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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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commit/galaxy-central: richard_burhans: don't show metadata items that are not visible
by Bitbucket 07 Jun '11

07 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2b4d50205705/ changeset: 2b4d50205705 user: richard_burhans date: 2011-06-07 20:30:52 summary: don't show metadata items that are not visible affected #: 1 file (105 bytes) --- a/templates/library/common/ldda_info.mako Tue Jun 07 11:32:11 2011 -0400 +++ b/templates/library/common/ldda_info.mako Tue Jun 07 14:30:52 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. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Commit versions of tools from the last_gen tool shed in order of oldest -> newest in the next-gen tool shed. Fixes issue # 578.
by Bitbucket 07 Jun '11

07 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/063ac2ef7a5e/ changeset: 063ac2ef7a5e branches: user: greg date: 2011-06-07 17:32:11 summary: Commit versions of tools from the last_gen tool shed in order of oldest -> newest in the next-gen tool shed. Fixes issue # 578. affected #: 1 file (0 bytes) --- a/scripts/tool_shed/migrate_tools_to_repositories.py Tue Jun 07 11:06:50 2011 -0400 +++ b/scripts/tool_shed/migrate_tools_to_repositories.py Tue Jun 07 11:32:11 2011 -0400 @@ -59,12 +59,12 @@ this_item = item while item.newer_version: if item.newer_version.state in valid_states: - versions.insert( 0, item.newer_version ) + versions.append( item.newer_version ) item = item.newer_version item = this_item while item.older_version: if item.older_version[ 0 ].state in valid_states: - versions.append( item.older_version[ 0 ] ) + versions.insert( 0, item.older_version[ 0 ] ) item = item.older_version[ 0 ] return versions 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: Add the ability to download repository files in tar.gz, tar.bz2 or zip format from the tool shed.
by Bitbucket 07 Jun '11

07 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1119959f40cc/ changeset: 1119959f40cc branches: user: greg date: 2011-06-07 17:06:50 summary: Add the ability to download repository files in tar.gz, tar.bz2 or zip format from the tool shed. affected #: 8 files (4.6 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Tue Jun 07 10:46:52 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Tue Jun 07 11:06:50 2011 -0400 @@ -611,6 +611,23 @@ rra=rra, message=message, status=status ) + @web.expose + def download( self, trans, repository_id, file_type, **kwd ): + # Download an archive of the repository files compressed as zip, gz or bz2. + params = util.Params( kwd ) + repository = get_repository( trans, repository_id ) + # Allow hgweb to handle the download. This requires the tool shed + # server account's .hgrc file to include the following setting: + # [web] + # allow_archive = bz2, gz, zip + if file_type == 'zip': + file_type_str = 'tip.zip' + elif file_type == 'bz2': + file_type_str = 'tip.tar.bz2' + elif file_type == 'gz': + file_type_str = 'tip.tar.gz' + download_url = '/repos/%s/%s/archive/%s' % ( repository.user.username, repository.name, file_type_str ) + return trans.response.send_redirect( download_url ) @web.json def open_folder( self, trans, repository_id, key ): # TODO: The tool shed includes a repository source file browser, which currently depends upon --- a/lib/galaxy/webapps/community/controllers/upload.py Tue Jun 07 10:46:52 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Tue Jun 07 11:06:50 2011 -0400 @@ -119,11 +119,12 @@ repo.dirstate.add( file_path ) files_to_commit.append( file_path ) else: - # We're uploading files to a repository with existing - # contents, so clone the repository to a temporary location. - tmp_dir, cloned_repo_dir = self.__handle_hg_clone( trans, repository, upload_point, uploaded_file, file_data, repo_dir, current_working_dir, istar, tar=tar ) + # Clone the repository to a temporary location. + tmp_dir, cloned_repo_dir = self.__hg_clone( trans, repository, repo_dir, current_working_dir ) + # Move the uploaded files to the upload_point within the cloned repository. + self.__move_to_upload_point( upload_point, uploaded_file, file_data, cloned_repo_dir, istar, tar ) # Commit and push the changes from the cloned repo to the master repo. - self.__handle_hg_push( trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ) + self.__hg_push( trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ) if ok: if files_to_commit: repo.dirstate.write() @@ -147,7 +148,7 @@ commit_message=commit_message, message=message, status=status ) - def __handle_hg_clone( self, trans, repository, upload_point, uploaded_file, file_data, repo_dir, current_working_dir, istar, tar=None ): + def __hg_clone( self, trans, repository, repo_dir, current_working_dir ): tmp_dir = tempfile.mkdtemp() tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) if not os.path.exists( tmp_archive_dir ): @@ -158,20 +159,8 @@ os.system( cmd ) os.chdir( current_working_dir ) cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) - if upload_point is not None: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) - else: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) - if istar: - # Extract the uploaded tarball to the load_point within the cloned repository hierarchy - tar.extractall( path=full_path ) - tar.close() - uploaded_file.close() - else: - # Move the uploaded file to the load_point within the cloned repository hierarchy - shutil.move( uploaded_file.name, full_path ) return tmp_dir, cloned_repo_dir - def __handle_hg_push( self, trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ): + def __hg_push( self, trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ): # We want these change sets to be associated with the owner of the repository, so we'll # set the HGUSER environment variable accordingly. os.environ[ 'HGUSER' ] = trans.user.username @@ -198,6 +187,19 @@ action='browse_repository', message=message, id=trans.security.encode_id( repository.id ) ) ) + def __move_to_upload_point( self, upload_point, uploaded_file, file_data, cloned_repo_dir, istar, tar ): + if upload_point is not None: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) + else: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) + if istar: + # Extract the uploaded tarball to the load_point within the cloned repository hierarchy + tar.extractall( path=full_path ) + tar.close() + uploaded_file.close() + else: + # Move the uploaded file to the load_point within the cloned repository hierarchy + shutil.move( uploaded_file.name, full_path ) def __check_archive( self, archive ): for member in archive.getmembers(): # Allow regular files and directories only --- a/templates/webapps/community/repository/browse_repository.mako Tue Jun 07 10:46:52 2011 -0400 +++ b/templates/webapps/community/repository/browse_repository.mako Tue Jun 07 11:06:50 2011 -0400 @@ -79,6 +79,9 @@ %if can_rate: <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> %endif + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div> %endif </ul> --- a/templates/webapps/community/repository/manage_repository.mako Tue Jun 07 10:46:52 2011 -0400 +++ b/templates/webapps/community/repository/manage_repository.mako Tue Jun 07 11:06:50 2011 -0400 @@ -76,6 +76,9 @@ %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse repository</a> %endif + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div> %endif </ul> --- a/templates/webapps/community/repository/rate_repository.mako Tue Jun 07 10:46:52 2011 -0400 +++ b/templates/webapps/community/repository/rate_repository.mako Tue Jun 07 11:06:50 2011 -0400 @@ -81,6 +81,9 @@ %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse repository</a> %endif + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div> %endif </ul> --- a/templates/webapps/community/repository/view_changelog.mako Tue Jun 07 10:46:52 2011 -0400 +++ b/templates/webapps/community/repository/view_changelog.mako Tue Jun 07 11:06:50 2011 -0400 @@ -50,6 +50,9 @@ %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse repository</a> %endif + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div></ul> --- a/templates/webapps/community/repository/view_changeset.mako Tue Jun 07 10:46:52 2011 -0400 +++ b/templates/webapps/community/repository/view_changeset.mako Tue Jun 07 11:06:50 2011 -0400 @@ -54,6 +54,9 @@ %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse repository</a> %endif + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div></ul> --- a/templates/webapps/community/repository/view_repository.mako Tue Jun 07 10:46:52 2011 -0400 +++ b/templates/webapps/community/repository/view_repository.mako Tue Jun 07 11:06:50 2011 -0400 @@ -76,6 +76,9 @@ %if can_browse_contents: <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">Browse repository</a> %endif + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), file_type='zip' )}">Download as a zip file</a></div> %endif </ul> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for Select All / Unselect All functionality when more than one set of checkboxes is present on a page.
