanced Search | + <a href=""# onclick="javascript:$('#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 + + ${render_grid_column_filter(column)} + %endif + %endfor + </table> </div> </%def> \ No newline at end of file diff -r 736b4ebcd9db -r cc3e5d4538db templates/history/grid.mako --- a/templates/history/grid.mako Mon Nov 09 12:21:32 2009 -0500 +++ b/templates/history/grid.mako Mon Nov 09 14:07:16 2009 -0500 @@ -1,311 +1,1 @@ -<%! from galaxy.web.framework.helpers.grids import TextColumn, GridColumnFilter %> - -<%inherit file="/base.mako"/> -<%def name="title()">${grid.title}</%def> - -%if message: - <p> - <div class="${message_type}message transient-message">${message}</div> - <div style="clear: both"></div> - </p> -%endif - -<%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() { - $(".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 ); - }); - }) - }); - - // Set up autocomplete for tag filter input. - var t = $("#input-tags-filter"); - - var autocomplete_options = - { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; - - t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='History' )}", autocomplete_options); - - // Set up autocomplete for name filter input. - var t2 = $("#input-name-filter"); - - var autocomplete_options = - { selectFirst: false, autoFill: false, highlight: false, mustMatch: false }; - - t2.autocomplete("${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 - - // 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( controller='history', 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; - } - - </script> -</%def> - -<%def name="stylesheets()"> - ${h.css( "base", "autocomplete_tagging" )} - <style> - ## Not generic to all grids -- move to base? - .count-box { - min-width: 1.1em; - padding: 5px; - border-width: 1px; - border-style: solid; - text-align: center; - display: inline-block; - } - </style> -</%def> - -<%namespace file="../grid_common.mako" import="*" /> - -## Print grid header. -${render_grid_filters()} - -## Print grid. -<form name="history_actions" action="${url()}" method="post" > - <input type="hidden" name="page" value="${cur_page_num}"> - <table class="grid"> - <thead> - <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\ - %if column.ncells > 1: - colspan="${column.ncells}" - %endif - > - %if href: - <a href="${href}">${column.label}</a> - %else: - ${column.label} - %endif - <span>${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=${trans.security.encode_id( item.id )} class="grid-row-select-checkbox" /> - </td> - ## Data columns - %for column in grid.columns: - %if column.visible: - <% - # Link - link = column.get_link( trans, grid, item ) - if link: - href = url( **link ) - else: - href = None - # Value (coerced to list so we can loop) - value = column.get_value( trans, grid, item ) - if column.ncells == 1: - value = [ value ] - %> - %for cellnum, v in enumerate( value ): - <% - # Attach popup menu? - if column.attach_popup and cellnum == 0: - extra = '<a id="grid-%d-popup" class="arrow" style="display: none;"><span>▼</span></a>' % i - else: - extra = "" - %> - %if href: - <td><div class="menubutton split" style="float: left;"><a class="label" href="${href}">${v}</a>${extra}</td> - %else: - <td >${v}${extra}</td> - %endif - %endfor - %endif - %endfor - ## Actions column - <td> - <div popupmenu="grid-${i}-popup"> - %for operation in grid.operations: - %if operation.allowed( item ): - <a class="action-button" href="${url( operation=operation.label, id=item.id )}">${operation.label}</a> - %endif - %endfor - </div> - </td> - </tr> - %endfor - </tbody> - <tfoot> - ## Row for navigating among pages. - %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 histories on one page</a></span> - - - </td> - </tr> - %endif - %if grid.operations: - <tr> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected histories: - %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 - </tfoot> - </table> -</form> +<%inherit file="/grid_base.mako"/>

1 0

[hg] galaxy 2984: enable history renaming functionality to handl...
by Nate Coraor 09 Nov '09

