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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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commit/galaxy-central: jmchilton: Refactor job status checking logic into its own module.
by commits-noreply＠bitbucket.org 10 Oct '13

10 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c78f3f687fbc/ Changeset: c78f3f687fbc User: jmchilton Date: 2013-10-10 07:17:17 Summary: Refactor job status checking logic into its own module. Add unit tests for some basic behaviors. Affected #: 5 files diff -r ba45d14a2c8fe72554390872deb5f4ffdd66170f -r c78f3f687fbc8592d32a67738e57d847c00ce0c6 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -25,6 +25,7 @@ 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__ ) @@ -1079,158 +1080,7 @@ self.cleanup() def check_tool_output( self, 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 + return check_output( self.tool, stdout, stderr, tool_exit_code, job ) def cleanup( self ): # remove temporary files diff -r ba45d14a2c8fe72554390872deb5f4ffdd66170f -r c78f3f687fbc8592d32a67738e57d847c00ce0c6 lib/galaxy/jobs/error_level.py --- /dev/null +++ b/lib/galaxy/jobs/error_level.py @@ -0,0 +1,25 @@ + + +# 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 ba45d14a2c8fe72554390872deb5f4ffdd66170f -r c78f3f687fbc8592d32a67738e57d847c00ce0c6 lib/galaxy/jobs/output_checker.py --- /dev/null +++ b/lib/galaxy/jobs/output_checker.py @@ -0,0 +1,164 @@ +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 ba45d14a2c8fe72554390872deb5f4ffdd66170f -r c78f3f687fbc8592d32a67738e57d847c00ce0c6 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -34,6 +34,7 @@ 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 @@ -64,33 +65,11 @@ 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 ba45d14a2c8fe72554390872deb5f4ffdd66170f -r c78f3f687fbc8592d32a67738e57d847c00ce0c6 test/unit/test_job_output_checker.py --- /dev/null +++ b/test/unit/test_job_output_checker.py @@ -0,0 +1,62 @@ +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: martenson: user activation flow tweaked, link at the masthead message providing activation resending
by commits-noreply＠bitbucket.org 09 Oct '13

