October 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Filter tool dependency installation to only those that were checked when installing them from the Manage tool dependencies page for an installed tool shed repository.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ab9f5cb3acd8/ Changeset: ab9f5cb3acd8 User: greg Date: 2013-10-10 20:11:09 Summary: Filter tool dependency installation to only those that were checked when installing them from the Manage tool dependencies page for an installed tool shed repository. Affected #: 3 files diff -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -701,11 +701,11 @@ installed_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans, tool_shed_repository=tool_shed_repository, name='inst_td_ids', - uninstalled=False ) + uninstalled_only=False ) uninstalled_tool_dependencies_select_field = suc.build_tool_dependencies_select_field( trans, tool_shed_repository=tool_shed_repository, name='uninstalled_tool_dependency_ids', - uninstalled=True ) + uninstalled_only=True ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository_tool_dependencies.mako', repository=tool_shed_repository, installed_tool_dependencies_select_field=installed_tool_dependencies_select_field, diff -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -429,6 +429,10 @@ will be installed in: ~/<app.config.tool_dependency_dir>/<package_name>/<package_version>/<repo_owner>/<repo_name>/<repo_installed_changeset_revision> """ + # The received list of tool_dependencies are the database records for those dependencies defined in the received tool_dependencies_config + # that should be installed. This allows for filtering out dependencies that have not been checked for installation on the 'Manage tool + # dependencies' page for an installed tool shed repository. + attr_tups_of_dependencies_for_install = [ ( td.name, td.version, td.type ) for td in tool_dependencies ] sa_session = app.model.context.current installed_tool_dependencies = [] # Parse the tool_dependencies.xml config. @@ -439,19 +443,43 @@ fabric_version_checked = False for elem in root: if elem.tag == 'package': - # Only install the tool_dependency if it is not already installed. + # Only install the tool_dependency if it is not already installed and it is associated with a database record in the received + # tool_dependencies. package_name = elem.get( 'name', None ) package_version = elem.get( 'version', None ) if package_name and package_version: - for tool_dependency in tool_dependencies: - if tool_dependency.name==package_name and tool_dependency.version==package_version: - break - if tool_dependency.can_install: + attr_tup = ( package_name, package_version, 'package' ) + try: + index = attr_tups_of_dependencies_for_install.index( attr_tup ) + except Exception, e: + index = None + if index is not None: + tool_dependency = tool_dependencies[ index ] + if tool_dependency.can_install: + try: + tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies ) + except Exception, e: + error_message = "Error installing tool dependency %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) ) + log.exception( error_message ) + if tool_dependency: + tool_dependency.status = app.model.ToolDependency.installation_status.ERROR + tool_dependency.error_message = error_message + sa_session.add( tool_dependency ) + sa_session.flush() + if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, + app.model.ToolDependency.installation_status.ERROR ]: + installed_tool_dependencies.append( tool_dependency ) + elif elem.tag == 'set_environment': + env_var_name = env_var_elem.get( 'name', None ) + if env_var_name: + # Tool dependencies of type "set_environmnet" always have the version attribute set to None. + attr_tup = ( env_var_name, None, 'set_environment' ) + if attr_tup in attr_tups_of_dependencies_for_install: try: - tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies ) + tool_dependency = set_environment( app, elem, tool_shed_repository ) except Exception, e: - error_message = "Error installing tool dependency %s version %s: %s" % ( str( package_name ), str( package_version ), str( e ) ) - log.exception( error_message ) + error_message = "Error setting environment for tool dependency: %s" % str( e ) + log.debug( error_message ) if tool_dependency: tool_dependency.status = app.model.ToolDependency.installation_status.ERROR tool_dependency.error_message = error_message @@ -460,20 +488,6 @@ if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) - elif elem.tag == 'set_environment': - try: - tool_dependency = set_environment( app, elem, tool_shed_repository ) - except Exception, e: - error_message = "Error setting environment for tool dependency: %s" % str( e ) - log.debug( error_message ) - if tool_dependency: - tool_dependency.status = app.model.ToolDependency.installation_status.ERROR - tool_dependency.error_message = error_message - sa_session.add( tool_dependency ) - sa_session.flush() - if tool_dependency and tool_dependency.status in [ app.model.ToolDependency.installation_status.INSTALLED, - app.model.ToolDependency.installation_status.ERROR ]: - installed_tool_dependencies.append( tool_dependency ) return installed_tool_dependencies def repository_dependency_needed_only_for_compiling_tool_dependency( repository, repository_dependency ): diff -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 -r ab9f5cb3acd8dcfe30fc5b92fc4a792c9815c877 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -144,13 +144,18 @@ repositories_select_field.add_option( option_label, option_value ) return repositories_select_field -def build_tool_dependencies_select_field( trans, tool_shed_repository, name, multiple=True, display='checkboxes', uninstalled=False ): +def build_tool_dependencies_select_field( trans, tool_shed_repository, name, multiple=True, display='checkboxes', uninstalled_only=False ): """Method called from Galaxy to generate the current list of tool dependency ids for an installed tool shed repository.""" tool_dependencies_select_field = SelectField( name=name, multiple=multiple, display=display ) for tool_dependency in tool_shed_repository.tool_dependencies: - if uninstalled and tool_dependency.status not in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED, - trans.model.ToolDependency.installation_status.UNINSTALLED ]: - continue + if uninstalled_only: + if tool_dependency.status not in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED, + trans.model.ToolDependency.installation_status.UNINSTALLED ]: + continue + else: + if tool_dependency.status in [ trans.model.ToolDependency.installation_status.NEVER_INSTALLED, + trans.model.ToolDependency.installation_status.UNINSTALLED ]: + continue option_label = '%s version %s' % ( str( tool_dependency.name ), str( tool_dependency.version ) ) option_value = trans.security.encode_id( tool_dependency.id ) tool_dependencies_select_field.add_option( option_label, option_value ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Update of the new upload front end, fix data viewer