by Bitbucket 07 Jun '11

07 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9d268e6d85f3/ changeset: 9d268e6d85f3 branches: user: dan date: 2011-06-07 16:46:52 summary: Fix for Select All / Unselect All functionality when more than one set of checkboxes is present on a page. affected #: 1 file (2 bytes) --- a/templates/tool_form.mako Tue Jun 07 09:04:55 2011 -0400 +++ b/templates/tool_form.mako Tue Jun 07 10:46:52 2011 -0400 @@ -51,7 +51,7 @@ }); function checkUncheckAll( name, check ) { - $("input[name=" + name + "][type='checkbox']").attr('checked', !!check); + $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check); } // Inserts the Select All / Unselect All buttons for checkboxes Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for incorrect variable name reuse ('roles'), occurring when importing multiple datasets from a history into a library.
by Bitbucket 07 Jun '11

07 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/eeb9fdfcbe00/ changeset: eeb9fdfcbe00 branches: user: dan date: 2011-06-07 15:04:55 summary: Fix for incorrect variable name reuse ('roles'), occurring when importing multiple datasets from a history into a library. affected #: 1 file (40 bytes) --- a/lib/galaxy/web/controllers/library_common.py Mon Jun 06 16:17:09 2011 -0400 +++ b/lib/galaxy/web/controllers/library_common.py Tue Jun 07 09:04:55 2011 -0400 @@ -1221,7 +1221,7 @@ # it exists, then we need to apply the LIBRARY_MANAGE permission to the library dataset. dataset_manage_permissions_action = trans.app.security_agent.get_action( 'DATASET_MANAGE_PERMISSIONS' ).action flush_needed = False - for action, roles in dataset_permissions_dict.items(): + for action, dataset_permissions_roles in dataset_permissions_dict.items(): if isinstance( action, Action ): action = action.action if action == dataset_manage_permissions_action: @@ -1229,7 +1229,7 @@ action = trans.app.security_agent.get_action( 'LIBRARY_MANAGE' ).action # Allow the permissions inherited from the folder to over-ride the same permissions on the dataset. if action not in current_library_dataset_actions: - for ldp in [ trans.model.LibraryDatasetPermissions( action, ldda.library_dataset, role ) for role in roles ]: + for ldp in [ trans.model.LibraryDatasetPermissions( action, ldda.library_dataset, role ) for role in dataset_permissions_roles ]: trans.sa_session.add( ldp ) flush_needed = True if flush_needed: 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: Fix GFF3 reader bug.
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1f9173561795/ changeset: 1f9173561795 branches: user: jgoecks date: 2011-06-06 22:17:09 summary: Fix GFF3 reader bug. affected #: 1 file (10 bytes) --- a/lib/galaxy/datatypes/util/gff_util.py Mon Jun 06 15:45:16 2011 -0400 +++ b/lib/galaxy/datatypes/util/gff_util.py Mon Jun 06 16:17:09 2011 -0400 @@ -217,7 +217,7 @@ # GFF3 test: parent_id = interval.attributes.get( 'Parent', None ) cur_id = interval.attributes.get( 'ID', None ) - if feature_id and parent_id != feature_parent_id and feature_id != cur_id: + if ( cur_id and cur_id != feature_id ) or ( parent_id and parent_id != feature_id ): break # GTF test: gene_id = interval.attributes.get( 'gene_id', None ) 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: Code cleanup for uploading files to a repo in the tool shed.
