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commit/galaxy-central: jgoecks: Include post-job actions when importing and exporting workflows. Fixes #518
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/576e78ba4141/ changeset: 576e78ba4141 user: jgoecks date: 2011-06-08 21:16:20 summary: Include post-job actions when importing and exporting workflows. Fixes #518 affected #: 1 file (926 bytes) --- a/lib/galaxy/web/controllers/workflow.py Wed Jun 08 14:41:45 2011 -0400 +++ b/lib/galaxy/web/controllers/workflow.py Wed Jun 08 15:16:20 2011 -0400 @@ -1592,6 +1592,15 @@ 'annotation' : annotation_str } + # Add post-job actions to step dict. + if module.type == 'tool': + pja_dict = {} + for pja in step.post_job_actions: + pja_dict[pja.action_type+pja.output_name] = dict( action_type = pja.action_type, + output_name = pja.output_name, + action_arguments = pja.action_arguments ) + step_dict[ 'post_job_actions' ] = pja_dict + # Data inputs step_dict['inputs'] = [] if module.type == "data_input": @@ -1695,6 +1704,12 @@ if annotation: annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) self.add_item_annotation( trans.sa_session, trans.get_user(), step, annotation ) + # Unpack and add post-job actions. + post_job_actions = step_dict.get( 'post_job_actions', {} ) + for name, pja_dict in post_job_actions.items(): + pja = PostJobAction( pja_dict[ 'action_type' ], + step, pja_dict[ 'output_name' ], + pja_dict[ 'action_arguments' ] ) # Second pass to deal with connections between steps for step in steps: # Input connections Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 08 Jun '11

08 Jun '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8166f7585484/ changeset: 8166f7585484 user: natefoo date: 2011-06-08 19:25:45 summary: Don't provde the output filename to the upload tool if it's outside Galaxy's files_path, since this means we're only linking data and the output paths are not used (and may contain non-shell-safe characters). Fixes issue #533. affected #: 1 file (299 bytes) --- a/tools/data_source/upload.xml Wed Jun 08 12:46:11 2011 -0400 +++ b/tools/data_source/upload.xml Wed Jun 08 13:25:45 2011 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> -<tool name="Upload File" id="upload1" version="1.1.2"> +<tool name="Upload File" id="upload1" version="1.1.3"><description> from your computer </description> @@ -11,7 +11,12 @@ #while $varExists('output%i' % $outnum): #set $output = $getVar('output%i' % $outnum) #set $outnum += 1 - ${output.dataset.dataset.id}:${output.files_path}:${output} + #set $file_name = $output.file_name + ## FIXME: This is not future-proof for other uses of external_filename (other than for use by the library upload's "link data" feature) + #if $output.dataset.dataset.external_filename: + #set $file_name = "None" + #end if + ${output.dataset.dataset.id}:${output.files_path}:${file_name} #end while </command><inputs nginx_upload="true"> http://bitbucket.org/galaxy/galaxy-central/changeset/b2fa1535d02e/ changeset: b2fa1535d02e user: natefoo date: 2011-06-08 19:26:06 summary: merge. affected #: 6 files (2.7 KB) --- a/lib/galaxy/tools/__init__.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Jun 08 13:26:06 2011 -0400 @@ -756,13 +756,14 @@ case.inputs = self.parse_input_elem( ElementTree.XML( "<when>%s</when>" % case_inputs ), enctypes, context ) else: - case.inputs = {} + case.inputs = odict() group.cases.append( case ) else: # Should have one child "input" which determines the case input_elem = elem.find( "param" ) assert input_elem is not None, "<conditional> must have a child <param>" group.test_param = self.parse_param_elem( input_elem, enctypes, context ) + possible_cases = list( group.test_param.legal_values ) #store possible cases, undefined whens will have no inputs # Must refresh when test_param changes group.test_param.refresh_on_change = True # And a set of possible cases @@ -771,6 +772,16 @@ case.value = case_elem.get( "value" ) case.inputs = self.parse_input_elem( case_elem, enctypes, context ) group.cases.append( case ) + try: + possible_cases.remove( case.value ) + except: + log.warning( "A when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % ( group.name, group.test_param.name, case.value ) ) + for unspecified_case in possible_cases: + log.warning( "A when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % ( group.name, group.test_param.name, unspecified_case ) ) + case = ConditionalWhen() + case.value = unspecified_case + case.inputs = odict() + group.cases.append( case ) rval[group.name] = group elif elem.tag == "upload_dataset": group = UploadDataset() --- a/lib/galaxy/tools/parameters/basic.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Wed Jun 08 13:26:06 2011 -0400 @@ -318,7 +318,7 @@ checked = self.checked if value is not None: checked = form_builder.CheckboxField.is_checked( value ) - return form_builder.CheckboxField( self.name, checked ) + return form_builder.CheckboxField( self.name, checked, refresh_on_change = self.refresh_on_change ) def from_html( self, value, trans=None, other_values={} ): return form_builder.CheckboxField.is_checked( value ) def to_python( self, value, app ): @@ -330,6 +330,9 @@ return self.truevalue else: return self.falsevalue + @property + def legal_values( self ): + return [ self.truevalue, self.falsevalue ] class FileToolParameter( ToolParameter ): """ --- a/lib/galaxy/tools/parameters/grouping.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Wed Jun 08 13:26:06 2011 -0400 @@ -414,7 +414,10 @@ return "Conditional (%s)" % self.name def get_current_case( self, value, trans ): # Convert value to user representation - str_value = self.test_param.filter_value( value, trans ) + if isinstance( value, bool ): + str_value = self.test_param.to_param_dict_string( value ) + else: + str_value = self.test_param.filter_value( value, trans ) # Find the matching case for index, case in enumerate( self.cases ): if str_value == case.value: --- a/lib/galaxy/web/form_builder.py Wed Jun 08 13:25:45 2011 -0400 +++ b/lib/galaxy/web/form_builder.py Wed Jun 08 13:26:06 2011 -0400 @@ -88,9 +88,17 @@ >>> print CheckboxField( "bar", checked="yes" ).get_html() <input type="checkbox" id="bar" name="bar" value="true" checked="checked"><input type="hidden" name="bar" value="true"> """ - def __init__( self, name, checked=None ): + def __init__( self, name, checked=None, refresh_on_change = False, refresh_on_change_values = None ): self.name = name self.checked = ( checked == True ) or ( isinstance( checked, basestring ) and ( checked.lower() in ( "yes", "true", "on" ) ) ) + self.refresh_on_change = refresh_on_change + self.refresh_on_change_values = refresh_on_change_values or [] + if self.refresh_on_change: + self.refresh_on_change_text = ' refresh_on_change="true" ' + if self.refresh_on_change_values: + self.refresh_on_change_text = '%s refresh_on_change_values="%s" ' % ( self.refresh_on_change_text, ",".join( self.refresh_on_change_values ) ) + else: + self.refresh_on_change_text = '' def get_html( self, prefix="", disabled=False ): if self.checked: checked_text = ' checked="checked"' @@ -102,8 +110,8 @@ # parsing the request, the value 'true' in the hidden field actually means it is NOT checked. # See the is_checked() method below. The prefix is necessary in each case to ensure functional # correctness when the param is inside a conditional. - return '<input type="checkbox" id="%s" name="%s" value="true"%s%s><input type="hidden" name="%s%s" value="true"%s>' \ - % ( id_name, id_name, checked_text, self.get_disabled_str( disabled ), prefix, self.name, self.get_disabled_str( disabled ) ) + return '<input type="checkbox" id="%s" name="%s" value="true"%s%s%s><input type="hidden" name="%s%s" value="true"%s>' \ + % ( id_name, id_name, checked_text, self.get_disabled_str( disabled ), self.refresh_on_change_text, prefix, self.name, self.get_disabled_str( disabled ) ) @staticmethod def is_checked( value ): if value == True: @@ -253,7 +261,7 @@ <div><input type="checkbox" name="bar" value="3" id="bar|3"><label class="inline" for="bar|3">automatic</label></div><div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label class="inline" for="bar|4">bazooty</label></div> """ - def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=[], size=None ): + def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=None, size=None ): self.name = name self.multiple = multiple or False self.size = size @@ -266,7 +274,7 @@ raise Exception, "Unknown display type: %s" % display self.display = display self.refresh_on_change = refresh_on_change - self.refresh_on_change_values = refresh_on_change_values + self.refresh_on_change_values = refresh_on_change_values or [] if self.refresh_on_change: self.refresh_on_change_text = ' refresh_on_change="true"' if self.refresh_on_change_values: --- a/static/scripts/galaxy.base.js Wed Jun 08 13:25:45 2011 -0400 +++ b/static/scripts/galaxy.base.js Wed Jun 08 13:26:06 2011 -0400 @@ -588,6 +588,23 @@ select_field.get(0).form.submit(); }); + // checkboxes refresh on change + $(":checkbox[refresh_on_change='true']").click( function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + select_field.get(0).form.submit(); + }); + // Links with confirmation $( "a[confirm]" ).click( function() { return confirm( $(this).attr("confirm") ); --- a/static/scripts/packed/galaxy.base.js Wed Jun 08 13:25:45 2011 -0400 +++ b/static/scripts/packed/galaxy.base.js Wed Jun 08 13:26:06 2011 -0400 @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return 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f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:b,minChars:0,hideForLessThanMinChars:false};c.autocomplete(e,f);d.replaceWith(c);var k=function(){var o=c.attr("value");var n=i[o];if(n!==null&&n!==undefined){c.attr("value",n)}else{if(m!==""){c.attr("value",m)}else{c.attr("value","?")}}};c.parents("form").submit(function(){k()});$(document).bind("convert_to_values",function(){k()});if(d.attr("refresh_on_change")=="true"){var h=d.attr("refresh_on_change_values"),l=d.attr("last_selected_value");if(h!==undefined){h=h.split(",")}var j=function(){var n=i[c.attr("value")];if(l!==n&&n!==null&&n!==undefined){if(h!==undefined&&$.inArray(n,h)===-1&&$.inArray(l,h)===-1){return}c.attr("value",n);$(window).trigger("refresh_on_change");c.parents("form").submit()}};c.bind("result",j);c.keyup(function(n){if(n.keyCode===13){j()}});c.keydown(function(n){if(n.keyCode===13){return false}})}})}function 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h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search 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b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))});if($.fn.tipsy){$(".tooltip").tipsy({gravity:"s"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file Repository URL: 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commit/galaxy-central: 2 new changesets
by Bitbucket 08 Jun '11

08 Jun '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/3d876a5e313b/ changeset: 3d876a5e313b user: dan date: 2011-06-08 19:04:57 summary: Allow conditional statements to not define a 'when' tag for all cases. When a 'when' is not defined, sub-inputs will be empty. Resolves #465. affected #: 1 file (885 bytes) --- a/lib/galaxy/tools/__init__.py Wed Jun 08 12:46:11 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Wed Jun 08 13:04:57 2011 -0400 @@ -756,13 +756,14 @@ case.inputs = self.parse_input_elem( ElementTree.XML( "<when>%s</when>" % case_inputs ), enctypes, context ) else: - case.inputs = {} + case.inputs = odict() group.cases.append( case ) else: # Should have one child "input" which determines the case input_elem = elem.find( "param" ) assert input_elem is not None, "<conditional> must have a child <param>" group.test_param = self.parse_param_elem( input_elem, enctypes, context ) + possible_cases = list( group.test_param.legal_values ) #store possible cases, undefined whens will have no inputs # Must refresh when test_param changes group.test_param.refresh_on_change = True # And a set of possible cases @@ -771,6 +772,16 @@ case.value = case_elem.get( "value" ) case.inputs = self.parse_input_elem( case_elem, enctypes, context ) group.cases.append( case ) + try: + possible_cases.remove( case.value ) + except: + log.warning( "A when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % ( group.name, group.test_param.name, case.value ) ) + for unspecified_case in possible_cases: + log.warning( "A when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % ( group.name, group.test_param.name, unspecified_case ) ) + case = ConditionalWhen() + case.value = unspecified_case + case.inputs = odict() + group.cases.append( case ) rval[group.name] = group elif elem.tag == "upload_dataset": group = UploadDataset() http://bitbucket.org/galaxy/galaxy-central/changeset/91b35c84d7ce/ changeset: 91b35c84d7ce user: dan date: 2011-06-08 19:05:03 summary: Allow boolean inputs (checkbox) to be used as the parameter selector for conditional grouping inputs. Resolves #393. affected #: 5 files (1.9 KB) --- a/lib/galaxy/tools/parameters/basic.py Wed Jun 08 13:04:57 2011 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Wed Jun 08 13:05:03 2011 -0400 @@ -318,7 +318,7 @@ checked = self.checked if value is not None: checked = form_builder.CheckboxField.is_checked( value ) - return form_builder.CheckboxField( self.name, checked ) + return form_builder.CheckboxField( self.name, checked, refresh_on_change = self.refresh_on_change ) def from_html( self, value, trans=None, other_values={} ): return form_builder.CheckboxField.is_checked( value ) def to_python( self, value, app ): @@ -330,6 +330,9 @@ return self.truevalue else: return self.falsevalue + @property + def legal_values( self ): + return [ self.truevalue, self.falsevalue ] class FileToolParameter( ToolParameter ): """ --- a/lib/galaxy/tools/parameters/grouping.py Wed Jun 08 13:04:57 2011 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Wed Jun 08 13:05:03 2011 -0400 @@ -414,7 +414,10 @@ return "Conditional (%s)" % self.name def get_current_case( self, value, trans ): # Convert value to user representation - str_value = self.test_param.filter_value( value, trans ) + if isinstance( value, bool ): + str_value = self.test_param.to_param_dict_string( value ) + else: + str_value = self.test_param.filter_value( value, trans ) # Find the matching case for index, case in enumerate( self.cases ): if str_value == case.value: --- a/lib/galaxy/web/form_builder.py Wed Jun 08 13:04:57 2011 -0400 +++ b/lib/galaxy/web/form_builder.py Wed Jun 08 13:05:03 2011 -0400 @@ -88,9 +88,17 @@ >>> print CheckboxField( "bar", checked="yes" ).get_html() <input type="checkbox" id="bar" name="bar" value="true" checked="checked"><input type="hidden" name="bar" value="true"> """ - def __init__( self, name, checked=None ): + def __init__( self, name, checked=None, refresh_on_change = False, refresh_on_change_values = None ): self.name = name self.checked = ( checked == True ) or ( isinstance( checked, basestring ) and ( checked.lower() in ( "yes", "true", "on" ) ) ) + self.refresh_on_change = refresh_on_change + self.refresh_on_change_values = refresh_on_change_values or [] + if self.refresh_on_change: + self.refresh_on_change_text = ' refresh_on_change="true" ' + if self.refresh_on_change_values: + self.refresh_on_change_text = '%s refresh_on_change_values="%s" ' % ( self.refresh_on_change_text, ",".join( self.refresh_on_change_values ) ) + else: + self.refresh_on_change_text = '' def get_html( self, prefix="", disabled=False ): if self.checked: checked_text = ' checked="checked"' @@ -102,8 +110,8 @@ # parsing the request, the value 'true' in the hidden field actually means it is NOT checked. # See the is_checked() method below. The prefix is necessary in each case to ensure functional # correctness when the param is inside a conditional. - return '<input type="checkbox" id="%s" name="%s" value="true"%s%s><input type="hidden" name="%s%s" value="true"%s>' \ - % ( id_name, id_name, checked_text, self.get_disabled_str( disabled ), prefix, self.name, self.get_disabled_str( disabled ) ) + return '<input type="checkbox" id="%s" name="%s" value="true"%s%s%s><input type="hidden" name="%s%s" value="true"%s>' \ + % ( id_name, id_name, checked_text, self.get_disabled_str( disabled ), self.refresh_on_change_text, prefix, self.name, self.get_disabled_str( disabled ) ) @staticmethod def is_checked( value ): if value == True: @@ -253,7 +261,7 @@ <div><input type="checkbox" name="bar" value="3" id="bar|3"><label class="inline" for="bar|3">automatic</label></div><div><input type="checkbox" name="bar" value="4" id="bar|4" checked='checked'><label class="inline" for="bar|4">bazooty</label></div> """ - def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=[], size=None ): + def __init__( self, name, multiple=None, display=None, refresh_on_change=False, refresh_on_change_values=None, size=None ): self.name = name self.multiple = multiple or False self.size = size @@ -266,7 +274,7 @@ raise Exception, "Unknown display type: %s" % display self.display = display self.refresh_on_change = refresh_on_change - self.refresh_on_change_values = refresh_on_change_values + self.refresh_on_change_values = refresh_on_change_values or [] if self.refresh_on_change: self.refresh_on_change_text = ' refresh_on_change="true"' if self.refresh_on_change_values: --- a/static/scripts/galaxy.base.js Wed Jun 08 13:04:57 2011 -0400 +++ b/static/scripts/galaxy.base.js Wed Jun 08 13:05:03 2011 -0400 @@ -588,6 +588,23 @@ select_field.get(0).form.submit(); }); + // checkboxes refresh on change + $(":checkbox[refresh_on_change='true']").click( function() { + var select_field = $(this), + select_val = select_field.val(), + refresh = false, + ref_on_change_vals = select_field.attr("refresh_on_change_values"); + if (ref_on_change_vals) { + ref_on_change_vals = ref_on_change_vals.split(','); + var last_selected_value = select_field.attr("last_selected_value"); + if ($.inArray(select_val, ref_on_change_vals) === -1 && $.inArray(last_selected_value, ref_on_change_vals) === -1) { + return; + } + } + $(window).trigger("refresh_on_change"); + select_field.get(0).form.submit(); + }); + // Links with confirmation $( "a[confirm]" ).click( function() { return confirm( $(this).attr("confirm") ); --- a/static/scripts/packed/galaxy.base.js Wed Jun 08 13:04:57 2011 -0400 +++ b/static/scripts/packed/galaxy.base.js Wed Jun 08 13:05:03 2011 -0400 @@ -1,1 +1,1 @@ -if(!Array.indexOf){Array.prototype.indexOf=function(c){for(var b=0,a=this.length;b<a;b++){if(this[b]==c){return b}}return -1}}function obj_length(c){if(c.length!==undefined){return c.length}var b=0;for(var a in c){b++}return 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https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Disable grid controls and content when new content is being fetched. Fixes #272
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c6b9d40bdd0e/ changeset: c6b9d40bdd0e user: jgoecks date: 2011-06-08 18:46:11 summary: Disable grid controls and content when new content is being fetched. Fixes #272 affected #: 1 file (8 bytes) --- a/templates/grid_base.mako Wed Jun 08 12:10:51 2011 -0400 +++ b/templates/grid_base.mako Wed Jun 08 12:46:11 2011 -0400 @@ -689,7 +689,7 @@ width : 100%; height : 100%; z-index : 14000; - position : absolute; + position : fixed; display: none; } ## If page is displayed in panels, pad from edges for readability. @@ -708,6 +708,7 @@ <%namespace file="./grid_common.mako" import="*" /><%def name="make_grid( grid )"> + <div class="loading-elt-overlay"></div><table><tr><td width="75%">${self.render_grid_header( grid )}</td> @@ -769,9 +770,7 @@ if show_item_checkboxes or multiple_item_ops_exist: show_item_checkboxes = True %> - <form action="${url()}" method="post" onsubmit="return false;"> - <div class="loading-elt-overlay"></div><table id="grid-table" class="grid"><thead id="grid-table-header"><tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Remove hardcoding of universe_wsgi.ini, fixes issue #358 (except for the sample cleanup scripts which, as samples, are expected to be modified by the site anyway).