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/450c04224d6c/ Changeset: 450c04224d6c User: guerler Date: 2013-10-10 19:34:36 Summary: Update of the new upload front end, fix data viewer Affected #: 6 files diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -11,13 +11,16 @@ // base element elMain: '#everything', - // defaults inputs + // defaults options optionsDefault: { title : "galaxy-modal", body : "", backdrop : true }, + // options + options : {}, + // initialize initialize : function(options) { // create @@ -31,16 +34,18 @@ this.initialize(options); // fix height - this.$body.css('max-height', $(document).height() / 2); + var maxHeight = $(document).height() / 2; + this.$body.css('max-height', maxHeight); - // set max-height so that modal does not exceed window size and is in middle of page. - /*/ TODO: this could perhaps be handled better using CSS. - this.$body.css( "max-height", - $(window).height() - - this.$footer.outerHeight() - - this.$header.outerHeight() - - parseInt( this.$dialog.css( "padding-top" ), 10 ) - - parseInt( this.$dialog.css( "padding-bottom" ), 10 ));*/ + // fix height if available + if (this.options.height < maxHeight) + this.$body.css('height', this.options.height); + else + this.$body.css('height', maxHeight); + + // remove scroll bar + if (this.options.height) + this.$body.css('overflow', 'hidden'); // show if (this.visible) @@ -64,18 +69,18 @@ // create create: function(options) { // configure options - options = _.defaults(options, this.optionsDefault); + this.options = _.defaults(options, this.optionsDefault); // check for progress bar request - if (options.body == 'progress') - options.body = $('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'); + if (this.options.body == 'progress') + this.options.body = $('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'); // remove former element if (this.$el) this.$el.remove(); // create new element - this.setElement(this.template(options.title)); + this.setElement(this.template(this.options.title)); // link elements this.$body = (this.$el).find('.modal-body'); @@ -84,24 +89,20 @@ this.$backdrop = (this.$el).find('.modal-backdrop'); // append body - this.$body.html(options.body); - - // fix height if available - if (options.height) - this.$body.css('height', options.height); + this.$body.html(this.options.body); // fix min-width so that modal cannot shrink considerably if new content is loaded. this.$body.css('min-width', this.$body.width()); // configure background - if (!options.backdrop) + if (!this.options.backdrop) this.$backdrop.removeClass('in'); // append buttons - if (options.buttons) { + if (this.options.buttons) { // link functions var self = this; - $.each(options.buttons, function(name, value) { + $.each(this.options.buttons, function(name, value) { self.$buttons.append($('<button id="' + String(name).toLowerCase() + '"></button>').text(name).click(value)).append(" "); }); } else diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -19,15 +19,16 @@ // extension types select_extension : { - '' : 'Auto-detect', + 'auto' : 'Auto-detect', 'bed' : 'bed', 'ab1' : 'ab1' }, // states state : { - init : 'fa-icon-trash', - done : 'fa-icon-caret-down' + init : 'fa-icon-trash', + success : 'fa-icon-ok', + error : 'fa-icon-warning-sign' }, // counter @@ -94,7 +95,7 @@ var id = '#upload-' + index; // add upload item - $(this.el).append(this.template_file(id, this.select_extension)); + $(this.el).find('tbody:last').append(this.template_row(id, this.select_extension)); // scroll to bottom //$(this.el).scrollTop($(this.el).prop('scrollHeight')); @@ -106,15 +107,15 @@ it.fadeIn(); // update title - it.find('.title').html(file.name); - - // configure select field - //it.find('#extension').select2(); + it.find('#title').html(file.name); + + // update info + it.find('#size').html(this.size_to_string (file.size)); // add functionality to remove button var self = this; - it.find('.symbol').on('click', function() { self.event_remove (index) }); - + it.find('#symbol').on('click', function() { self.event_remove (index) }); + // initialize progress this.event_progress(index, file, 0); @@ -141,6 +142,10 @@ extension : it.find('#extension').val() } + // configure url + var current_history = Galaxy.currHistoryPanel.model.get('id'); + this.uploadbox.configure({url : galaxy_config.root + "api/histories/" + current_history + "/contents"}); + // return additional data to be send with file return data; }, @@ -157,8 +162,8 @@ // update progress it.find('.progress-bar').css({ width : percentage + '%' }); - // update info - it.find('.info').html(percentage + '% of ' + this.size_to_string (file.size)); + // update value + it.find('#percentage').html(percentage + '%'); }, // success @@ -184,16 +189,15 @@ var it = this.get_upload_item(index); // update progress frame - it.addClass('panel-success'); - it.removeClass('panel-default'); + it.addClass('success'); // update icon - var sy = it.find('.symbol'); + var sy = it.find('#symbol'); sy.removeClass('fa-icon-spin'); sy.removeClass('fa-icon-spinner'); // set status - sy.addClass(this.state.done); + sy.addClass(this.state.success); }, // error @@ -216,22 +220,21 @@ var it = this.get_upload_item(index); // update progress frame - it.addClass('panel-danger'); - it.removeClass('panel-default'); + it.addClass('danger'); // remove progress bar it.find('.progress').remove(); // write error message - it.find('.error').html('<strong>Failed:</strong> ' + message); + it.find('#info').html('<strong>Failed: </strong>' + message).show(); // update icon - var sy = it.find('.symbol'); + var sy = it.find('#symbol'); sy.removeClass('fa-icon-spin'); sy.removeClass('fa-icon-spinner'); // set status - sy.addClass(this.state.done); + sy.addClass(this.state.error); }, // start upload process @@ -242,27 +245,22 @@ return; // switch icons for new uploads + var items = $(this.el).find('.upload-item'); var self = this; - $(this.el).find('.symbol').each(function() + items.each(function() { - if($(this).hasClass(self.state.init)) + var symbol = $(this).find('#symbol'); + if(symbol.hasClass(self.state.init)) { - $(this).removeClass(self.state.init); - $(this).addClass('fa-icon-spinner'); - $(this).addClass('fa-icon-spin'); + symbol.removeClass(self.state.init); + symbol.addClass('fa-icon-spinner'); + symbol.addClass('fa-icon-spin'); } }); - // hide configuration - $(this.el).find('.panel-body').hide(); - // update running this.counter.running = this.counter.announce; this.update_screen(); - - // configure url - var current_history = Galaxy.currHistoryPanel.model.get('id'); - this.uploadbox.configure({url : galaxy_config.root + "api/histories/" + current_history + "/contents"}); // initiate upload procedure in plugin this.uploadbox.upload(); @@ -283,9 +281,9 @@ if (this.counter.running == 0) { // remove from screen - var panels = $(this.el).find('.panel'); - panels.fadeOut({complete: function() { panels.remove(); }}); - + var items = $(this.el).find('.upload-item'); + $(this.el).find('table').fadeOut({ complete : function() { items.remove(); }}); + // reset counter this.counter.reset(); @@ -302,18 +300,18 @@ { // get item var it = this.get_upload_item(index); - var sy = it.find('.symbol'); + var sy = it.find('#symbol'); // only remove from queue if not in processing line - if (sy.hasClass(this.state.init) || sy.hasClass(this.state.done)) + if (sy.hasClass(this.state.init) || sy.hasClass(this.state.success) || sy.hasClass(this.state.error)) { // reduce counter - if (it.hasClass('panel-default')) + if (it.hasClass('success')) + this.counter.success--; + else if (it.hasClass('danger')) + this.counter.error--; + else this.counter.announce--; - else if (it.hasClass('panel-success')) - this.counter.success--; - else if (it.hasClass('panel-danger')) - this.counter.error--; // show on screen info this.update_screen(); @@ -340,14 +338,14 @@ this.modal = new mod_modal.GalaxyModal( { title : 'Upload files from your local drive', - body : this.template('upload-box'), + body : this.template('upload-box', 'upload-info'), buttons : { 'Select' : function() {self.uploadbox.select()}, 'Upload' : function() {self.event_upload()}, 'Reset' : function() {self.event_reset()}, 'Close' : function() {self.modal.hide()} }, - height : '250px' + height : '350' }); // set element @@ -441,45 +439,61 @@ this.modal.enableButton('Select'); else this.modal.disableButton('Select'); + + // table visibility + if (this.counter.announce + this.counter.success + this.counter.error > 0) + $(this.el).find('table').show(); + else + $(this.el).find('table').hide(); }, // load html template - template: function(id) + template: function(id, idInfo) { - return '<div id="' + id + '" class="upload-box"></div><h6 id="upload-info" class="upload-info"></h6>'; + return '<div id="' + id + '" class="upload-box">' + + '<table class="table table-striped" style="display: none;">' + + '<thead>' + + '<tr>' + + '<th>Name</th>' + + '<th>Size</th>' + + '<th>Type</th>' + + '<th>Space→Tab</th>' + + '<th>Progress</th>' + + '<th></th>' + + '</tr>' + + '</thead>' + + '<tbody></tbody>' + + '</table>' + + '</div>' + + '<h6 id="' + idInfo + '" class="upload-info"></h6>'; }, - // load html template - template_file: function(id, select_extension) + template_row: function(id, select_extension) { - // start template - var tmpl = '<div id="' + id.substr(1) + '" class="panel panel-default">' + - '<div class="panel-heading">' + - '<h5 class="title"></h5>' + - '<h5 class="info"></h5>' + - '<div class="symbol ' + this.state.init + '"></div>' + - '</div>' + - '<div class="panel-body">' + - '<div class="menu">' + - 'Select file type: ' + - '<select id="extension">'; - + // construct template + var tmpl = '<tr id="' + id.substr(1) + '" class="upload-item">' + + '<td><div id="title" class="title"></div></td>' + + '<td><div id="size" class="size"></div></td>' + + '<td>' + + '<select id="extension">'; + // add file types to selection for (key in select_extension) - tmpl += '<option value="' + key + '">' + select_extension[key] + '</option>'; - - // continue template - tmpl += '</select>, ' + - '<span>Convert space to tabs: <input id="space_to_tabs" type="checkbox"></input></span>' + + tmpl += '<option value="' + key + '">' + select_extension[key] + '</option>'; + + tmpl += '</select>' + + '</td>' + + '<td><input id="space_to_tabs" type="checkbox"></input></td>' + + '<td>' + + '<div id="info" class="info">' + + '<div class="progress">' + + '<div class="progress-bar progress-bar-success"></div>' + + '<div id="percentage" class="percentage">0%</div>' + + '</div>' + '</div>' + - '</div>' + - '<div class="panel-footer">' + - '<div class="progress">' + - '<div class="progress-bar progress-bar-success"></div>' + - '</div>' + - '<h6 class="error"></h6>' + - '</div>' + - '</div>'; + '</td>' + + '<td><div id="symbol" class="symbol ' + this.state.init + '"></div></td>' + + '</tr>'; // return html string return tmpl; diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/scripts/mvc/data.js --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -183,10 +183,12 @@ var column_types = this.model.get_metadata('column_types'); if (colspan !== undefined) { $cell.attr('colspan', colspan).addClass('stringalign'); - } else if (column_types !== undefined && index < column_types.length) { - if (column_types[index] === 'str' || column_types === 'list') { - /* Left align all str columns, right align the rest */ - $cell.addClass('stringalign'); + } else if (column_types) { + if (index < column_types.length) { + if (column_types[index] === 'str' || column_types === 'list') { + /* Left align all str columns, right align the rest */ + $cell.addClass('stringalign'); + } } } return $cell; diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -20,8 +20,7 @@ success : function() {}, error : function(index, file, message) { alert(message); }, complete : function() {}, - error_browser : "Your browser does not support drag-and-drop file uploads.", - error_filesize : "This file is too large (>250MB). Please use an FTP client to upload it.", + error_filesize : "File exceeds 250MB. Please use an FTP client.", error_default : "Please make sure the file is available." } diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1125,12 +1125,14 @@ .galaxy-frame .frame .f-pin{left:6px;top:1px} .galaxy-frame .frame .f-resize{background:#fff;width:16px;height:16px;color:#2c3143;right:0px;bottom:0px;text-align:center;line-height:16px;border:0px} .upload-info{font-weight:normal;text-align:center} -.upload-box{width:100%;height:95%;max-height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:20px}.upload-box .panel{display:none}.upload-box .panel .panel-heading{position:relative;height:19px;padding:5px}.upload-box .panel .panel-heading .title{position:absolute;top:2px;font-weight:normal;text-align:left;margin:0px;max-width:300px;overflow:hidden} -.upload-box .panel .panel-heading .info{position:absolute;top:3px;font-weight:normal;right:20px;text-align:right;margin:0px} -.upload-box .panel .panel-heading .symbol{position:absolute;cursor:pointer;top:0px;right:3px} -.upload-box .panel .panel-body{position:relative;padding:5px} -.upload-box .panel .panel-footer{position:relative;height:20px;padding:0px}.upload-box .panel .panel-footer .progress{height:10px;margin:5px} -.upload-box .panel .panel-footer .error{font-weight:normal;margin:2px} +.upload-box{width:100%;height:90%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px}.upload-box .table{width:100%} +.upload-box .table th{text-align:center;white-space:nowrap} +.upload-box .table td{margin:0px;paddign:0px} +.upload-box .title{width:150px;word-wrap:break-word;font-size:11px} +.upload-box .size{white-space:nowrap} +.upload-box .info{width:130px;font-size:11px}.upload-box .info .progress{top:1px;position:relative;width:100%;padding:0px;margin:0px}.upload-box .info .progress .progress-bar{border-radius:inherit;-moz-border-radius:inherit} +.upload-box .info .progress .percentage{position:absolute;text-align:center;width:100%;color:#fff} +.upload-box .symbol{cursor:pointer} .unselectable{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none} .parent-width{-webkit-box-sizing:border-box;-moz-box-sizing:border-box;box-sizing:border-box;width:100%;*width:90%} .clear:before,.clear:after{content:" ";display:table;} diff -r 33af3a5b36df7207ec469d635779329a73117f73 -r 450c04224d6cd0f2c8c7964cedcd0eeafd98c873 static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -7,8 +7,7 @@ .upload-box { width : 100%; - height : 95%; - max-height : 95%; + height : 90%; text-align : center; overflow : scroll; font-size : @font-size-base; @@ -16,71 +15,58 @@ -moz-border-radius: @border-radius-large; border-radius : @border-radius-large; border : 1px dashed @btn-default-border; - padding : 20px; + padding : 10px; + + .table { + width : 100%; + } + + .table th { + text-align: center; + white-space: nowrap; + } + + .table td { + margin: 0px; + paddign: 0px; + } + + .title { + width: 150px; + word-wrap: break-word; + font-size : @font-size-small; + } + + .size { + white-space: nowrap; + } + + .info { + width: 130px; + font-size : @font-size-small; - .panel - { - display: none; - - .panel-heading - { + .progress { + top:1px; position: relative; - height: 19px; - padding: 5px; - - .title - { - position: absolute; - top: 2px; - font-weight: normal; - text-align: left; - margin: 0px; - max-width: 300px; - overflow: hidden; - } - - .info - { - position: absolute; - top: 3px; - font-weight: normal; - right: 20px; - text-align: right; - margin: 0px; - } - - .symbol - { - position: absolute; - cursor: pointer; - top: 0px; - right: 3px; - } - } - - .panel-body - { - position: relative; - padding: 5px; - } - - .panel-footer - { - position:relative; - height: 20px; + width: 100%; padding: 0px; + margin: 0px; - .progress - { - height: 10px; - margin: 5px; + .progress-bar { + border-radius: inherit; + -moz-border-radius: inherit; } - .error - { - font-weight: normal; - margin: 2px; + .percentage { + position: absolute; + text-align: center; + width: 100%; + color: @white; } } } + + .symbol { + cursor: pointer; + } } \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3d2ca877e2c4/ Changeset: 3d2ca877e2c4 User: natefoo Date: 2013-10-10 18:48:07 Summary: Convert DOS line endings. Affected #: 1 file diff -r 1706b14098fc7e88e9aa1c54f28857a818beec4d -r 3d2ca877e2c4d7a17c4113be333ec2431b066a7c tools/data_source/microbial_import_code.py --- a/tools/data_source/microbial_import_code.py +++ b/tools/data_source/microbial_import_code.py @@ -1,154 +1,154 @@ - -def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ): - # FIXME: this function is duplicated in the DynamicOptions class. It is used here only to - # set data.name in exec_after_process(). - microbe_info= {} - orgs = {} - - filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR - for i, line in enumerate( open( filename ) ): - line = line.rstrip( '\r\n' ) - if line and not line.startswith( '#' ): - fields = line.split( sep ) - #read each line, if not enough fields, go to next line - try: - info_type = fields.pop(0) - if info_type.upper() == "ORG": - #ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dop… - org_num = fields.pop(0) - name = fields.pop(0) - kingdom = fields.pop(0) - group = fields.pop(0) - chromosomes = fields.pop(0) - info_url = fields.pop(0) - link_site = fields.pop(0) - if org_num not in orgs: - orgs[ org_num ] = {} - orgs[ org_num ][ 'chrs' ] = {} - orgs[ org_num ][ 'name' ] = name - orgs[ org_num ][ 'kingdom' ] = kingdom - orgs[ org_num ][ 'group' ] = group - orgs[ org_num ][ 'chromosomes' ] = chromosomes - orgs[ org_num ][ 'info_url' ] = info_url - orgs[ org_num ][ 'link_site' ] = link_site - elif info_type.upper() == "CHR": - #CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1 - org_num = fields.pop(0) - chr_acc = fields.pop(0) - name = fields.pop(0) - length = fields.pop(0) - gi = fields.pop(0) - gb = fields.pop(0) - info_url = fields.pop(0) - chr = {} - chr[ 'name' ] = name - chr[ 'length' ] = length - chr[ 'gi' ] = gi - chr[ 'gb' ] = gb - chr[ 'info_url' ] = info_url - if org_num not in orgs: - orgs[ org_num ] = {} - orgs[ org_num ][ 'chrs' ] = {} - orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr - elif info_type.upper() == "DATA": - #DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed - uid = fields.pop(0) - org_num = fields.pop(0) - chr_acc = fields.pop(0) - feature = fields.pop(0) - filetype = fields.pop(0) - path = fields.pop(0) - data = {} - data[ 'filetype' ] = filetype - data[ 'path' ] = path - data[ 'feature' ] = feature - - if org_num not in orgs: - orgs[ org_num ] = {} - orgs[ org_num ][ 'chrs' ] = {} - if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]: - orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {} - orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data - else: continue - except: continue - for org_num in orgs: - org = orgs[ org_num ] - if org[ 'kingdom' ] not in microbe_info: - microbe_info[ org[ 'kingdom' ] ] = {} - if org_num not in microbe_info[ org[ 'kingdom' ] ]: - microbe_info[ org[ 'kingdom' ] ][org_num] = org - return microbe_info - -#post processing, set build for data and add additional data to history -from galaxy import datatypes, config, jobs, tools -from shutil import copyfile - -def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): - base_dataset = out_data.items()[0][1] - history = base_dataset.history - if history == None: - print "unknown history!" - return - kingdom = param_dict.get( 'kingdom', None ) - #group = param_dict.get( 'group', None ) - org = param_dict.get( 'org', None ) - - #if not (kingdom or group or org): - if not (kingdom or org): - print "Parameters are not available." + +def load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ): + # FIXME: this function is duplicated in the DynamicOptions class. It is used here only to + # set data.name in exec_after_process(). + microbe_info= {} + orgs = {} + + filename = "%s/microbial_data.loc" % GALAXY_DATA_INDEX_DIR + for i, line in enumerate( open( filename ) ): + line = line.rstrip( '\r\n' ) + if line and not line.startswith( '#' ): + fields = line.split( sep ) + #read each line, if not enough fields, go to next line + try: + info_type = fields.pop(0) + if info_type.upper() == "ORG": + #ORG 12521 Clostridium perfringens SM101 bacteria Firmicutes CP000312,CP000313,CP000314,CP000315 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=genomeprj&cmd=Retrieve&dop… + org_num = fields.pop(0) + name = fields.pop(0) + kingdom = fields.pop(0) + group = fields.pop(0) + chromosomes = fields.pop(0) + info_url = fields.pop(0) + link_site = fields.pop(0) + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + orgs[ org_num ][ 'name' ] = name + orgs[ org_num ][ 'kingdom' ] = kingdom + orgs[ org_num ][ 'group' ] = group + orgs[ org_num ][ 'chromosomes' ] = chromosomes + orgs[ org_num ][ 'info_url' ] = info_url + orgs[ org_num ][ 'link_site' ] = link_site + elif info_type.upper() == "CHR": + #CHR 12521 CP000315 Clostridium perfringens phage phiSM101, complete genome 38092 110684521 CP000315.1 + org_num = fields.pop(0) + chr_acc = fields.pop(0) + name = fields.pop(0) + length = fields.pop(0) + gi = fields.pop(0) + gb = fields.pop(0) + info_url = fields.pop(0) + chr = {} + chr[ 'name' ] = name + chr[ 'length' ] = length + chr[ 'gi' ] = gi + chr[ 'gb' ] = gb + chr[ 'info_url' ] = info_url + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + orgs[ org_num ][ 'chrs' ][ chr_acc ] = chr + elif info_type.upper() == "DATA": + #DATA 12521_12521_CDS 12521 CP000315 CDS bed /home/djb396/alignments/playground/bacteria/12521/CP000315.CDS.bed + uid = fields.pop(0) + org_num = fields.pop(0) + chr_acc = fields.pop(0) + feature = fields.pop(0) + filetype = fields.pop(0) + path = fields.pop(0) + data = {} + data[ 'filetype' ] = filetype + data[ 'path' ] = path + data[ 'feature' ] = feature + + if org_num not in orgs: + orgs[ org_num ] = {} + orgs[ org_num ][ 'chrs' ] = {} + if 'data' not in orgs[ org_num ][ 'chrs' ][ chr_acc ]: + orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ] = {} + orgs[ org_num ][ 'chrs' ][ chr_acc ][ 'data' ][ uid ] = data + else: continue + except: continue + for org_num in orgs: + org = orgs[ org_num ] + if org[ 'kingdom' ] not in microbe_info: + microbe_info[ org[ 'kingdom' ] ] = {} + if org_num not in microbe_info[ org[ 'kingdom' ] ]: + microbe_info[ org[ 'kingdom' ] ][org_num] = org + return microbe_info + +#post processing, set build for data and add additional data to history +from galaxy import datatypes, config, jobs, tools +from shutil import copyfile + +def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): + base_dataset = out_data.items()[0][1] + history = base_dataset.history + if history == None: + print "unknown history!" + return + kingdom = param_dict.get( 'kingdom', None ) + #group = param_dict.get( 'group', None ) + org = param_dict.get( 'org', None ) + + #if not (kingdom or group or org): + if not (kingdom or org): + print "Parameters are not available." #workflow passes galaxy.tools.parameters.basic.UnvalidatedValue instead of values if isinstance( kingdom, tools.parameters.basic.UnvalidatedValue ): - kingdom = kingdom.value + kingdom = kingdom.value if isinstance( org, tools.parameters.basic.UnvalidatedValue ): org = org.value - GALAXY_DATA_INDEX_DIR = app.config.tool_data_path - microbe_info = load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ) - new_stdout = "" - split_stdout = stdout.split("\n") - basic_name = "" - for line in split_stdout: - fields = line.split("\t") - if fields[0] == "#File1": - description = fields[1] - chr = fields[2] - dbkey = fields[3] - file_type = fields[4] - name, data = out_data.items()[0] - data.set_size() - basic_name = data.name - data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for " + microbe_info[kingdom][org]['name'] + ":" + chr + ")" - data.dbkey = dbkey - data.info = data.name - data = app.datatypes_registry.change_datatype( data, file_type ) - data.init_meta() - data.set_peek() - app.model.context.add( data ) - app.model.context.flush() - elif fields[0] == "#NewFile": - description = fields[1] - chr = fields[2] - dbkey = fields[3] - filepath = fields[4] - file_type = fields[5] - newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context ) #This import should become a library - newdata.set_size() - newdata.extension = file_type - newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")" - app.model.context.add( newdata ) - app.model.context.flush() - app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset ) - history.add_dataset( newdata ) - app.model.context.add( history ) - app.model.context.flush() - try: - copyfile(filepath,newdata.file_name) - newdata.info = newdata.name - newdata.state = jobs.JOB_OK - except: - newdata.info = "The requested file is missing from the system." - newdata.state = jobs.JOB_ERROR - newdata.dbkey = dbkey - newdata.init_meta() - newdata.set_peek() - app.model.context.flush() + GALAXY_DATA_INDEX_DIR = app.config.tool_data_path + microbe_info = load_microbial_data( GALAXY_DATA_INDEX_DIR, sep='\t' ) + new_stdout = "" + split_stdout = stdout.split("\n") + basic_name = "" + for line in split_stdout: + fields = line.split("\t") + if fields[0] == "#File1": + description = fields[1] + chr = fields[2] + dbkey = fields[3] + file_type = fields[4] + name, data = out_data.items()[0] + data.set_size() + basic_name = data.name + data.name = data.name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for " + microbe_info[kingdom][org]['name'] + ":" + chr + ")" + data.dbkey = dbkey + data.info = data.name + data = app.datatypes_registry.change_datatype( data, file_type ) + data.init_meta() + data.set_peek() + app.model.context.add( data ) + app.model.context.flush() + elif fields[0] == "#NewFile": + description = fields[1] + chr = fields[2] + dbkey = fields[3] + filepath = fields[4] + file_type = fields[5] + newdata = app.model.HistoryDatasetAssociation( create_dataset = True, sa_session = app.model.context ) #This import should become a library + newdata.set_size() + newdata.extension = file_type + newdata.name = basic_name + " (" + microbe_info[kingdom][org]['chrs'][chr]['data'][description]['feature'] +" for "+microbe_info[kingdom][org]['name']+":"+chr + ")" + app.model.context.add( newdata ) + app.model.context.flush() + app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset ) + history.add_dataset( newdata ) + app.model.context.add( history ) + app.model.context.flush() + try: + copyfile(filepath,newdata.file_name) + newdata.info = newdata.name + newdata.state = jobs.JOB_OK + except: + newdata.info = "The requested file is missing from the system." + newdata.state = jobs.JOB_ERROR + newdata.dbkey = dbkey + newdata.init_meta() + newdata.set_peek() + app.model.context.flush() https://bitbucket.org/galaxy/galaxy-central/commits/33af3a5b36df/ Changeset: 33af3a5b36df User: natefoo Date: 2013-10-10 18:53:10 Summary: Fix outdated usage of states in microbial dataset post-job hook. Affected #: 1 file diff -r 3d2ca877e2c4d7a17c4113be333ec2431b066a7c -r 33af3a5b36df7207ec469d635779329a73117f73 tools/data_source/microbial_import_code.py --- a/tools/data_source/microbial_import_code.py +++ b/tools/data_source/microbial_import_code.py @@ -80,7 +80,7 @@ return microbe_info #post processing, set build for data and add additional data to history -from galaxy import datatypes, config, jobs, tools +from galaxy import datatypes, config, tools from shutil import copyfile def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr): @@ -144,10 +144,10 @@ try: copyfile(filepath,newdata.file_name) newdata.info = newdata.name - newdata.state = jobs.JOB_OK + newdata.state = newdata.states.OK except: newdata.info = "The requested file is missing from the system." - newdata.state = jobs.JOB_ERROR + newdata.state = newdata.states.ERROR newdata.dbkey = dbkey newdata.init_meta() newdata.set_peek() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Backout of c78f3f687fbc. I'm sure it is fine, but @natefoo got in my head and I don't want to break anything.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1706b14098fc/ Changeset: 1706b14098fc User: jmchilton Date: 2013-10-10 18:16:20 Summary: Backout of c78f3f687fbc. I'm sure it is fine, but @natefoo got in my head and I don't want to break anything. Affected #: 5 files diff -r 0f9ac20283c65288daa887508594ae67049047d0 -r 1706b14098fc7e88e9aa1c54f28857a818beec4d lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -25,7 +25,6 @@ from galaxy.util.bunch import Bunch from galaxy.util.expressions import ExpressionContext from galaxy.util.json import from_json_string -from .output_checker import check_output log = logging.getLogger( __name__ ) @@ -1080,7 +1079,158 @@ self.cleanup() def check_tool_output( self, stdout, stderr, tool_exit_code, job ): - return check_output( self.tool, stdout, stderr, tool_exit_code, job ) + """ + Check the output of a tool - given the stdout, stderr, and the tool's + exit code, return True if the tool exited succesfully and False + otherwise. No exceptions should be thrown. If this code encounters + an exception, it returns True so that the workflow can continue; + otherwise, a bug in this code could halt workflow progress. + Note that, if the tool did not define any exit code handling or + any stdio/stderr handling, then it reverts back to previous behavior: + if stderr contains anything, then False is returned. + Note that the job id is just for messages. + """ + # By default, the tool succeeded. This covers the case where the code + # has a bug but the tool was ok, and it lets a workflow continue. + success = True + + try: + # Check exit codes and match regular expressions against stdout and + # stderr if this tool was configured to do so. + # If there is a regular expression for scanning stdout/stderr, + # then we assume that the tool writer overwrote the default + # behavior of just setting an error if there is *anything* on + # stderr. + if ( len( self.tool.stdio_regexes ) > 0 or + len( self.tool.stdio_exit_codes ) > 0 ): + # Check the exit code ranges in the order in which + # they were specified. Each exit_code is a StdioExitCode + # that includes an applicable range. If the exit code was in + # that range, then apply the error level and add a message. + # If we've reached a fatal error rule, then stop. + max_error_level = galaxy.tools.StdioErrorLevel.NO_ERROR + if tool_exit_code != None: + for stdio_exit_code in self.tool.stdio_exit_codes: + if ( tool_exit_code >= stdio_exit_code.range_start and + tool_exit_code <= stdio_exit_code.range_end ): + # Tack on a generic description of the code + # plus a specific code description. For example, + # this might prepend "Job 42: Warning (Out of Memory)\n". + code_desc = stdio_exit_code.desc + if ( None == code_desc ): + code_desc = "" + tool_msg = ( "%s: Exit code %d (%s)" % ( + galaxy.tools.StdioErrorLevel.desc( stdio_exit_code.error_level ), + tool_exit_code, + code_desc ) ) + log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) ) + stderr = tool_msg + "\n" + stderr + max_error_level = max( max_error_level, + stdio_exit_code.error_level ) + if ( max_error_level >= + galaxy.tools.StdioErrorLevel.FATAL ): + break + + if max_error_level < galaxy.tools.StdioErrorLevel.FATAL: + # We'll examine every regex. Each regex specifies whether + # it is to be run on stdout, stderr, or both. (It is + # possible for neither stdout nor stderr to be scanned, + # but those regexes won't be used.) We record the highest + # error level, which are currently "warning" and "fatal". + # If fatal, then we set the job's state to ERROR. + # If warning, then we still set the job's state to OK + # but include a message. We'll do this if we haven't seen + # a fatal error yet + for regex in self.tool.stdio_regexes: + # If ( this regex should be matched against stdout ) + # - Run the regex's match pattern against stdout + # - If it matched, then determine the error level. + # o If it was fatal, then we're done - break. + # Repeat the stdout stuff for stderr. + # TODO: Collapse this into a single function. + if ( regex.stdout_match ): + regex_match = re.search( regex.match, stdout, + re.IGNORECASE ) + if ( regex_match ): + rexmsg = self.regex_err_msg( regex_match, regex) + log.info( "Job %s: %s" + % ( job.get_id_tag(), rexmsg ) ) + stdout = rexmsg + "\n" + stdout + max_error_level = max( max_error_level, + regex.error_level ) + if ( max_error_level >= + galaxy.tools.StdioErrorLevel.FATAL ): + break + + if ( regex.stderr_match ): + regex_match = re.search( regex.match, stderr, + re.IGNORECASE ) + if ( regex_match ): + rexmsg = self.regex_err_msg( regex_match, regex) + log.info( "Job %s: %s" + % ( job.get_id_tag(), rexmsg ) ) + stderr = rexmsg + "\n" + stderr + max_error_level = max( max_error_level, + regex.error_level ) + if ( max_error_level >= + galaxy.tools.StdioErrorLevel.FATAL ): + break + + # If we encountered a fatal error, then we'll need to set the + # job state accordingly. Otherwise the job is ok: + if max_error_level >= galaxy.tools.StdioErrorLevel.FATAL: + success = False + else: + success = True + + # When there are no regular expressions and no exit codes to check, + # default to the previous behavior: when there's anything on stderr + # the job has an error, and the job is ok otherwise. + else: + # TODO: Add in the tool and job id: + # log.debug( "Tool did not define exit code or stdio handling; " + # + "checking stderr for success" ) + if stderr: + success = False + else: + success = True + + # On any exception, return True. + except: + tb = traceback.format_exc() + log.warning( "Tool check encountered unexpected exception; " + + "assuming tool was successful: " + tb ) + success = True + + # Store the modified stdout and stderr in the job: + if None != job: + job.stdout = stdout + job.stderr = stderr + + return success + + def regex_err_msg( self, match, regex ): + """ + Return a message about the match on tool output using the given + ToolStdioRegex regex object. The regex_match is a MatchObject + that will contain the string matched on. + """ + # Get the description for the error level: + err_msg = galaxy.tools.StdioErrorLevel.desc( regex.error_level ) + ": " + # If there's a description for the regular expression, then use it. + # Otherwise, we'll take the first 256 characters of the match. + if None != regex.desc: + err_msg += regex.desc + else: + mstart = match.start() + mend = match.end() + err_msg += "Matched on " + # TODO: Move the constant 256 somewhere else besides here. + if mend - mstart > 256: + err_msg += match.string[ mstart : mstart+256 ] + "..." + else: + err_msg += match.string[ mstart: mend ] + return err_msg def cleanup( self ): # remove temporary files diff -r 0f9ac20283c65288daa887508594ae67049047d0 -r 1706b14098fc7e88e9aa1c54f28857a818beec4d lib/galaxy/jobs/error_level.py --- a/lib/galaxy/jobs/error_level.py +++ /dev/null @@ -1,25 +0,0 @@ - - -# These determine stdio-based error levels from matching on regular expressions -# and exit codes. They are meant to be used comparatively, such as showing -# that warning < fatal. This is really meant to just be an enum. -class StdioErrorLevel( object ): - NO_ERROR = 0 - LOG = 1 - WARNING = 2 - FATAL = 3 - MAX = 3 - descs = { - NO_ERROR: 'No error', - LOG: 'Log', - WARNING: 'Warning', - FATAL: 'Fatal error', - } - - @staticmethod - def desc( error_level ): - err_msg = "Unknown error" - if ( error_level > 0 and - error_level <= StdioErrorLevel.MAX ): - err_msg = StdioErrorLevel.descs[ error_level ] - return err_msg diff -r 0f9ac20283c65288daa887508594ae67049047d0 -r 1706b14098fc7e88e9aa1c54f28857a818beec4d lib/galaxy/jobs/output_checker.py --- a/lib/galaxy/jobs/output_checker.py +++ /dev/null @@ -1,164 +0,0 @@ -import re -from .error_level import StdioErrorLevel -import traceback - -from logging import getLogger -log = getLogger( __name__ ) - - -def check_output( tool, stdout, stderr, tool_exit_code, job ): - """ - Check the output of a tool - given the stdout, stderr, and the tool's - exit code, return True if the tool exited succesfully and False - otherwise. No exceptions should be thrown. If this code encounters - an exception, it returns True so that the workflow can continue; - otherwise, a bug in this code could halt workflow progress. - - Note that, if the tool did not define any exit code handling or - any stdio/stderr handling, then it reverts back to previous behavior: - if stderr contains anything, then False is returned. - - Note that the job id is just for messages. - """ - # By default, the tool succeeded. This covers the case where the code - # has a bug but the tool was ok, and it lets a workflow continue. - success = True - - try: - # Check exit codes and match regular expressions against stdout and - # stderr if this tool was configured to do so. - # If there is a regular expression for scanning stdout/stderr, - # then we assume that the tool writer overwrote the default - # behavior of just setting an error if there is *anything* on - # stderr. - if ( len( tool.stdio_regexes ) > 0 or - len( tool.stdio_exit_codes ) > 0 ): - # Check the exit code ranges in the order in which - # they were specified. Each exit_code is a StdioExitCode - # that includes an applicable range. If the exit code was in - # that range, then apply the error level and add a message. - # If we've reached a fatal error rule, then stop. - max_error_level = StdioErrorLevel.NO_ERROR - if tool_exit_code != None: - for stdio_exit_code in tool.stdio_exit_codes: - if ( tool_exit_code >= stdio_exit_code.range_start and - tool_exit_code <= stdio_exit_code.range_end ): - # Tack on a generic description of the code - # plus a specific code description. For example, - # this might prepend "Job 42: Warning (Out of Memory)\n". - code_desc = stdio_exit_code.desc - if ( None == code_desc ): - code_desc = "" - tool_msg = ( "%s: Exit code %d (%s)" % ( - StdioErrorLevel.desc( stdio_exit_code.error_level ), - tool_exit_code, - code_desc ) ) - log.info( "Job %s: %s" % (job.get_id_tag(), tool_msg) ) - stderr = tool_msg + "\n" + stderr - max_error_level = max( max_error_level, - stdio_exit_code.error_level ) - if ( max_error_level >= - StdioErrorLevel.FATAL ): - break - - if max_error_level < StdioErrorLevel.FATAL: - # We'll examine every regex. Each regex specifies whether - # it is to be run on stdout, stderr, or both. (It is - # possible for neither stdout nor stderr to be scanned, - # but those regexes won't be used.) We record the highest - # error level, which are currently "warning" and "fatal". - # If fatal, then we set the job's state to ERROR. - # If warning, then we still set the job's state to OK - # but include a message. We'll do this if we haven't seen - # a fatal error yet - for regex in tool.stdio_regexes: - # If ( this regex should be matched against stdout ) - # - Run the regex's match pattern against stdout - # - If it matched, then determine the error level. - # o If it was fatal, then we're done - break. - # Repeat the stdout stuff for stderr. - # TODO: Collapse this into a single function. - if ( regex.stdout_match ): - regex_match = re.search( regex.match, stdout, - re.IGNORECASE ) - if ( regex_match ): - rexmsg = __regex_err_msg( regex_match, regex) - log.info( "Job %s: %s" - % ( job.get_id_tag(), rexmsg ) ) - stdout = rexmsg + "\n" + stdout - max_error_level = max( max_error_level, - regex.error_level ) - if ( max_error_level >= - StdioErrorLevel.FATAL ): - break - - if ( regex.stderr_match ): - regex_match = re.search( regex.match, stderr, - re.IGNORECASE ) - if ( regex_match ): - rexmsg = __regex_err_msg( regex_match, regex) - log.info( "Job %s: %s" - % ( job.get_id_tag(), rexmsg ) ) - stderr = rexmsg + "\n" + stderr - max_error_level = max( max_error_level, - regex.error_level ) - if ( max_error_level >= - StdioErrorLevel.FATAL ): - break - - # If we encountered a fatal error, then we'll need to set the - # job state accordingly. Otherwise the job is ok: - if max_error_level >= StdioErrorLevel.FATAL: - success = False - else: - success = True - - # When there are no regular expressions and no exit codes to check, - # default to the previous behavior: when there's anything on stderr - # the job has an error, and the job is ok otherwise. - else: - # TODO: Add in the tool and job id: - # log.debug( "Tool did not define exit code or stdio handling; " - # + "checking stderr for success" ) - if stderr: - success = False - else: - success = True - - # On any exception, return True. - except: - tb = traceback.format_exc() - log.warning( "Tool check encountered unexpected exception; " - + "assuming tool was successful: " + tb ) - success = True - - # Store the modified stdout and stderr in the job: - if None != job: - job.stdout = stdout - job.stderr = stderr - - return success - - -def __regex_err_msg( match, regex ): - """ - Return a message about the match on tool output using the given - ToolStdioRegex regex object. The regex_match is a MatchObject - that will contain the string matched on. - """ - # Get the description for the error level: - err_msg = StdioErrorLevel.desc( regex.error_level ) + ": " - # If there's a description for the regular expression, then use it. - # Otherwise, we'll take the first 256 characters of the match. - if None != regex.desc: - err_msg += regex.desc - else: - mstart = match.start() - mend = match.end() - err_msg += "Matched on " - # TODO: Move the constant 256 somewhere else besides here. - if mend - mstart > 256: - err_msg += match.string[ mstart : mstart + 256 ] + "..." - else: - err_msg += match.string[ mstart: mend ] - return err_msg diff -r 0f9ac20283c65288daa887508594ae67049047d0 -r 1706b14098fc7e88e9aa1c54f28857a818beec4d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -34,7 +34,6 @@ from sqlalchemy import and_ from galaxy import jobs, model -from galaxy.jobs.error_level import StdioErrorLevel from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper from galaxy.jobs import ParallelismInfo from galaxy.tools.actions import DefaultToolAction @@ -65,11 +64,33 @@ from tool_shed.util import shed_util_common from .loader import load_tool, template_macro_params - log = logging.getLogger( __name__ ) WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile( '''\$\{.+?\}''' ) +# These determine stdio-based error levels from matching on regular expressions +# and exit codes. They are meant to be used comparatively, such as showing +# that warning < fatal. This is really meant to just be an enum. +class StdioErrorLevel( object ): + NO_ERROR = 0 + LOG = 1 + WARNING = 2 + FATAL = 3 + MAX = 3 + descs = { + NO_ERROR : 'No error', + LOG: 'Log', + WARNING : 'Warning', + FATAL : 'Fatal error' + } + @staticmethod + def desc( error_level ): + err_msg = "Unknown error" + if ( error_level > 0 and + error_level <= StdioErrorLevel.MAX ): + err_msg = StdioErrorLevel.descs[ error_level ] + return err_msg + class ToolNotFoundException( Exception ): pass diff -r 0f9ac20283c65288daa887508594ae67049047d0 -r 1706b14098fc7e88e9aa1c54f28857a818beec4d test/unit/test_job_output_checker.py --- a/test/unit/test_job_output_checker.py +++ /dev/null @@ -1,62 +0,0 @@ -from unittest import TestCase -from galaxy.util.bunch import Bunch -from galaxy.jobs.output_checker import check_output -from galaxy.jobs.error_level import StdioErrorLevel - - -class OutputCheckerTestCase( TestCase ): - - def setUp( self ): - self.tool = Bunch( - stdio_regexes=[], - stdio_exit_codes=[], - ) - self.job = Bunch( - stdout=None, - stderr=None, - get_id_tag=lambda: "test_id", - ) - self.stdout = '' - self.stderr = '' - self.tool_exit_code = None - - def test_default_no_stderr_success( self ): - self.__assertSuccessful() - - def test_default_stderr_failure( self ): - self.stderr = 'foo' - self.__assertNotSuccessful() - - def test_exit_code_error( self ): - mock_exit_code = Bunch( range_start=1, range_end=1, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_exit_codes.append( mock_exit_code ) - self.tool_exit_code = 1 - self.__assertNotSuccessful() - - def test_exit_code_success( self ): - mock_exit_code = Bunch( range_start=1, range_end=1, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_exit_codes.append( mock_exit_code ) - self.tool_exit_code = 0 - self.__assertSuccessful() - - def test_problematic_strings( self ): - problematic_str = '\x80abc' - regex_rule = Bunch( match=r'.abc', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_regexes = [ regex_rule ] - self.stderr = problematic_str - self.__assertNotSuccessful() - - problematic_str = '\x80abc' - regex_rule = Bunch( match=r'.abcd', stdout_match=False, stderr_match=True, error_level=StdioErrorLevel.FATAL, desc=None ) - self.tool.stdio_regexes = [ regex_rule ] - self.stderr = problematic_str - self.__assertSuccessful() - - def __assertSuccessful( self ): - self.assertTrue( self.__check_output() ) - - def __assertNotSuccessful( self ): - self.assertFalse( self.__check_output() ) - - def __check_output( self ): - return check_output( self.tool, self.stdout, self.stderr, self.tool_exit_code, self.job ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add status code 404 to response in tool_runner when a tool does not exist.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0f9ac20283c6/ Changeset: 0f9ac20283c6 User: dan Date: 2013-10-10 17:45:42 Summary: Add status code 404 to response in tool_runner when a tool does not exist. Affected #: 1 file diff -r 0226b3a74e2a64ddca1ce166de3d7c491315c4a5 -r 0f9ac20283c65288daa887508594ae67049047d0 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -61,6 +61,7 @@ if not tool: log.error( "index called with tool id '%s' but no such tool exists", tool_id ) trans.log_event( "Tool id '%s' does not exist" % tool_id ) + trans.response.status = 404 return "Tool '%s' does not exist, kwd=%s " % ( tool_id, kwd ) if tool.require_login and not trans.user: message = "You must be logged in to use this tool." 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: Remove test/unit/test_tool_loader.pyc added in 10286:edef166c163f.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0226b3a74e2a/ Changeset: 0226b3a74e2a User: dan Date: 2013-10-10 16:58:47 Summary: Remove test/unit/test_tool_loader.pyc added in 10286:edef166c163f. Affected #: 1 file diff -r 41c165399d53a643a62774f6e4e0e0da4280074f -r 0226b3a74e2a64ddca1ce166de3d7c491315c4a5 test/unit/test_tool_loader.pyc Binary file test/unit/test_tool_loader.pyc has changed 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 DiskObjectStore Docstring unit test.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41c165399d53/ Changeset: 41c165399d53 User: dan Date: 2013-10-10 16:54:34 Summary: Fix for DiskObjectStore Docstring unit test. Affected #: 2 files diff -r c05bc0400aa788bf71fd5da21b42faabded70120 -r 41c165399d53a643a62774f6e4e0e0da4280074f lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -187,7 +187,7 @@ >>> import tempfile >>> file_path=tempfile.mkdtemp() >>> obj = Bunch(id=1) - >>> s = DiskObjectStore(Bunch(umask=077, job_working_directory=file_path, new_file_path=file_path), file_path=file_path) + >>> s = DiskObjectStore(Bunch(umask=077, job_working_directory=file_path, new_file_path=file_path, object_store_check_old_style=False), file_path=file_path) >>> s.create(obj) >>> s.exists(obj) True diff -r c05bc0400aa788bf71fd5da21b42faabded70120 -r 41c165399d53a643a62774f6e4e0e0da4280074f test/unit/test_tool_loader.pyc Binary file test/unit/test_tool_loader.pyc has changed 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: Temporarily remove graph datatypes (necessary to avoid autodetection problems) until their sniffers are fixed. See also: a60d756aeb5d