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e0de7ec40a80/ changeset: e0de7ec40a80 branches: user: greg date: 2011-06-06 21:45:16 summary: Code cleanup for uploading files to a repo in the tool shed. affected #: 3 files (8.8 KB) --- a/lib/galaxy/webapps/community/controllers/repository.py Mon Jun 06 15:30:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Mon Jun 06 15:45:16 2011 -0400 @@ -16,9 +16,12 @@ # Characters that must be html escaped MAPPED_CHARS = { '>' :'>', - '<' :'<' } + '<' :'<', + '"' : '"', + '&' : '&', + '\'' : ''' } MAX_CONTENT_SIZE = 32768 -VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;" ) +VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) class CategoryListGrid( grids.Grid ): @@ -673,7 +676,7 @@ for i, line in enumerate( open( file_path ) ): to_html = '%s%s' % ( to_html, self.to_html_str( line ) ) if len( to_html ) > MAX_CONTENT_SIZE: - large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %d\n' % MAX_CONTENT_SIZE + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) to_html = '%s%s' % ( to_html, self.to_html_str( large_str ) ) break return to_html @@ -706,9 +709,9 @@ translated.append( ' ' ) elif c == '\t': translated.append( '    ' ) - elif c in [ '\r\n', '\n' ]: + elif c == '\n': translated.append( '<br/>' ) - else: + elif c not in [ '\r' ]: translated.append( 'X' ) return ''.join( translated ) def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ): --- a/lib/galaxy/webapps/community/controllers/upload.py Mon Jun 06 15:30:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/upload.py Mon Jun 06 15:45:16 2011 -0400 @@ -60,12 +60,9 @@ elif file_data not in ( '', None ): uploaded_file = file_data.file if uploaded_file: - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we update without passing the -r null flag (see below). When - # we're uploading more files, we have to clean out the repo root directory - # so we can move them into it. We need to eliminate all this when we figure - # out how to browse the repository files. + # Our current support for browsing repo contents requires a copy of the + # repository files in the repo root directory. To produce these copies, + # we update without passing the "-r null" flag. os.chdir( repo_dir ) os.system( 'hg update -r null > /dev/null 2>&1' ) os.chdir( current_working_dir ) @@ -76,16 +73,16 @@ tar = tarfile.open( uploaded_file.name ) istar = True except tarfile.ReadError, e: + tar = None istar = False - if istar: - ok, message = self.__check_archive( tar ) - if ok: - if repository.is_new: + if repository.is_new: + if istar: + # We have an archive ( a tarball ) + ok, message = self.__check_archive( tar ) + if ok: tar.extractall( path=repo_dir ) tar.close() uploaded_file.close() - # TODO: The following will only work on new, empty repos, - # need to also handle repos with existing contents for root, dirs, files in os.walk( repo_dir, topdown=False ): # Don't visit .hg directories and don't include hgrc files in commit. if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: @@ -109,78 +106,9 @@ repo.dirstate.add( file_path ) files_to_commit.append( file_path ) else: - # The repo already contains the file, so we need to make sure the file being - # uploaded is different from the file in the repo. This is a temporary brute- - # force method. - # Make a clone of the repository in a temporary location - tmp_dir = tempfile.mkdtemp() - tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) - if not os.path.exists( tmp_archive_dir ): - os.makedirs( tmp_archive_dir ) - cmd = "hg clone %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( tmp_archive_dir ) - os.system( cmd ) - os.chdir( current_working_dir ) - cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) - if upload_point is not None: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) - else: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) - # Extract the uploaded tarball to the load_point within the cloned repository hierarchy - tar.extractall( path=full_path ) tar.close() - uploaded_file.close() - # We want these change sets to be associated with the owner of the repository, so we'll - # set the HGUSER environment variable accordingly. - os.environ[ 'HGUSER' ] = trans.user.username - # Add the file to the cloned repository. If it's already tracked, this should do nothing. - os.chdir( cloned_repo_dir ) - os.system( 'hg add > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - os.chdir( cloned_repo_dir ) - # Commit the change set to the cloned repository - os.system( "hg commit -m '%s' > /dev/null 2>&1" % commit_message ) - os.chdir( current_working_dir ) - # Push the change set to the master repository - cmd = "hg push %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( cloned_repo_dir ) - os.system( cmd ) - # Change the current working directory to the original - os.chdir( current_working_dir ) - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. - os.chdir( repo_dir ) - os.system( 'hg update > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - # Remove tmp directory - shutil.rmtree( tmp_dir ) - message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename - trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repository', - message=message, - id=trans.security.encode_id( repository.id ) ) ) - - else: - tar.close() - else: - """ - # TODO: This segment uses the mercurial api (and works), but we need the - # api section below to be functional in order for this segment to be used. - # In the meantime, we use the repository.is_new check below... - repo_contains = file_path in [ i for i in ctx.manifest() ] - if not repo_contains: - repo.dirstate.add( file_path ) - files_to_commit.append( file_path ) - """ - if repository.is_new: - # We're uploading a single file + # We have a single file if upload_point is not None: full_path = os.path.abspath( os.path.join( upload_point, file_data.filename ) ) file_path = os.path.join( upload_point, file_data.filename ) @@ -190,98 +118,18 @@ shutil.move( uploaded_file.name, full_path ) repo.dirstate.add( file_path ) files_to_commit.append( file_path ) - else: - """ - # TODO: This segment attempts to use the mercurial api, but is not functional. - # Until we get it working, we're using the brute force method below it. - fctx = None - for changeset in repo.changelog: - ctx = repo.changectx( changeset ) - if file_path not in ctx.files(): - continue - fctx = ctx[ file_path ] - break - # We now have the parent version of the upload file. - if fctx: - data = fctx.data() - # TODO: obviously very bad way of comparing files... - file_path_data = open( full_path ).read() - different = data != file_path_data - if different: - # TODO: how do you insert a new version of an existing file using the mercurial api??? - # the follwoin gis not correct! - #repo.dirstate.normallookup( file_path ) - #files_to_commit.append( file_path ) - pass - """ - # The repo already contains the file, so we need to make sure the file being - # uploaded is different from the file in the repo. This is a temporary brute- - # force method. - # Make a clone of the repository in a temporary location - tmp_dir = tempfile.mkdtemp() - tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) - if not os.path.exists( tmp_archive_dir ): - os.makedirs( tmp_archive_dir ) - cmd = "hg clone %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( tmp_archive_dir ) - os.system( cmd ) - os.chdir( current_working_dir ) - cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) - if upload_point is not None: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) - else: - full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) - # Move the uploaded file to the load_point within the cloned repository hierarchy - shutil.move( uploaded_file.name, full_path ) - # We want these change sets to be associated with the owner of the repository, so we'll - # set the HGUSER environment variable accordingly. - os.environ[ 'HGUSER' ] = trans.user.username - # Add the file to the cloned repository. If it's already tracked, this should do nothing. - os.chdir( cloned_repo_dir ) - os.system( 'hg add > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - os.chdir( cloned_repo_dir ) - # Commit the change set to the cloned repository - os.system( "hg commit -m '%s' > /dev/null 2>&1" % commit_message ) - os.chdir( current_working_dir ) - # Push the change set to the master repository - cmd = "hg push %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) - os.chdir( cloned_repo_dir ) - os.system( cmd ) - os.chdir( current_working_dir ) - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. - os.chdir( repo_dir ) - os.system( 'hg update > /dev/null 2>&1' ) - os.chdir( current_working_dir ) - # Remove tmp directory - shutil.rmtree( tmp_dir ) - message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename - trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repository', - message=message, - id=trans.security.encode_id( repository.id ) ) ) + else: + # We're uploading files to a repository with existing + # contents, so clone the repository to a temporary location. + tmp_dir, cloned_repo_dir = self.