09 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/736b4ebcd9db changeset: 2984:736b4ebcd9db user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Mon Nov 09 12:21:32 2009 -0500 description: enable history renaming functionality to handle unicode strings. diffstat: lib/galaxy/web/controllers/history.py | 6 +++--- templates/history/rename.mako | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diffs (46 lines): diff -r 144abb3b14bc -r 736b4ebcd9db lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Sat Nov 07 10:30:20 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Mon Nov 09 12:21:32 2009 -0500 @@ -106,7 +106,7 @@ grids.MulticolFilterColumn( "Search", cols_to_filter=[ columns[0], columns[2] ], - key="free-text-search", visible=False, filterable="default" ) + key="free-text-search", visible=False, filterable="standard" ) ) operations = [ @@ -807,13 +807,13 @@ history = get_history( trans, history_id ) if history and history.user_id == user.id: histories.append( history ) - cur_names.append( history.name ) + cur_names.append( history.get_display_name() ) if not name or len( histories ) != len( name ): return trans.fill_template( "/history/rename.mako", histories=histories ) change_msg = "" for i in range(len(histories)): if histories[i].user_id == user.id: - if name[i] == histories[i].name: + if name[i] == histories[i].get_display_name(): change_msg = change_msg + "<p>History: "+cur_names[i]+" is already named: "+name[i]+"</p>" elif name[i] not in [None,'',' ']: name[i] = escape(name[i]) diff -r 144abb3b14bc -r 736b4ebcd9db templates/history/rename.mako --- a/templates/history/rename.mako Sat Nov 07 10:30:20 2009 -0500 +++ b/templates/history/rename.mako Mon Nov 09 12:21:32 2009 -0500 @@ -18,11 +18,11 @@ %for history in histories: <tr> <td> - <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> - ${history.name} + <input type="hidden" name="id" value="${trans.security.encode_id( history.id )}"> + ${history.get_display_name()} </td> <td> - <input type="text" name="name" value="${history.name}" size="40"> + <input type="text" name="name" value="${history.get_display_name()}" size="40"> </td> </tr> %endfor

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Re: [galaxy-dev] [galaxy-bugs] Galaxy tool error report from u4705270@hotmail.com
by Kelly Vincent 09 Nov '09

09 Nov '09

Hi, Could you possibly share your history with me (making sure to include all of the files you used to get to the point where it fails) at kpvincent(a)bx.psu.edu ? I can't really tell what the problem is from this error. There appear to be a couple of things wrong (the index of the BAM file doesn't get created and then Samtools seg faults when it tries to index the reference file). With your actual files, I can look into the failures in more depth. Regards, Kelly On Nov 8, 2009, at 9:50 PM, galaxy-bugs(a)bx.psu.edu wrote: > > GALAXY TOOL ERROR REPORT > ------------------------ > > This error report was sent from the Galaxy instance hosted on the > server > "main.g2.bx.psu.edu" > ----------------------------------------------------------------------------- > This is in reference to output dataset 913904. > ----------------------------------------------------------------------------- > The user 'u4705270(a)hotmail.com' provided the following information: > I have problem when I use SAM file from BWA to transform to BAM in > SAM tool. > sh: line 1: 32286 Segmentation fault samtools faidx /galaxy/ > home/g2main/galaxy_main/database/tmp/framework/tmpGSqkyx 2> /dev/null > sh: line 1: 32291 Segmentation fault samtools sort /galaxy/home/ > g2main/galaxy_main/database/tmp/framework/tmpdokBYv /galaxy/home/ > g2main/galaxy_main/database/tmp/framework/tmpU-Dbdm 2> /dev/null > lseek: Invalid argument > [bam_header_read] read from pipe; skip EOF checking. > There was a problem creating the index for the BAM file > > ----------------------------------------------------------------------------- > job id: 676933 > tool id: sam_to_bam > ----------------------------------------------------------------------------- > job stderr: > sh: line 1: 32286 Segmentation fault samtools faidx /galaxy/ > home/g2main/galaxy_main/database/tmp/framework/tmpGSqkyx 2> /dev/null > sh: line 1: 32291 Segmentation fault samtools sort /galaxy/home/ > g2main/galaxy_main/database/tmp/framework/tmpdokBYv /galaxy/home/ > g2main/galaxy_main/database/tmp/framework/tmpU-Dbdm 2> /dev/null > lseek: Invalid argument > [bam_header_read] read from pipe; skip EOF checking. > There was a problem creating the index for the BAM file > > ----------------------------------------------------------------------------- > job stdout: > > ----------------------------------------------------------------------------- > job info: > None > ----------------------------------------------------------------------------- > job traceback: > None > ----------------------------------------------------------------------------- > (This is an automated message). > _______________________________________________ > galaxy-bugs mailing list > galaxy-bugs(a)bx.psu.edu > http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-bugs