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c05bc0400aa7/ Changeset: c05bc0400aa7 User: natefoo Date: 2013-10-10 16:42:56 Summary: Temporarily remove graph datatypes (necessary to avoid autodetection problems) until their sniffers are fixed. See also: a60d756aeb5d Affected #: 1 file diff -r 641cb928bd4bf3c9c209f880472b14b202ef1d5d -r c05bc0400aa788bf71fd5da21b42faabded70120 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -245,10 +245,6 @@ <datatype extension="snpmatrix" type="galaxy.datatypes.genetics:SNPMatrix" display_in_upload="true"/><datatype extension="xls" type="galaxy.datatypes.tabular:Tabular"/> -  - <datatype extension="xgmml" type="galaxy.datatypes.graph:Xgmml" display_in_upload="true"/> - <datatype extension="sif" type="galaxy.datatypes.graph:Sif" display_in_upload="true"/> - <datatype extension="rdf" type="galaxy.datatypes.graph:Rdf" display_in_upload="true"/></registration><sniffers><!-- 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: Fixes and code cleanup for installing tool dependencies defined in tool shed repository definition file via fabric.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/641cb928bd4b/ Changeset: 641cb928bd4b User: greg Date: 2013-10-10 16:35:37 Summary: Fixes and code cleanup for installing tool dependencies defined in tool shed repository definition file via fabric. Affected #: 2 files diff -r f86731617df8422ac7364bc299c7a53978af16e6 -r 641cb928bd4bf3c9c209f880472b14b202ef1d5d lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -16,49 +16,55 @@ eggs.require( 'Fabric' ) from fabric.api import env +from fabric.api import hide from fabric.api import lcd from fabric.api import local from fabric.api import settings -from fabric.api import hide log = logging.getLogger( __name__ ) INSTALLATION_LOG = 'INSTALLATION.log' VIRTUALENV_URL = 'https://pypi.python.org/packages/source/v/virtualenv/virtualenv-1.9.1.tar.gz' -def add_to_env_shell_file( text, env_shell_file ): +def check_fabric_version(): + version = env.version + if int( version.split( "." )[ 0 ] ) < 1: + raise NotImplementedError( "Install Fabric version 1.0 or later." ) + +def file_append( text, file_path, skip_if_contained=True, make_executable=True ): ''' - Append a line to a file, if this line does not already exist in the file. Creates the file and sets the mode to - executable if the file does not exist. Equivalent to a local version of fabric.contrib.files.append. + Append a line to a file unless skip_if_contained is True and the line already exists in the file. This method creates the file + if it doesn't exist. If make_executable is True, the permissions on the file are set to executable by the owner. This method + is similar to a local version of fabric.contrib.files.append. ''' - if not os.path.exists( env_shell_file ): - local( 'touch %s' % env_shell_file ) - # Explicitly set env.sh executable. - with settings( hide( 'everything' ), warn_only=True ): - local( 'chmod +x %s' % env_shell_file ) + if not os.path.exists( file_path ): + local( 'touch %s' % file_path ) + if make_executable: + # Explicitly set the file to the received mode if valid. + with settings( hide( 'everything' ), warn_only=True ): + local( 'chmod +x %s' % file_path ) return_code = 0 - # Convert the contents to a list, in order to support adding one or more lines to env.sh. + # Convert the received text to a list, in order to support adding one or more lines to the file. if isinstance( text, basestring ): text = [ text ] for line in text: # Build a regex to search for the relevant line in env.sh. regex = td_common_util.egrep_escape( line ) - # If the line exists, egrep will return a success. - with settings( hide( 'everything' ), warn_only=True ): - egrep_cmd = 'egrep "^%s$" %s' % ( regex, env_shell_file ) - contains_line = local( egrep_cmd ).succeeded - if contains_line: - continue - # If not, then append the line, escaping any single quotes in the shell command. + if skip_if_contained: + # If the line exists in the file, egrep will return a success. + with settings( hide( 'everything' ), warn_only=True ): + egrep_cmd = 'egrep "^%s$" %s' % ( regex, file_path ) + contains_line = local( egrep_cmd ).succeeded + if contains_line: + continue + # Append the current line to the file, escaping any single quotes in the line. line = line.replace( "'", r"'\\''" ) - return_code = local( "echo '%s' >> %s" % ( line, env_shell_file ) ).return_code + return_code = local( "echo '%s' >> %s" % ( line, file_path ) ).return_code + if return_code: + # Return upon the first error encountered. + return return_code return return_code -def check_fabric_version(): - version = env.version - if int( version.split( "." )[ 0 ] ) < 1: - raise NotImplementedError( "Install Fabric version 1.0 or later." ) - def filter_actions_after_binary_installation( actions ): '''Filter out actions that should not be processed if a binary download succeeded.''' filtered_actions = [] @@ -331,7 +337,7 @@ # Check for the presence of the $ENV[] key string and populate it if possible. env_var_dict = handle_environment_variables( app, tool_dependency, install_dir, env_var_dict, cmds ) env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) - return_code = add_to_env_shell_file( env_entry, env_file ) + return_code = file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) if return_code: return elif action_type == 'set_environment_for_install': @@ -373,13 +379,13 @@ log.error( "virtualenv's site-packages directory '%s' does not exist", output.stdout ) return modify_env_command_dict = dict( name="PYTHONPATH", action="prepend_to", value=output.stdout ) - env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) - return_code = add_to_env_shell_file( env_entry, env_file ) + env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict ) + return_code = file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) if return_code: return modify_env_command_dict = dict( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) ) env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict ) - return_code = add_to_env_shell_file( env_entry, env_file ) + return_code = file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) if return_code: return elif action_type == 'shell_command': diff -r f86731617df8422ac7364bc299c7a53978af16e6 -r 641cb928bd4bf3c9c209f880472b14b202ef1d5d lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -823,7 +823,7 @@ env_entry, env_file = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) if env_var_version == '1.0': # Handle setting environment variables using a fabric method. - fabric_util.add_to_env_shell_file( env_entry, env_file ) + fabric_util.file_append( env_entry, env_file, skip_if_contained=True, make_executable=True ) sa_session.refresh( tool_dependency ) if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Add Pythonic FASTQ to FASTA converter back into tool_conf.xml.main removed in 10720:870b10eaa4cf.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f86731617df8/ Changeset: f86731617df8 User: dan Date: 2013-10-10 16:00:13 Summary: Add Pythonic FASTQ to FASTA converter back into tool_conf.xml.main removed in 10720:870b10eaa4cf. Affected #: 1 file diff -r c78f3f687fbc8592d32a67738e57d847c00ce0c6 -r f86731617df8422ac7364bc299c7a53978af16e6 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -55,6 +55,7 @@ <section id="convert" name="Convert Formats"><tool file="filters/bed2gff.xml" /><tool file="fasta_tools/fasta_to_tabular.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /><tool file="filters/gff2bed.xml" /><tool file="maf/maf_to_bed.xml" /><tool file="maf/maf_to_interval.xml" /> @@ -226,6 +227,7 @@ <tool file="fastq/fastq_trimmer_by_quality.xml" /><tool file="fastq/fastq_masker_by_quality.xml" /><tool file="fastq/fastq_manipulation.xml" /> + <tool file="fastq/fastq_to_fasta.xml" /><tool file="fastq/fastq_to_tabular.xml" /><tool file="fastq/tabular_to_fastq.xml" /><label id="fastx_toolkit_fastq" text="FASTX-Toolkit for FASTQ data" /> 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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