__handle_hg_clone( trans, repository, upload_point, uploaded_file, file_data, repo_dir, current_working_dir, istar, tar=tar ) + # Commit and push the changes from the cloned repo to the master repo. + self.__handle_hg_push( trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ) if ok: if files_to_commit: repo.dirstate.write() repo.commit( text=commit_message ) - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. os.chdir( repo_dir ) os.system( 'hg update > /dev/null 2>&1' ) - #os.system( 'hg update -r null' ) os.chdir( current_working_dir ) message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename trans.response.send_redirect( web.url_for( controller='repository', @@ -290,17 +138,8 @@ id=trans.security.encode_id( repository.id ) ) ) else: status = 'error' - # Since we extracted the archive into repo_dir, a copy of the archive's - # files remains there. The following will remove them. It would be - # more ideal if we could use the mercurial api to do this, but I haven't - # yet discovered a way to pass the -r null flag to repo.update(). - # TODO: our current support for browsing repo contents requires a copy - # of the repository files in the repo root directory. To produce these - # copies, we'll update without passing the -r null flag. When we figure - # out how to browse the repository files, uncomment the -r flag below. os.chdir( repo_dir ) os.system( 'hg update > /dev/null 2>&1' ) - #os.system( 'hg update -r null' ) os.chdir( current_working_dir ) selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/repository/upload.mako', @@ -308,6 +147,57 @@ commit_message=commit_message, message=message, status=status ) + def __handle_hg_clone( self, trans, repository, upload_point, uploaded_file, file_data, repo_dir, current_working_dir, istar, tar=None ): + tmp_dir = tempfile.mkdtemp() + tmp_archive_dir = os.path.join( tmp_dir, 'tmp_archive_dir' ) + if not os.path.exists( tmp_archive_dir ): + os.makedirs( tmp_archive_dir ) + # Make a clone of the repository in a temporary location + cmd = "hg clone %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) + os.chdir( tmp_archive_dir ) + os.system( cmd ) + os.chdir( current_working_dir ) + cloned_repo_dir = os.path.join( tmp_archive_dir, 'repo_%d' % repository.id ) + if upload_point is not None: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, upload_point, file_data.filename ) ) + else: + full_path = os.path.abspath( os.path.join( cloned_repo_dir, file_data.filename ) ) + if istar: + # Extract the uploaded tarball to the load_point within the cloned repository hierarchy + tar.extractall( path=full_path ) + tar.close() + uploaded_file.close() + else: + # Move the uploaded file to the load_point within the cloned repository hierarchy + shutil.move( uploaded_file.name, full_path ) + return tmp_dir, cloned_repo_dir + def __handle_hg_push( self, trans, repository, file_data, commit_message, current_working_dir, cloned_repo_dir, repo_dir, tmp_dir ): + # We want these change sets to be associated with the owner of the repository, so we'll + # set the HGUSER environment variable accordingly. + os.environ[ 'HGUSER' ] = trans.user.username + # Add the file to the cloned repository. If it's already tracked, this should do nothing. + os.chdir( cloned_repo_dir ) + os.system( 'hg add > /dev/null 2>&1' ) + os.chdir( current_working_dir ) + os.chdir( cloned_repo_dir ) + # Commit the change set to the cloned repository + os.system( "hg commit -m '%s' > /dev/null 2>&1" % commit_message ) + os.chdir( current_working_dir ) + # Push the change set to the master repository + cmd = "hg push %s > /dev/null 2>&1" % os.path.abspath( repo_dir ) + os.chdir( cloned_repo_dir ) + os.system( cmd ) + os.chdir( current_working_dir ) + # Make a copy of the updated repository files for browsing. + os.chdir( repo_dir ) + os.system( 'hg update > /dev/null 2>&1' ) + os.chdir( current_working_dir ) + shutil.rmtree( tmp_dir ) + message = "The file '%s' has been successfully uploaded to the repository." % file_data.filename + trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repository', + message=message, + id=trans.security.encode_id( repository.id ) ) ) def __check_archive( self, archive ): for member in archive.getmembers(): # Allow regular files and directories only --- a/templates/webapps/community/upload/upload.mako Mon Jun 06 15:30:02 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,242 +0,0 @@ -<%namespace file="/message.mako" import="render_msg" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/community/base_panels.mako' - else: - return '/base.mako' -%> - -<%inherit file="${inherit(context)}"/> - -<% - if selected_upload_type == 'tool': - title = 'Upload a tool archive' - type_label = 'tool' - elif selected_upload_type == 'toolsuite': - title = 'Upload a tool suite archive' - type_label = 'tool suite' -%> - -<%def name="title()"> - ${title} -</%def> - -<%def name="javascripts()"> - ${parent.javascripts()} - <script type="text/javascript"> - $( function() { - $( "select[refresh_on_change='true']").change( function() { - $( "#upload_form" ).submit(); - }); - }); - </script> -</%def> - -<h2>${title}</h2> - -%if message: - ${render_msg( message, status )} -%endif - -<div class="toolForm"> - <div class="toolFormTitle">${title}</div> - <div class="toolFormBody"> - ## TODO: nginx - <form id="upload_form" name="upload_form" action="${h.url_for( controller='tool_upload', action='upload' )}" enctype="multipart/form-data" method="post"> - %if replace_id is not None: - <input type='hidden' name="replace_id" value="${replace_id}"/> - %endif - <div class="form-row"> - <label>Upload Type</label> - <div class="form-row-input"> - ${upload_type_select_list.get_html()} - </div> - <div class="toolParamHelp" style="clear: both;"> - Need help creating a ${type_label} archive? See details below. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>File:</label> - <div class="form-row-input"><input type="file" name="file_data"/></div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Category</label> - <div class="form-row-input"> - <select name="category_id" multiple> - %for category in categories: - %if category.id in selected_categories: - <option value="${trans.security.encode_id( category.id )}" selected>${category.name}</option> - %else: - <option value="${trans.security.encode_id( category.id )}">${category.name}</option> - %endif - %endfor - </select> - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>URL:</label> - <div class="form-row-input"><input type="text" name="url" style="width: 100%;"/></div> - <div class="toolParamHelp" style="clear: both;"> - Instead of uploading directly from your computer, you may instruct Galaxy to download the file from a Web or FTP address. - </div> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <input type="submit" class="primary-button" name="upload_button" value="Upload"> - </div> - </form> - </div> -</div> -<p/> -<div class="toolFormTitle">Creating an archive containing a tool or a suite of tools</div> -<p> - A tool or tool suite archive is a tar-format file (bzipped or gzipped tar are valid) - containing all the files necessary to load the tool(s) into a Galaxy instance. -</p> -%if selected_upload_type == 'toolsuite': - <h3>Tool Suite