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/73daddf1324d/ changeset: 73daddf1324d user: natefoo date: 2011-06-08 18:10:51 summary: Remove hardcoding of universe_wsgi.ini, fixes issue #358 (except for the sample cleanup scripts which, as samples, are expected to be modified by the site anyway). affected #: 10 files (2.6 KB) --- a/lib/galaxy/app.py Wed Jun 08 11:52:42 2011 -0400 +++ b/lib/galaxy/app.py Wed Jun 08 12:10:51 2011 -0400 @@ -29,7 +29,7 @@ db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database # Initialize database / check for appropriate schema version from galaxy.model.migrate.check import create_or_verify_database - create_or_verify_database( db_url, self.config.database_engine_options ) + create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) # Setup the database engine and ORM from galaxy.model import mapping self.model = mapping.init( self.config.file_path, --- a/lib/galaxy/eggs/__init__.py Wed Jun 08 11:52:42 2011 -0400 +++ b/lib/galaxy/eggs/__init__.py Wed Jun 08 12:10:51 2011 -0400 @@ -247,7 +247,7 @@ Reads the eggs.ini file for use with checking and fetching. """ config_file = os.path.join( galaxy_dir, 'eggs.ini' ) - def __init__( self, platform=None ): + def __init__( self, galaxy_config_file, platform=None ): self.eggs = {} self.config = CaseSensitiveConfigParser() self.repo = None @@ -256,7 +256,7 @@ self.py_platform = None if platform is not None: self.py_platform = platform.split( '-' )[0] - self.galaxy_config = GalaxyConfig() + self.galaxy_config = GalaxyConfig( galaxy_config_file ) self.parse() def parse( self ): self.config.read( Crate.config_file ) @@ -349,12 +349,14 @@ raise EggNotFetchable( missing ) class GalaxyConfig( object ): - config_file = os.path.join( galaxy_dir, "universe_wsgi.ini" ) always_conditional = ( 'GeneTrack', 'pysam', 'ctypes', 'python_daemon' ) - def __init__( self ): - self.config = ConfigParser.ConfigParser() - if self.config.read( GalaxyConfig.config_file ) == []: - raise Exception( "error: unable to read Galaxy config from %s" % GalaxyConfig.config_file ) + def __init__( self, config_file ): + if config_file is None: + self.config = None + else: + self.config = ConfigParser.ConfigParser() + if self.config.read( config_file ) == []: + raise Exception( "error: unable to read Galaxy config from %s" % config_file ) def check_conditional( self, egg_name ): def check_pysam(): # can't build pysam on solaris < 10 @@ -364,6 +366,10 @@ if int( minor ) < 10: return False return True + # If we're using require() we may not have a Galaxy config file, but if + # we're using require(), we don't care about conditionals. + if self.config is None: + return True if egg_name == "pysqlite": # SQLite is different since it can be specified in two config vars and defaults to True try: @@ -396,7 +402,7 @@ env = get_env() def require( req_str ): - c = Crate() + c = Crate( None ) req = pkg_resources.Requirement.parse( req_str ) # TODO: This breaks egg version requirements. Not currently a problem, but # it could become one. --- a/lib/galaxy/eggs/dist.py Wed Jun 08 11:52:42 2011 -0400 +++ b/lib/galaxy/eggs/dist.py Wed Jun 08 12:10:51 2011 -0400 @@ -39,10 +39,10 @@ Holds eggs with info on how to build them for distribution. """ dist_config_file = os.path.join( galaxy_dir, 'dist-eggs.ini' ) - def __init__( self, build_on='all' ): + def __init__( self, galaxy_config_file, build_on='all' ): self.dist_config = CaseSensitiveConfigParser() self.build_on = build_on - ScrambleCrate.__init__( self ) + ScrambleCrate.__init__( self, galaxy_config_file ) def parse( self ): self.dist_config.read( DistScrambleCrate.dist_config_file ) self.hosts = dict( self.dist_config.items( 'hosts' ) ) --- a/lib/galaxy/model/migrate/check.py Wed Jun 08 11:52:42 2011 -0400 +++ b/lib/galaxy/model/migrate/check.py Wed Jun 08 12:10:51 2011 -0400 @@ -20,7 +20,7 @@ "mysql" : "MySQL_python" } -def create_or_verify_database( url, engine_options={} ): +def create_or_verify_database( url, galaxy_config_file, engine_options={} ): """ Check that the database is use-able, possibly creating it if empty (this is the only time we automatically create tables, otherwise we force the @@ -98,8 +98,11 @@ # Verify that the code and the DB are in sync db_schema = schema.ControlledSchema( engine, migrate_repository ) if migrate_repository.versions.latest != db_schema.version: - raise Exception( "Your database has version '%d' but this code expects version '%d'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'." - % ( db_schema.version, migrate_repository.versions.latest ) ) + config_arg = '' + if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file: + config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' ) + raise Exception( "Your database has version '%d' but this code expects version '%d'. Please backup your database and then migrate the schema by running 'sh manage_db.sh%s upgrade'." + % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) else: log.info( "At database version %d" % db_schema.version ) @@ -123,4 +126,4 @@ finally: for message in "".join( sys.stdout.buffer ).split( "\n" ): log.info( message ) - sys.stdout = old_stdout \ No newline at end of file + sys.stdout = old_stdout --- a/run.sh Wed Jun 08 11:52:42 2011 -0400 +++ b/run.sh Wed Jun 08 12:10:51 2011 -0400 @@ -32,7 +32,7 @@ [ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0; break done if [ $FETCH_EGGS -eq 1 ]; then - python ./scripts/check_eggs.py quiet + python ./scripts/check_eggs.py -q if [ $? -ne 0 ]; then echo "Some eggs are out of date, attempting to fetch..." python ./scripts/fetch_eggs.py --- a/scripts/check_eggs.py Wed Jun 08 11:52:42 2011 -0400 +++ b/scripts/check_eggs.py Wed Jun 08 12:10:51 2011 -0400 @@ -3,27 +3,35 @@ usage: check_eggs.py """ import os, sys, logging +from optparse import OptionParser + +parser = OptionParser() +parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' ) +parser.add_option( '-q', '--quiet', dest='quiet', action="store_true", help='Quiet (no output, only set return code)', default=False ) +( options, args ) = parser.parse_args() + +if not os.path.exists( options.config ): + print "Config file does not exist (see 'python %s --help'): %s" % ( sys.argv[0], options.config ) + sys.exit( 1 ) root = logging.getLogger() root.setLevel( 10 ) root.addHandler( logging.StreamHandler( sys.stdout ) ) +config_arg = '' +if options.config != 'universe_wsgi.ini': + config_arg = '-c %s' % options.config + lib = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "lib" ) ) sys.path.append( lib ) -try: - assert sys.argv[1] == 'quiet' - quiet = True -except: - quiet = False - from galaxy.eggs import Crate -c = Crate() +c = Crate( options.config ) if c.config_missing: - if not quiet: + if not options.quiet: print "Some of your Galaxy eggs are out of date. Please update them" print "by running:" - print " python scripts/fetch_eggs.py" + print " python scripts/fetch_eggs.py %s" % config_arg sys.exit( 1 ) sys.exit( 0 ) --- a/scripts/dist-scramble.py Wed Jun 08 11:52:42 2011 -0400 +++ b/scripts/dist-scramble.py Wed Jun 08 12:10:51 2011 -0400 @@ -1,11 +1,10 @@ -""" -usage: dist-scramble.py <egg_name> [platform] - egg_name - The egg to scramble (as defined in eggs.ini) - platform - The platform to scramble on (as defined in - dist-eggs.ini). Leave blank for all. - Platform-inspecific eggs ignore this argument. -""" import os, sys, logging +from optparse import OptionParser + +parser = OptionParser() +parser.add_option( '-e', '--egg-name', dest='egg_name', help='Egg name (as defined in eggs.ini) to scramble (required)' ) +parser.add_option( '-p', '--platform', dest='platform', help='Scramble for a specific platform (by default, eggs are scrambled for all platforms, see dist-eggs.ini for platform names)' ) +( options, args ) = parser.parse_args() root = logging.getLogger() root.setLevel( 10 ) @@ -17,18 +16,20 @@ from galaxy.eggs.dist import DistScrambleCrate, ScrambleFailure from galaxy.eggs import EggNotFetchable -if len( sys.argv ) > 3 or len( sys.argv ) < 2: - print __doc__ +if not options.egg_name: + print "ERROR: You must specify an egg to scramble (-e)" + parser.print_help() sys.exit( 1 ) -elif len( sys.argv ) == 3: - c = DistScrambleCrate( sys.argv[2] ) + +if options.platform: + c = DistScrambleCrate( None, options.platform ) else: - c = DistScrambleCrate() + c = DistScrambleCrate( None ) try: - eggs = c[sys.argv[1]] + eggs = c[options.egg_name] except: - print "error: %s not in eggs.ini" % sys.argv[1] + print "ERROR: %s not in eggs.ini" % options.egg_name sys.exit( 1 ) failed = [] for egg in eggs: --- a/scripts/fetch_eggs.py Wed Jun 08 11:52:42 2011 -0400 +++ b/scripts/fetch_eggs.py Wed Jun 08 12:10:51 2011 -0400 @@ -1,15 +1,15 @@ -""" -usage: fetch_eggs.py [egg_name] [platform] - With no arguments, fetches all eggs necessary according to the - settings in universe_wsgi.ini. - egg_name - Fetch only this egg (as defined in eggs.ini) or 'all' for - all eggs (even those not required by your settings). - platform - Fetch eggs for a specific platform (if not provided, fetch - eggs for *this* platform). Useful for fetching eggs for cluster - nodes which are of a different architecture than the head node. - Platform name can be determined with the get_platforms.py script. -""" import os, sys, logging +from optparse import OptionParser + +parser = OptionParser() +parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' ) +parser.add_option( '-e', '--egg-name', dest='egg_name', help='Egg name (as defined in eggs.ini) to fetch, or "all" for all eggs, even those not needed by your