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Re: [galaxy-dev] OS X dev build attempt
by Art Poon 09 Nov '09

09 Nov '09

Dear colleagues, I'm attempting to install a local instance of Galaxy for development purposes on my Mac. The Galaxy build script issued the following warning: > Your platform (py2.5-macosx-10.6-i386-ucs2) is not supported. > Pre-built galaxy eggs are not available from the Galaxy developers for > your platform. You may be able to build them by hand with: > python scripts/scramble.py Upon running scramble.py, it turned out that the link to pysqlite in eggs.ini is broken: http://initd.org/pub/software/pysqlite/releases/2.3/2.3.5/pysqlite-2.3.5.ta… so I replaced the corresponding line in the eggs.ini file with: http://pysqlite.googlecode.com/files/pysqlite-2.5.5.tar.gz http://www.sqlite.org/sqlite-source-3_5_4.zip (I haven't yet located a link to pysqlite 2.3.5 on the web.) This immediately created a problem with SQLAlchemy and sqlalchemy_migrate: > File "/Users/apoon/Source/galaxy/eggs/py2.5-noplatform/ > SQLAlchemy-0.4.7p1-py2.5.egg/sqlalchemy/engine/base.py", line 942, > in _handle_dbapi_exception > raise exceptions.DBAPIError.instance(statement, parameters, e, > connection_invalidated=is_disconnect) > ProgrammingError: (ProgrammingError) Cannot operate on a closed > cursor. None None Googled the respective error messages and found that there's a version conflict with pysqlite 2.5.5. So those got updated as well, with the corresponding line edits to eggs.ini. So far so good. But then run.sh exited with another problem: > File "lib/galaxy/model/migrate/versions/ > 0005_cleanup_datasets_fix.py", line 665, in upgrade > for dataset in context.query( Dataset ).filter( and_ > ( Dataset.c.deleted == True, Dataset.c.purged == False ) ): > AttributeError: type object 'Dataset' has no attribute 'c' I poked around in that script and found that while class Dataset has no attribute 'c', it sure has attributes 'deleted' and 'purged'. So I changed that line to: > for dataset in context.query( Dataset ).filter( and_ > ( Dataset.deleted == True, Dataset.purged == False ) ): Re-ran run.sh, got asked to migrate the database scheme, so sh manage_db.sh upgrade it is, followed with another run.sh and hey, presto! My Mac is running Galaxy. ^_^ Cheers, - Art.

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setting per-tools parameters for SGE job runner
by Andreas Kuntzagk 09 Nov '09

09 Nov '09

Hi, I have galaxy running now with SGE job runners. I also managed to set PATH now using .sge_request. What I want to do now is to set some SGE parameters for some special tools which need special parameters (e.q. a parallel env. ) Is there a way to set them in galaxy (maybe using the job runner URL)? Or do I need to write wrappers? thanks, Andreas

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Error message in executing NGS tool Quality format converter
by Vipin TS 09 Nov '09

09 Nov '09

Hi all, I am working on a local instance of Galaxy NGS tools system. I am using a tool 'Quality format converter' but it fails to give the result. Here is the error message. An error occurred running this job: */home/galaxy/galaxy-2/database/pbs/galaxy_16459.sh: line 13: fastq_quality_converter: command not found* >From this I understood that 'fastq_quality_converter' script/file is missing. if I am wrong please let me know. Also I am not finding such a script/file in my local instance galaxy tool directory. Many thanks in advance, Vipin T S

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