Archive</h3> - <p> - A tools suite must include a file named <code>suite_config.xml</code> which provides information about the id, name, - version and description of the tool suite, as well as the id, name, version and description of each tool - in the suite. Here is an example <code>suite_config.xml</code> file. - </p> - <p> -<pre> - <suite id="lastz_toolsuite" name="Suite of Lastz tools" version="1.0.0"> - <description>This suite contains all of my Lastz tools for Galaxy</description> - <tool id="lastz_wrapper_2" name="Lastz" version="1.1.0"> - <description> map short reads against reference sequence</description> - </tool> - <tool id="lastz_paired_reads_wrapper" name="Lastz paired reads" version="1.0.0"> - <description> map short paired reads against reference sequence</description> - </tool> - </suite> -</pre> - </p> - </p> - <p> - New versions of the suite can be uploaded, replacing an older version of the suite, but the version attribute - of the <suite> tag must be altered the same way that the version attribute of a single tool config must be altered - if uploading a new version of a tool. - </p> - <p> - The id, name and version attributes of each <tool> tag in the <code>suite_config.xml</code> file must exactly match the same - attributes in each associated tool config in the archive or you will not be allowed to upload the archive. - </p> - <p> - In addition to the <code>suite_config.xml</code> file, the archive must include all - <a href="http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax" target="_blank">tool config files</a>, - executables, functional test data (if your tool config includes functional tests) and other files needed for each - of the tools in your suite to function within Galaxy. See the information about single tool archives below for - additional hints to enable ease-of-use when others download your suite of tools. - </p> - <p> - For example, to package the above Lastz suite of tools: -<pre> - user@host:~% tar jcvf ~/Desktop/galaxy_lastz_toolsuite.tar.bz2 lastzsuite - lastzsuite/ - lastzsuite/README - lastzsuite/suite_config.xml - lastzsuite/lastz_paired_reads_wrapper.py - lastzsuite/lastz_paired_reads_wrapper.xml - lastzsuite/lastz_wrapper.py - lastzsuite/lastz_wrapper.xml - lastzsuite/lastz-distrib-1.02.00/ - lastzsuite/lastz-distrib-1.02.00/src/ - lastzsuite/lastz-distrib-1.02.00/src/Makefile - lastzsuite/lastz-distrib-1.02.00/src/version.mak - lastzsuite/lastz-distrib-1.02.00/src/lastz.c - lastzsuite/lastz-distrib-1.02.00/src/lastz.h - ... -</pre> - ~/Desktop/galaxy_lastz_tool.tar.bz2 is now ready to be uploaded. - </p> -%endif -<h3>Single Tool Archive</h3> -<p> - A single tool archive must include a - <a href="http://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax" target="_blank">tool config file</a> - and will probably also include a tool script. If any steps are necessary to install your tool beyond the basic - instructions below, include a README file to provide details. If the tool (or parts of it) are written in C, - the source code can be included (or put links to the source in the README). Do not include pre-compiled binaries - without source since Galaxy is run on a wide variety of platforms. Also, if you are only wrapping or providing a - Galaxy config for a tool that is not your own, be sure the license allows for redistribution before including any - part of that tool in the archive. -</p> -<p> - There are no requirements about the directory structure inside the archive, but for ease of use it's generally - a good idea to put everything inside a sub-directory, instead of directly at the top level. -</p> -<p> - For example, to package the Lastz tool's config file, Galaxy wrapper, and the C source: -<pre> - user@host:~% tar jcvf ~/Desktop/galaxy_lastz_tool.tar.bz2 lastz - lastz/ - lastz/README - lastz/lastz_wrapper.py - lastz/lastz_wrapper.xml - lastz/lastz-distrib-1.02.00/ - lastz/lastz-distrib-1.02.00/src/ - lastz/lastz-distrib-1.02.00/src/Makefile - lastz/lastz-distrib-1.02.00/src/version.mak - lastz/lastz-distrib-1.02.00/src/lastz.c - lastz/lastz-distrib-1.02.00/src/lastz.h - ... -</pre> - ~/Desktop/galaxy_lastz_tool.tar.bz2 is now ready to be uploaded. -</p> -<h3>Editing Information, Categories, and Submitting For Approval</h3> -<p> - Simply uploading a tool to the Galaxy too shed will not allow other users to find and download your tool. It will - need to be approved by an administrator before it appears in the tool list. -</p> -<p> - After your archive has successfully uploaded, you will be redirected to the Edit Tool page. Provide a detailed - description of what the tool does - this will be used by administrators to understand the tool before approving it - for display on the site. Once approved, this information will be displayed to users who view your tool. In addition, - the site administrators will have configured a number of categories with which you can associate your tool to make it - easy to find by users looking to solve specific problems. Associate as many categories as are relevant to your tool. - You may change the description and associated categories as often as you'd like until you click the "<strong>Submit for - approval</strong>" button. Once submitted, the tool will be approved or rejected by an administrator. If the tool is - rejected, you will see information about why it was rejected, and you can make appropriate changes to the archive and - re-submit it for approval. When it is approved, your archive will be visible to everyone. At that point, the description - and associated categories can only be changed by an administrator. -</p> -<p> - When the tool has been approved or rejected, you may upload a new version by browsing to the tool's "View Tool" page, - clicking the "Tool actions" menu in the upper right corner of the page, and selecting "Upload a new version" from the - menu. -</p> -<hr/> -<h3>Downloading and Installing Tools</h3> -<p> - A tool's download link will send you the tool archive. Once downloaded, unpack the tool on your local Galaxy instance's server: -<pre> - user@host:~% tar xvf galaxy_lastz_tool.tar - ... - user@host:~% tar zxvf galaxy_lastz_tool.tar.gz - ... - user@host:~% tar jxvf galaxy_lastz_tool.tar.bz2 - ... -</pre> - If the archive includes a README file, consult it for installation instructions. If not, follow these basic steps: - <ol> - <li>Create a directory under <code>galaxy_dist/tools/</code> to house downloaded tool(s).</li> - <li>In the new directory, place the XML and any script file(s) which were contained in the archive.</li> - <li> - If the tool includes binaries, you'll need to copy them to a directory on your <code>$PATH</code>. If the tool depends on - C binaries but does not come with them (only source), you'll need to compile the source first. - </li> - <li>Add the tool to <code>galaxy_dist/tool_conf.xml</code>.</li> - <li>Restart your Galaxy server process.</li> - </ol> -</p> -<p> - In the near future, we plan to implement a more direct method to install tools via the Galaxy administrator user interface instead - of placing files on the filesystem and manually managing the <code>tool_conf.xml</code> file. -</p> 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: kanwei: Improve docs for Grouping tool. Closes #576
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d34c83a1301e/ changeset: d34c83a1301e branches: user: kanwei date: 2011-06-06 21:30:02 summary: Improve docs for Grouping tool. Closes #576 affected #: 1 file (364 bytes) --- a/tools/stats/grouping.xml Mon Jun 06 13:17:18 2011 -0400 +++ b/tools/stats/grouping.xml Mon Jun 06 15:30:02 2011 -0400 @@ -88,7 +88,11 @@ **Syntax** -This tool allows you to group the input dataset by a particular column and perform aggregate functions: Mean, Median, Mode, Sum, Max, Min, Count, Randomly pick, and Concatenate on any column. +This tool allows you to group the input dataset by a particular column and perform aggregate functions: Mean, Median, Mode, Sum, Max, Min, Count, Concatenate, and Randomly pick on any column(s). + +The Concatenate function will take, for each group, each item in the specified column and build a comma delimited list. Concatenate Unique will do the same but will build a list of unique items with no repetition. + +Count and Count Unique are equivalent to Concatenate and Concatenate Unique, but will only count the number of items and will return an integer. - If multiple modes are present, all are reported. 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: kanwei: trackster: Fix VCF data provider