configuration' ) +parser.add_option( '-p', '--platform', dest='platform', help='Fetch for a specific platform (by default, eggs are fetched for *this* platform' ) +( options, args ) = parser.parse_args() + +if not os.path.exists( options.config ): + print "Config file does not exist (see 'python %s --help'): %s" % ( sys.argv[0], options.config ) + sys.exit( 1 ) root = logging.getLogger() root.setLevel( 10 ) @@ -21,18 +21,18 @@ from galaxy.eggs import Crate, EggNotFetchable import pkg_resources +if options.platform: + c = Crate( options.config, platform = options.platform ) +else: + c = Crate( options.config ) try: - c = Crate( platform = sys.argv[2] ) -except: - c = Crate() -try: - if len( sys.argv ) == 1: + if not options.egg_name: c.resolve() # Only fetch eggs required by the config - elif sys.argv[1] == 'all': + elif options.egg_name == 'all': c.resolve( all=True ) # Fetch everything else: # Fetch a specific egg - name = sys.argv[1] + name = options.egg_name try: egg = c[name] except: @@ -41,12 +41,15 @@ dist = egg.resolve()[0] print "%s %s is installed at %s" % ( dist.project_name, dist.version, dist.location ) except EggNotFetchable, e: + config_arg = '' + if options.config != 'universe_wsgi.ini': + config_arg = '-c %s ' % options.config try: - assert sys.argv[1] != 'all' + assert options.egg_name != 'all' egg = e.eggs[0] print "%s %s couldn't be downloaded automatically. You can try" % ( egg.name, egg.version ) print "building it by hand with:" - print " python scripts/scramble.py %s" + print " python scripts/scramble.py %s-e %s" % ( config_arg, egg.name ) except ( AssertionError, IndexError ): print "One or more of the python eggs necessary to run Galaxy couldn't be" print "downloaded automatically. You can try building them by hand (all" @@ -54,6 +57,6 @@ print " python scripts/scramble.py" print "Or individually:" for egg in e.eggs: - print " python scripts/scramble.py %s" % egg.name + print " python scripts/scramble.py %s-e %s" % ( config_arg, egg.name ) sys.exit( 1 ) sys.exit( 0 ) --- a/scripts/manage_db.py Wed Jun 08 11:52:42 2011 -0400 +++ b/scripts/manage_db.py Wed Jun 08 12:10:51 2011 -0400 @@ -21,7 +21,15 @@ config_file = 'community_wsgi.ini' repo = 'lib/galaxy/webapps/community/model/migrate' else: + # Poor man's optparse config_file = 'universe_wsgi.ini' + if '-c' in sys.argv: + pos = sys.argv.index( '-c' ) + sys.argv.pop(pos) + config_file = sys.argv.pop( pos ) + if not os.path.exists( config_file ): + print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file + sys.exit( 1 ) repo = 'lib/galaxy/model/migrate' cp = SafeConfigParser() --- a/scripts/scramble.py Wed Jun 08 11:52:42 2011 -0400 +++ b/scripts/scramble.py Wed Jun 08 12:10:51 2011 -0400 @@ -1,11 +1,14 @@ -""" -usage: scramble.py [egg_name] - With no arguments, scrambles all eggs necessary according to the - settings in universe_wsgi.ini. - egg_name - Scramble only this egg (as defined in eggs.ini) or 'all' - for all eggs (even those not required by your settings). -""" import os, sys, logging +from optparse import OptionParser + +parser = OptionParser() +parser.add_option( '-c', '--config', dest='config', help='Path to Galaxy config file (universe_wsgi.ini)', default='universe_wsgi.ini' ) +parser.add_option( '-e', '--egg-name', dest='egg_name', help='Egg name (as defined in eggs.ini) to fetch, or "all" for all eggs, even those not needed by your configuration' ) +( options, args ) = parser.parse_args() + +if not os.path.exists( options.config ): + print "Config file does not exist (see 'python %s --help'): %s" % ( sys.argv[0], options.config ) + sys.exit( 1 ) root = logging.getLogger() root.setLevel( 10 ) @@ -16,22 +19,25 @@ from galaxy.eggs.scramble import ScrambleCrate, ScrambleFailure, EggNotFetchable -c = ScrambleCrate() +c = ScrambleCrate( options.config ) try: - if len( sys.argv ) == 1: + if not options.egg_name: eggs = c.scramble() - elif sys.argv[1] == 'all': + elif options.egg_name == 'all': c.scramble( all=True ) else: # Scramble a specific egg - name = sys.argv[1] + name = options.egg_name try: egg = c[name] except: print "error: %s not in eggs.ini" % name sys.exit( 1 ) for dependency in egg.dependencies: + config_arg = '' + if options.config != 'universe_wsgi.ini': + config_arg = '-c %s' % options.config print "Checking %s dependency: %s" % ( egg.name, dependency ) try: c[dependency].require() @@ -39,7 +45,7 @@ degg = e.eggs[0] print "%s build dependency %s %s couldn't be downloaded" % ( egg.name, degg.name, degg.version ) print "automatically. You can try building it by hand with:" - print " python scripts/scramble.py %s" % degg.name + print " python scripts/scramble.py %s-e %s" % ( config_agr, degg.name ) sys.exit( 1 ) egg.scramble() sys.exit( 0 ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Unicode fixes and refactoring.
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6005fbf6fc4d/ changeset: 6005fbf6fc4d user: jgoecks date: 2011-06-08 17:32:55 summary: Unicode fixes and refactoring. affected #: 3 files (231 bytes) --- a/lib/galaxy/tools/search/__init__.py Wed Jun 08 11:15:42 2011 -0400 +++ b/lib/galaxy/tools/search/__init__.py Wed Jun 08 11:32:55 2011 -0400 @@ -1,4 +1,5 @@ from galaxy.eggs import require +from galaxy.web.framework.helpers import to_unicode # Whoosh is compatible with Python 2.5+ Try to import Whoosh and set flag to indicate whether tool search is enabled. try: require( "Whoosh" ) @@ -35,12 +36,6 @@ writer = self.index.writer() ## TODO: would also be nice to search section headers. for id, tool in self.toolbox.tools_by_id.iteritems(): - def to_unicode( a_basestr ): - if type( a_basestr ) is str: - return unicode( a_basestr, 'utf-8' ) - else: - return a_basestr - writer.add_document( id=id, title=to_unicode(tool.name), description=to_unicode(tool.description), help=to_unicode(tool.help) ) writer.commit() --- a/lib/galaxy/web/controllers/root.py Wed Jun 08 11:15:42 2011 -0400 +++ b/lib/galaxy/web/controllers/root.py Wed Jun 08 11:32:55 2011 -0400 @@ -8,6 +8,7 @@ from galaxy.util.sanitize_html import sanitize_html from galaxy.model.orm import * from galaxy.model.item_attrs import UsesAnnotations +from galaxy.web.framework.helpers import to_unicode log = logging.getLogger( __name__ ) @@ -329,7 +330,7 @@ trans.sa_session.flush() if trans.app.config.set_metadata_externally: trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming = { 'input1':data }, overwrite = False ) #overwrite is False as per existing behavior - return trans.show_ok_message( "Changed the type of dataset '%s' to %s" % ( data.name, params.datatype ), refresh_frames=['history'] ) + return trans.show_ok_message( "Changed the type of dataset '%s' to %s" % ( to_unicode( data.name ), params.datatype ), refresh_frames=['history'] ) else: return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( data.extension, params.datatype ) ) elif params.save: --- a/templates/dataset/copy_view.mako Wed Jun 08 11:15:42 2011 -0400 +++ b/templates/dataset/copy_view.mako Wed Jun 08 11:32:55 2011 -0400 @@ -66,7 +66,7 @@ %><div class="form-row"><input type="checkbox" name="source_dataset_ids" id="dataset_${encoded_id}" value="${encoded_id}"${checked}/> - <label for="dataset_${encoded_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${data.name}</label> + <label for="dataset_${encoded_id}" style="display: inline;font-weight:normal;"> ${data.hid}: ${h.to_unicode(data.name)}</label></div> %endfor %else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: afgane: Do not display non-functional buttons for editing tags/annotations on history Show Structure page
by Bitbucket 08 Jun '11

08 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5b5f693ca5cb/ changeset: 5b5f693ca5cb user: afgane date: 2011-06-08 17:15:42 summary: Do not display non-functional buttons for editing tags/annotations on history Show Structure page affected #: 2 files (106 bytes) --- a/templates/history/display_structured.mako Tue Jun 07 14:53:53 2011 -0400 +++ b/templates/history/display_structured.mako Wed Jun 08 11:15:42 2011 -0400 @@ -91,7 +91,7 @@ </%def><%def name="render_item_hda( hda, children )"> - ${render_dataset( hda, hda.hid )} + ${render_dataset( hda, hda.hid, display_structured=True )} </%def><%def name="render_item_job( job, children )"> --- a/templates/root/history_common.mako Tue Jun 07 14:53:53 2011 -0400 +++ b/templates/root/history_common.mako Wed Jun 08 11:15:42 2011 -0400 @@ -1,6 +1,6 @@ <% _=n_ %> ## Render the dataset `data` as history item, using `hid` as the displayed id -<%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True )"> +<%def name="render_dataset( data, hid, show_deleted_on_refresh = False, for_editing = True, display_structured = False )"><% dataset_id = trans.security.encode_id( data.id ) from galaxy.datatypes.metadata import FileParameter @@ -171,10 +171,12 @@ new-url="${h.url_for( controller='tracks', action='index', dataset_id=dataset_id, default_dbkey=data.dbkey)}" title="Visualize in Trackster"></a> %endif %if trans.user: - <div style="float: right"> - <a href="${h.url_for( controller='tag', action='retag', item_class=data.__class__.__name__, item_id=dataset_id )}" target="galaxy_main" title="Edit dataset tags" class="icon-button tags tooltip"></a> - <a href="${h.url_for( controller='dataset', action='annotate', id=dataset_id )}" target="galaxy_main" title="Edit dataset annotation" class="icon-button annotate tooltip"></a> - </div> + %if not display_structured: + <div style="float: right"> + <a href="${h.url_for( controller='tag', action='retag', item_class=data.__class__.__name__, item_id=dataset_id )}" target="galaxy_main" title="Edit dataset tags" class="icon-button tags tooltip"></a> + <a href="${h.url_for( controller='dataset', action='annotate', id=dataset_id )}" target="galaxy_main" title="Edit dataset annotation" class="icon-button annotate tooltip"></a> + </div> + %endif <div style="clear: both"></div><div class="tag-area" style="display: none"><strong>Tags:</strong> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Revert change set 2b4d50205705, adding a [missing] comment so all meta data items will always be displayed on the ldda_info page.
by Bitbucket 07 Jun '11

07 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/515151397bc5/ changeset: 515151397bc5 user: greg date: 2011-06-07 20:53:53 summary: Revert change set 2b4d50205705, adding a [missing] comment so all meta data items will always be displayed on the ldda_info page. affected #: 1 file (12 bytes) --- a/templates/library/common/ldda_info.mako Tue Jun 07 14:36:46 2011 -0400 +++ b/templates/library/common/ldda_info.mako Tue Jun 07 14:53:53 2011 -0400 @@ -135,23 +135,22 @@ <div class="form-row"><div>${ldda.blurb}</div></div> + ## We want to display all metadata item here, whether marked visible or not since they are all pretty useful %for name, spec in ldda.metadata.spec.items(): - %if spec.visible: - <div class="form-row"> - <label>${spec.desc.replace( ' (click box & select)', '' )}:</label> - <% - metadata_val = ldda.metadata.get( name ) - if isinstance( metadata_val, trans.model.MetadataFile ): - metadata_val = metadata_val.file_name - elif isinstance( metadata_val, list ): - # Make sure list items are strings - metadata_val = [ str( item ) for item in metadata_val ] - metadata_val = ', '.join( metadata_val ) - %> - ${metadata_val} - <div style="clear: both"></div> - </div> - %endif + <div class="form-row"> + <label>${spec.desc.replace( ' (click box & select)', '' )}:</label> + <% + metadata_val = ldda.metadata.get( name ) + if isinstance( metadata_val, trans.model.MetadataFile ): + metadata_val = metadata_val.file_name + elif isinstance( metadata_val, list ): + # Make sure list items are strings + metadata_val = [ str( item ) for item in metadata_val ] + metadata_val = ', '.join( metadata_val ) + %> + ${metadata_val} + <div style="clear: both"></div> + </div> %endfor %if ldda.peek != "no peek": <div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: richard_burhans: allow lines starting with arbitrary characters to be excluded from the peek