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/346ad6f83be1/ changeset: 346ad6f83be1 branches: user: kanwei date: 2011-06-06 19:17:18 summary: trackster: Fix VCF data provider affected #: 1 file (62 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Mon Jun 06 11:17:31 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Mon Jun 06 13:17:18 2011 -0400 @@ -607,12 +607,12 @@ out.write( line ) out.close() -class VcfDataProvider( TracksDataProvider ): +class VcfDataProvider( TabixDataProvider ): """ VCF data provider for the Galaxy track browser. Payload format: - [ uid (offset), start, end, ID, reference base(s), alternate base(s), quality score] + [ uid (offset), start, end, ID, reference base(s), alternate base(s), quality score ] """ col_name_data_attr_mapping = { 'Qual' : { 'index': 6 , 'name' : 'Qual' } } @@ -622,21 +622,20 @@ count = 0 message = None - reader = galaxy_utils.sequence.vcf.Reader( iterator ) - for line in reader: + for line in iterator: if count >= MAX_VALS: message = ERROR_MAX_VALS % "features" break count += 1 feature = line.split() - payload = [ hash(line), vcf_line.pos-1, vcf_line.pos, \ + payload = [ hash(line), int(feature[1])-1, int(feature[1]), # ID: - feature[2], \ + feature[2], # reference base(s): - feature[3], \ + feature[3], # alternative base(s) - feature[4], \ + feature[4], # phred quality score int( feature[5] )] rval.append(payload) 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: Trackster: use error padding only when needed by placing error messages in div above tiles rather than in tiles.
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b7c4c1bcf03d/ changeset: b7c4c1bcf03d branches: user: jgoecks date: 2011-06-06 17:17:31 summary: Trackster: use error padding only when needed by placing error messages in div above tiles rather than in tiles. affected #: 3 files (966 bytes) --- a/static/june_2007_style/blue/trackster.css Mon Jun 06 11:12:04 2011 -0400 +++ b/static/june_2007_style/blue/trackster.css Mon Jun 06 11:17:31 2011 -0400 @@ -26,6 +26,7 @@ .label-track .track-content{background:white;} .track-tile{background:white;} .track-tile canvas{position:relative;z-index:100;border:solid white;border-width:2px 0px 0px 0px;} +.tile-message {border-bottom:solid 1px red;text-align:center;color:red;background-color:white;} .track.error .track-content{background-color:#ECB4AF;background-image:none;} .track.nodata .track-content{background-color:#eee;background-image:none;} .track.pending .track-content{background-color:white;background-image:none;} --- a/static/june_2007_style/trackster.css.tmpl Mon Jun 06 11:12:04 2011 -0400 +++ b/static/june_2007_style/trackster.css.tmpl Mon Jun 06 11:17:31 2011 -0400 @@ -167,6 +167,13 @@ border-width: 2px 0px 0px 0px; } +.tile-message { + border-bottom: solid 1px red; + text-align: center; + color: red; + background-color: white; +} + .track.error .track-content { background-color: #ECB4AF; background-image: none; --- a/static/scripts/trackster.js Mon Jun 06 11:12:04 2011 -0400 +++ b/static/scripts/trackster.js Mon Jun 06 11:17:31 2011 -0400 @@ -172,7 +172,7 @@ // height of individual features within tracks. Feature height, then, should always be less // than track height. CHAR_HEIGHT_PX = 9, // FIXME: font size may not be static - ERROR_PADDING = 10, // Padding at the top of tracks for error messages + ERROR_PADDING = 15, // Padding at the top of tracks for error messages SUMMARY_TREE_TOP_PADDING = CHAR_HEIGHT_PX + 2, // Maximum number of rows un a slotted track MAX_FEATURE_DEPTH = 100, @@ -1507,8 +1507,9 @@ this.max_val = max_val; }; -var FeatureTrackTile = function(index, resolution, canvas) { +var FeatureTrackTile = function(index, resolution, canvas, message) { Tile.call(this, index, resolution, canvas); + this.message = message; }; /** @@ -1993,6 +1994,27 @@ } } + // + // If some tiles have messages, set padding of tiles without messages + // so features and rows align. + // + var messages_to_show = false; + for (var tile_index = 0; tile_index < drawn_tiles.length; tile_index++) { + if (drawn_tiles[tile_index].message) { + messages_to_show = true; + break; + } + } + if (messages_to_show) { + for (var tile_index = 0; tile_index < drawn_tiles.length; tile_index++) { + tile = drawn_tiles[tile_index]; + if (!tile.message) { + // Need to align with other tile(s) that have message(s). + tile.canvas.css("padding-top", ERROR_PADDING); + } + } + } + // Store initial canvas in case we need to use it for overview /* This is completely broken, just saves the first tile it sees regardless of if it should be the overview @@ -2620,8 +2642,7 @@ // Create painter, and canvas of sufficient size to contain all features // HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument var painter = new (this.painter)( filtered, tile_low, tile_high, this.prefs, mode, ref_seq ); - // FIXME: ERROR_PADDING is an ugly gap most of the time - var required_height = painter.get_required_height( slots_required ) + ERROR_PADDING; + var required_height = painter.get_required_height(slots_required); var canvas = this.view.canvas_manager.new_canvas(); canvas.width = width + left_offset; @@ -2634,31 +2655,26 @@ ctx.textAlign = "right"; this.container_div.find(".yaxislabel").remove(); - // If there is a message, draw it on canvas so that it moves around with canvas, and make the border red - // to indicate region where message is applicable + if (result.data) { + // Set example feature. This is needed so that track can update its UI based on feature attributes. + this.example_feature = (result.data.length ? result.data[0] : undefined); + + // Draw features. + painter.draw(ctx, width, required_height, slots); + } + + // If tile has a message, create container div with both a message div and the canvas. if (result.message) { - ctx.fillStyle = "red"; - ctx.textAlign = "left"; - var old_base = ctx.textBaseline; - ctx.textBaseline = "top"; - ctx.fillRect(left_offset, 0, canvas.width - left_offset, 1); - ctx.fillText(result.message, left_offset, 2); - ctx.textBaseline = old_base; - - // If there's no data, return. - if (!result.data) { - return new Tile(tile_index, resolution, canvas, required_height); - } + var container_div = $("<div/>"); + var message_div = $("<div/>").addClass("tile-message").text(result.message).css('width', canvas.width); + message_div.css({position: 'absolute', top: 0}); + $(canvas).css("top", 15); + container_div.append(message_div); + container_div.append(canvas); + canvas = container_div; } - // Set example feature. This is needed so that track can update its UI based on feature attributes. - this.example_feature = (result.data.length ? result.data[0] : undefined); - - // Draw features - ctx.translate(left_offset, ERROR_PADDING); - painter.draw(ctx, width, required_height, slots); - - return new FeatureTrackTile(tile_index, resolution, canvas); + return new FeatureTrackTile(tile_index, resolution, canvas, result.message); } }); 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: kanwei: Restore error icon for color-blindness; needs further testing
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/e4ef73d003f6/ changeset: e4ef73d003f6 branches: user: kanwei date: 2011-06-06 17:12:04 summary: Restore error icon for color-blindness; needs further testing affected #: 1 file (41 bytes) --- a/templates/root/history_common.mako Mon Jun 06 09:37:06 2011 -0400 +++ b/templates/root/history_common.mako Mon Jun 06 11:12:04 2011 -0400 @@ -69,6 +69,7 @@ <a class="icon-button delete tooltip" title="Delete" href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${data.id}"></a> %endif </div> + <span class="state-icon"></span><span class="historyItemTitle">${hid}: ${data.display_name()}</span></div> 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: Disable update check in cuffdiff wrapper.