by Bitbucket 07 Jun '11

07 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/bcc9c7aa5569/ changeset: bcc9c7aa5569 user: richard_burhans date: 2011-06-07 20:36:46 summary: allow lines starting with arbitrary characters to be excluded from the peek affected #: 1 file (243 bytes) --- a/lib/galaxy/datatypes/data.py Tue Jun 07 14:31:58 2011 -0400 +++ b/lib/galaxy/datatypes/data.py Tue Jun 07 14:36:46 2011 -0400 @@ -417,13 +417,13 @@ if line and not line.startswith( '#' ): data_lines += 1 return data_lines - def set_peek( self, dataset, line_count=None, is_multi_byte=False ): + def set_peek( self, dataset, line_count=None, is_multi_byte=False, skipchars=[] ): """ Set the peek. This method is used by various subclasses of Text. """ if not dataset.dataset.purged: # The file must exist on disk for the get_file_peek() method - dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte, skipchars=skipchars ) if line_count is None: # See if line_count is stored in the metadata if dataset.metadata.data_lines: @@ -461,7 +461,7 @@ path, name = os.path.split(__file__) full_path = os.path.join( path, 'test', fname ) return full_path -def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5 ): +def get_file_peek( file_name, is_multi_byte=False, WIDTH=256, LINE_COUNT=5, skipchars=[] ): """ Returns the first LINE_COUNT lines wrapped to WIDTH @@ -489,8 +489,14 @@ data_checked = True if file_type in [ 'gzipped', 'binary' ]: break - lines.append( line ) - count += 1 + skip_line = False + for skipchar in skipchars: + if line.startswith( skipchar ): + skip_line = True + break + if not skip_line: + lines.append( line ) + count += 1 temp.close() if file_type in [ 'gzipped', 'binary' ]: text = "%s file" % file_type Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 07 Jun '11

07 Jun '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dc97d0a852cb/ changeset: dc97d0a852cb user: jgoecks date: 2011-06-07 20:31:35 summary: Rename and reorder Cuffdiff outputs for clarity. affected #: 1 file (172 bytes) --- a/tools/ngs_rna/cuffdiff_wrapper.xml Tue Jun 07 11:32:11 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Tue Jun 07 14:31:35 2011 -0400 @@ -132,17 +132,17 @@ </inputs><outputs> - <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: isoform expression"/> - <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene expression"/> - <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups expression"/> - <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS Expression FPKM Tracking"/> - <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: isoform FPKM tracking"/> + <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing differential expression testing"/> + <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters differential expression testing"/> + <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS overloading diffential expression testing"/> + <data format="tabular" name="cds_exp_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM differential expression testing"/> + <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking"/> + <data format="tabular" name="tss_groups_exp" label="${tool.name} on ${on_string}: TSS groups differential expression testing"/> + <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" /> + <data format="tabular" name="genes_exp" label="${tool.name} on ${on_string}: gene differential expression testing"/><data format="tabular" name="genes_fpkm_tracking" label="${tool.name} on ${on_string}: gene FPKM tracking"/> - <data format="tabular" name="tss_groups_fpkm_tracking" label="${tool.name} on ${on_string}: TSS groups FPKM tracking" /> - <data format="tabular" name="cds_fpkm_tracking" label="${tool.name} on ${on_string}: CDS FPKM tracking"/> - <data format="tabular" name="splicing_diff" label="${tool.name} on ${on_string}: splicing diff"/> - <data format="tabular" name="promoters_diff" label="${tool.name} on ${on_string}: promoters diff"/> - <data format="tabular" name="cds_diff" label="${tool.name} on ${on_string}: CDS diff"/> + <data format="tabular" name="isoforms_exp" label="${tool.name} on ${on_string}: transcript differential expression testing"/> + <data format="tabular" name="isoforms_fpkm_tracking" label="${tool.name} on ${on_string}: transcript FPKM tracking"/></outputs><tests> @@ -164,17 +164,17 @@ Line diffs are needed because cuffdiff does not produce deterministic output. TODO: can we find datasets that lead to deterministic behavior? --> - <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/> - <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/> - <output name="tss_groups_exp" file="cuffdiff_out3.txt"/> - <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> - <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/> - <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/> - <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/> - <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/><output name="splicing_diff" file="cuffdiff_out9.txt"/><output name="promoters_diff" file="cuffdiff_out10.txt"/><output name="cds_diff" file="cuffdiff_out11.txt"/> + <output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/> + <output name="cds_fpkm_tracking" file="cuffdiff_out8.txt"/> + <output name="tss_groups_exp" file="cuffdiff_out3.txt"/> + <output name="tss_groups_fpkm_tracking" file="cuffdiff_out7.txt"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="200"/> + <output name="genes_fpkm_tracking" file="cuffdiff_out6.txt" lines_diff="200"/> + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="200"/> + <output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="200"/></test></tests> http://bitbucket.org/galaxy/galaxy-central/changeset/801a4a2a5921/ changeset: 801a4a2a5921 user: jgoecks date: 2011-06-07 20:31:58 summary: Merge. affected #: 1 file (105 bytes) --- a/templates/library/common/ldda_info.mako Tue Jun 07 14:31:35 2011 -0400 +++ b/templates/library/common/ldda_info.mako Tue Jun 07 14:31:58 2011 -0400 @@ -136,20 +136,22 @@ <div>${ldda.blurb}</div></div> %for name, spec in ldda.metadata.spec.items(): - <div class="form-row"> - <label>${spec.desc.replace( ' (click box & select)', '' )}:</label> - <% - metadata_val = ldda.metadata.get( name ) - if isinstance( metadata_val, trans.model.MetadataFile ): - metadata_val = metadata_val.file_name - elif isinstance( metadata_val, list ): - # Make sure list items are strings - metadata_val = [ str( item ) for item in metadata_val ] - metadata_val = ', '.join( metadata_val ) - %> - ${metadata_val} - <div style="clear: both"></div> - </div> + %if spec.visible: + <div class="form-row"> + <label>${spec.desc.replace( ' (click box & select)', '' )}:</label> + <% + metadata_val = ldda.metadata.get( name ) + if isinstance( metadata_val, trans.model.MetadataFile ): + metadata_val = metadata_val.file_name + elif isinstance( metadata_val, list ): + # Make sure list items are strings + metadata_val = [ str( item ) for item in metadata_val ] + metadata_val = ', '.join( metadata_val ) + %> + ${metadata_val} + <div style="clear: both"></div> + </div> + %endif %endfor %if ldda.peek != "no peek": <div class="form-row"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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