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1ab3dfb5d929/ changeset: 1ab3dfb5d929 branches: user: jgoecks date: 2011-06-06 15:37:06 summary: Disable update check in cuffdiff wrapper. affected #: 1 file (36 bytes) --- a/tools/ngs_rna/cuffdiff_wrapper.py Mon Jun 06 09:08:59 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.py Mon Jun 06 09:37:06 2011 -0400 @@ -101,7 +101,7 @@ try: tmp = tempfile.NamedTemporaryFile().name tmp_stdout = open( tmp, 'wb' ) - proc = subprocess.Popen( args='cuffdiff 2>&1', shell=True, stdout=tmp_stdout ) + proc = subprocess.Popen( args='cuffdiff --no-update-check 2>&1', shell=True, stdout=tmp_stdout ) tmp_stdout.close() returncode = proc.wait() stdout = None @@ -135,7 +135,7 @@ # Build command. # Base; always use quiet mode to avoid problems with storing log output. - cmd = "cuffdiff -q" + cmd = "cuffdiff --no-update-check -q" # Add options. if options.inner_dist_std_dev: 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: Removed unspecified build validators from Cufflinks/compare/diff tools as these cause trouble when running tools on custom genomes.
by Bitbucket 06 Jun '11

06 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/058a5d7a4f84/ changeset: 058a5d7a4f84 branches: user: jgoecks date: 2011-06-06 15:08:59 summary: Removed unspecified build validators from Cufflinks/compare/diff tools as these cause trouble when running tools on custom genomes. affected #: 3 files (205 bytes) --- a/tools/ngs_rna/cuffcompare_wrapper.xml Fri Jun 03 17:00:20 2011 -0400 +++ b/tools/ngs_rna/cuffcompare_wrapper.xml Mon Jun 06 09:08:59 2011 -0400 @@ -33,9 +33,7 @@ #end for </command><inputs> - <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""> - <validator type="unspecified_build" /> - </param> + <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/><repeat name="input_files" title="Additional GTF Input Files"><param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""><validator type="unspecified_build" /> --- a/tools/ngs_rna/cuffdiff_wrapper.xml Fri Jun 03 17:00:20 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Mon Jun 06 09:08:59 2011 -0400 @@ -67,9 +67,7 @@ </command><inputs> - <param format="gtf" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."> - <validator type="unspecified_build" /> - </param> + <param format="gtf" name="gtf_input" type="data" label="Transcripts" help="A transcript GTF file produced by cufflinks, cuffcompare, or other source."/><conditional name="group_analysis"><param name="do_groups" type="select" label="Perform replicate analysis" help="Perform cuffdiff with replicates in each group."><option value="No">No</option> --- a/tools/ngs_rna/cufflinks_wrapper.xml Fri Jun 03 17:00:20 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon Jun 06 09:08:59 2011 -0400 @@ -41,9 +41,7 @@ #end if </command><inputs> - <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""> - <validator type="unspecified_build" /> - </param> + <param format="sam,bam" name="input" type="data" label="SAM or BAM file of aligned RNA-Seq reads" help=""/><param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help=""/><param name="min_isoform_fraction" type="float" value="0.05" min="0" max="1" label="Min Isoform Fraction" help=""/><param name="pre_mrna_fraction" type="float" value="0.05" min="0" max="1" label="Pre MRNA Fraction" help=""/> 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: kanwei: Remove error icon in front of red datasets, since red clearly denotes fail already
by Bitbucket 03 Jun '11

03 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/aa55fc70f31e/ changeset: aa55fc70f31e branches: user: kanwei date: 2011-06-03 23:00:20 summary: Remove error icon in front of red datasets, since red clearly denotes fail already affected #: 1 file (36 bytes) --- a/templates/root/history_common.mako Fri Jun 03 16:46:14 2011 -0400 +++ b/templates/root/history_common.mako Fri Jun 03 17:00:20 2011 -0400 @@ -29,7 +29,6 @@ </div> %endif - ## Header row for history items (name, state, action buttons) <div style="overflow: hidden;" class="historyItemTitleBar"><div class="historyItemButtons"> @@ -70,7 +69,6 @@ <a class="icon-button delete tooltip" title="Delete" href="${h.url_for( action='delete', id=data.id, show_deleted_on_refresh=show_deleted_on_refresh )}" id="historyItemDeleter-${data.id}"></a> %endif </div> - <span class="state-icon"></span><span class="historyItemTitle">${hid}: ${data.display_name()}</span></div> @@ -192,7 +190,7 @@ ## icons. <div style="clear: both"></div> %endif - <div style="clear: both"></div> + <div style="clear: both"></div> %for display_app in data.datatype.get_display_types(): <% target_frame, display_links = data.datatype.get_display_links( data, display_app, app, request.base ) %> %if len( display_links ) > 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: greg: Clean up displaying content in the tool shed.
by Bitbucket 03 Jun '11

03 Jun '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/7c5dcf903d84/ changeset: 7c5dcf903d84 branches: user: greg date: 2011-06-03 22:46:14 summary: Clean up displaying content in the tool shed. affected #: 3 files (625 bytes) --- a/lib/galaxy/datatypes/checkers.py Fri Jun 03 16:22:02 2011 -0400 +++ b/lib/galaxy/datatypes/checkers.py Fri Jun 03 16:46:14 2011 -0400 @@ -25,9 +25,13 @@ temp.close() return False -def check_binary( file_path ): +def check_binary( name, file_path=True ): + # Handles files if file_path is True or text if file_path is False is_binary = False - temp = open( file_path, "U" ) + if file_path: + temp = open( name, "U" ) + else: + temp = name chars_read = 0 for chars in temp: for char in chars: @@ -39,7 +43,8 @@ break if chars_read > 100: break - temp.close() + if file_path: + temp.close() return is_binary def check_gzip( file_path ): @@ -94,6 +99,10 @@ return True return False +def is_bz2( file_path ): + is_bz2, is_valid = check_bz2( file_path ) + return is_bz2 + def is_gzip( file_path ): is_gzipped, is_valid = check_gzip( file_path ) - return is_gzipped and is_valid + return is_gzipped --- a/lib/galaxy/webapps/community/controllers/repository.py Fri Jun 03 16:22:02 2011 -0400 +++ b/lib/galaxy/webapps/community/controllers/repository.py Fri Jun 03 16:46:14 2011 -0400 @@ -3,6 +3,7 @@ from datetime import * from galaxy import util +from galaxy.datatypes.checkers import * from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.webapps.community.model import directory_hash_id @@ -13,12 +14,12 @@ log = logging.getLogger( __name__ ) -VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) -# Characters that are valid -VALID_CHARS = set( string.letters + string.digits ) # Characters that must be html escaped MAPPED_CHARS = { '>' :'>', '<' :'<' } +MAX_CONTENT_SIZE = 32768 +VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;" ) +VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) class CategoryListGrid( grids.Grid ): # TODO rename this class to be categoryListGrid when we eliminate all the tools stuff. @@ -173,17 +174,6 @@ repository_list_grid = RepositoryListGrid() category_list_grid = CategoryListGrid() - # TODO: These translations are costly, so figure out a better way... - def from_html_escaped( self, text ): - """Restores sanitized text""" - for key, value in MAPPED_CHARS.items(): - text = text.replace( value, key ) - return text - def to_html_escape_code( self, text ): - """Restricts the characters that are allowed in a text""" - for key, value in MAPPED_CHARS.items(): - text = text.replace( key, value ) - return text @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) @@ -567,23 +557,9 @@ ctx_parent = ctx.parents()[0] modified, added, removed, deleted, unknown, ignored, clean = repo.status( node1=ctx_parent.node(), node2=ctx.node() ) anchors = modified + added + removed + deleted + unknown + ignored + clean - def is_binary( chars ): - is_binary = False - chars_read = 0 - for char in chars: - chars_read += 1 - if ord( char ) > 128: - is_binary = True - break - return is_binary diffs = [] for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ): - if not util.is_multi_byte( diff ) and not is_binary( diff ): - # TODO: is there a better way? - diffs.append( self.to_html_escape_code( diff ) ) - else: - fixed_diff = diff.split( '\n' )[0] + '\nFile contains non-ascii characters that cannot be displayed\n' - diffs.append( fixed_diff ) + diffs.append( self.to_html_escaped( diff ) ) return trans.fill_template( '/webapps/community/repository/view_changeset.mako', repository=repository, ctx=ctx, @@ -681,28 +657,60 @@ message=message ) ) @web.json def get_file_contents( self, trans, file_path ): - def print_ticks( d ): - # pexpect timeout method - pass # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - if os.stat( file_path ).st_size > 32768: - return 'File size larger than maximum viewing size of 32 kb' - cmd = "cat %s" % file_path - # Handle the authentication message if ssh keys are not set - the message is - # something like: "Are you sure you want to continue connecting (yes/no)." - output = pexpect.run( cmd, - events={ pexpect.TIMEOUT : print_ticks }, - timeout=10 ) - output = self.to_html_escape_code( output ) - return unicode( output.replace( '\r\n', '<br/>' ).replace( ' ', ' ' ) ) + if is_gzip( file_path ): + to_html = self.to_html_str( '\ngzip compressed file\n' ) + elif is_bz2( file_path ): + to_html = self.to_html_str( '\nbz2 compressed file\n' ) + elif check_zip( file_path ): + to_html = self.to_html_str( '\nzip compressed file\n' ) + elif check_binary( file_path ): + to_html = self.to_html_str( '\nBinary file\n' ) + else: + to_html = '' + for i, line in enumerate( open( file_path ) ): + to_html = '%s%s' % ( to_html, self.to_html_str( line ) ) + if len( to_html ) > MAX_CONTENT_SIZE: + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %d\n' % MAX_CONTENT_SIZE + to_html = '%s%s' % ( to_html, self.to_html_str( large_str ) ) + break + return to_html @web.expose def help( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) return trans.fill_template( '/webapps/community/repository/help.mako', message=message, status=status, **kwd ) + def to_html_escaped( self, text ): + """Translates the characters in text to html values""" + translated = [] + for c in text: + if c in [ '\r\n', '\n', ' ', '\t' ] or c in VALID_CHARS: + translated.append( c ) + elif c in MAPPED_CHARS: + translated.append( MAPPED_CHARS[ c ] ) + else: + translated.append( 'X' ) + return ''.join( translated ) + def to_html_str( self, text ): + """Translates the characters in text to sn html string""" + translated = [] + for c in text: + if c in VALID_CHARS: + translated.append( c ) + elif c in MAPPED_CHARS: + translated.append( MAPPED_CHARS[ c ] ) + elif c == ' ': + translated.append( ' ' ) + elif c == '\t': + translated.append( '    ' ) + elif c in [ '\r\n', '\n' ]: + translated.append( '<br/>' ) + else: + translated.append( 'X' ) + return ''.join( translated ) def __build_allow_push_select_field( self, trans, current_push_list, selected_value='none' ): options = [] for user in trans.sa_session.query( trans.model.User ): --- a/templates/webapps/community/repository/common.mako Fri Jun 03 16:22:02 2011 -0400 +++ b/templates/webapps/community/repository/common.mako Fri Jun 03 16:46:14 2011 -0400 @@ -42,7 +42,6 @@ document.upload_form.upload_point.value = selKeys[0]; }, onActivate: function(dtnode) { - // TODO: certainly not ideal - find a better way to display the file contents. var cell = $("#file_contents"); var selected_value; if (dtnode.data.key == 'root') { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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