09 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ba45d14a2c8f/ Changeset: ba45d14a2c8f User: martenson Date: 2013-10-09 21:12:36 Summary: user activation flow tweaked, link at the masthead message providing activation resending Affected #: 3 files diff -r 9b738973adafffa45605e2c27ecb769ea21e8d94 -r ba45d14a2c8fe72554390872deb5f4ffdd66170f lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -153,11 +153,11 @@ if not trans.user.active and trans.app.config.user_activation_on: # Account activation is ON and the user is INACTIVE. if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON if self.is_outside_grace_period( trans, trans.user.create_time ): # User is outside the grace period. Login is disabled and he will have the activation email resent. - message = self.resend_verification_email( trans, trans.user.email ) + message, status = self.resend_verification_email( trans, trans.user.email, trans.user.username ) else: # User is within the grace period, let him log in. pass else: # Grace period is off. Login is disabled and user will have the activation email resent. - message = self.resend_verification_email( trans, trans.user.email ) + message, status = self.resend_verification_email( trans, trans.user.email, trans.user.username ) elif not user_openid.user or user_openid.user == trans.user: if openid_provider_obj.id: user_openid.provider = openid_provider_obj.id @@ -484,6 +484,7 @@ status = kwd.get( 'status', 'error' ) email = kwd.get( 'email', '' ) password = kwd.get( 'password', '' ) + username = kwd.get( 'username', '' ) redirect = kwd.get( 'redirect', trans.request.referer ).strip() success = False user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() @@ -502,11 +503,11 @@ elif trans.app.config.user_activation_on and not user.active: # activation is ON and the user is INACTIVE if ( trans.app.config.activation_grace_period != 0 ): # grace period is ON if self.is_outside_grace_period( trans, user.create_time ): # User is outside the grace period. Login is disabled and he will have the activation email resent. - message = self.resend_verification_email( trans, email ) + message, status = self.resend_verification_email( trans, email, username ) else: # User is within the grace period, let him log in. message, success, status = self.proceed_login( trans, user, redirect ) else: # Grace period is off. Login is disabled and user will have the activation email resent. - message = self.resend_verification_email( trans, email ) + message, status = self.resend_verification_email( trans, email, username ) else: # activation is OFF message, success, status = self.proceed_login( trans, user, redirect ) return ( message, status, user, success ) @@ -526,19 +527,36 @@ success = True status = 'done' return message, success, status - - def resend_verification_email( self, trans, email ): + + @web.expose + def resend_verification ( self, trans ): """ - Function resends the verification email in case user wants to log in with an inactive account. + Exposed function for use outside of the class. E.g. when user click on the resend link in the masthead. """ - is_activation_sent = self.send_verification_email( trans, email ) + message, status = self.resend_verification_email( trans, None, None ) + if status == 'done': + return trans.show_ok_message( message ) + else: + return trans.show_error_message( message ) + + def resend_verification_email( self, trans, email, username ): + """ + Function resends the verification email in case user wants to log in with an inactive account or he clicks the resend link. + """ + if email is None: # User is coming from outside registration form, load email from trans + email = trans.user.email + if username is None: # User is coming from outside registration form, load email from trans + username = trans.user.username + is_activation_sent = self.send_verification_email( trans, email, username) if is_activation_sent: - message = 'This account has not been activated yet. The activation link has been sent again. Please check your email address %s.<br>' % email + message = 'This account has not been activated yet. The activation link has been sent again. Please check your email address <b>%s</b> including the spam/trash folder.<br><a target="_top" href="%s">Return to the home page</a>.' % ( email, url_for( '/' ) ) + status = 'error' else: - message = 'This account has not been activated yet but we are unable to send the activation link. Please contact your local Galaxy administrator.' + message = 'This account has not been activated yet but we are unable to send the activation link. Please contact your local Galaxy administrator.<br><a target="_top" href="%s">Return to the home page</a>.' % url_for( '/' ) + status = 'error' if trans.app.config.error_email_to is not None: - message += ' Contact: %s' % trans.app.config.error_email_to - return message + message += '<br>Error contact: %s' % trans.app.config.error_email_to + return message, status def is_outside_grace_period ( self, trans, create_time ): """ @@ -729,9 +747,9 @@ success = False else: if trans.webapp.name == 'galaxy' and trans.app.config.user_activation_on: - is_activation_sent = self.send_verification_email( trans, email ) + is_activation_sent = self.send_verification_email( trans, email, username ) if is_activation_sent: - message = 'Now logged in as %s.<br>Verification email has been sent to your email address. Please verify it by clicking the activation link in the email.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) ) + message = 'Now logged in as %s.<br>Verification email has been sent to your email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.<br><a target="_top" href="%s">Return to the home page.</a>' % ( user.email, url_for( '/' ) ) success = True else: message = 'Unable to send activation email, please contact your local Galaxy administrator.' @@ -743,10 +761,12 @@ success = True return ( message, status, user, success ) - def send_verification_email( self, trans, email ): + def send_verification_email( self, trans, email, username ): """ Send the verification email containing the activation link to the user's email. """ + if username is None: + username = trans.user.username activation_link = self.prepare_activation_link( trans, email ) body = ("Hello %s,\n\n" @@ -755,7 +775,7 @@ "By clicking on the above link and opening a Galaxy account you are also confirming that you have read and agreed to Galaxy's Terms and Conditions for use of this service (%s). This includes a quota limit of one account per user. Attempts to subvert this limit by creating multiple accounts or through any other method may result in termination of all associated accounts and data.\n\n" "Please contact us if you need help with your account at: %s. You can also browse resources available at: %s. \n\n" "More about the Galaxy Project can be found at galaxyproject.org\n\n" - "Your Galaxy Team" % ( trans.user.username, email, datetime.utcnow().strftime( "%D" ), trans.request.host, activation_link,trans.app.config.terms_url, trans.app.config.error_email_to, trans.app.config.instance_resource_url )) + "Your Galaxy Team" % ( username, email, datetime.utcnow().strftime( "%D" ), trans.request.host, activation_link,trans.app.config.terms_url, trans.app.config.error_email_to, trans.app.config.instance_resource_url )) to = email frm = trans.app.config.activation_email subject = 'Galaxy Account Activation' diff -r 9b738973adafffa45605e2c27ecb769ea21e8d94 -r ba45d14a2c8fe72554390872deb5f4ffdd66170f lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -66,6 +66,7 @@ self.activation_grace_period = kwargs.get( 'activation_grace_period', None ) self.inactivity_box_content = kwargs.get( 'inactivity_box_content', None ) self.registration_warning_message = kwargs.get( 'registration_warning_message', None ) + self.terms_url = kwargs.get( 'terms_url', None ) self.blacklist_location = kwargs.get( 'blacklist_file', None ) self.blacklist_content = None self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) diff -r 9b738973adafffa45605e2c27ecb769ea21e8d94 -r ba45d14a2c8fe72554390872deb5f4ffdd66170f templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -312,7 +312,7 @@ </div> %if self.show_inactivity_warning: <div id="inactivebox" class="panel-warning-message"> - ${app.config.inactivity_box_content} + ${app.config.inactivity_box_content} <a href="${h.url_for( controller='user', action='resend_verification' )}">Resend verification.</a></div> %endif ${self.overlay(visible=self.overlay_visible)} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: Fix stdio return code handling that has been broken for a few releases.
by commits-noreply＠bitbucket.org 09 Oct '13

09 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9b738973adaf/ Changeset: 9b738973adaf User: jmchilton Date: 2013-10-09 19:48:26 Summary: Fix stdio return code handling that has been broken for a few releases. Affected #: 1 file diff -r 50f5157b063f5567fa2cea820d85bb4abd233f91 -r 9b738973adafffa45605e2c27ecb769ea21e8d94 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -167,16 +167,28 @@ if job_wrapper.dependency_shell_commands: commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) + # Coping work dir outputs or setting metadata will mask return code of + # tool command. If these are used capture the return code and ensure + # the last thing that happens is an exit with return code. + capture_return_code_command = "; return_code=$?" + captured_return_code = False + # Append commands to copy job outputs based on from_work_dir attribute. if include_work_dir_outputs: work_dir_outputs = self.get_work_dir_outputs( job_wrapper ) if work_dir_outputs: + if not captured_return_code: + commands += capture_return_code_command + captured_return_code = True commands += "; " + "; ".join( [ "if [ -f %s ] ; then cp %s %s ; fi" % ( source_file, source_file, destination ) for ( source_file, destination ) in work_dir_outputs ] ) # Append metadata setting commands, we don't want to overwrite metadata # that was copied over in init_meta(), as per established behavior if include_metadata and job_wrapper.requires_setting_metadata: + if not captured_return_code: + commands += capture_return_code_command + captured_return_code = True commands += "; cd %s; " % os.path.abspath( os.getcwd() ) commands += job_wrapper.setup_external_metadata( exec_dir = os.path.abspath( os.getcwd() ), @@ -185,6 +197,11 @@ output_fnames = job_wrapper.get_output_fnames(), set_extension = False, kwds = { 'overwrite' : False } ) + + + if captured_return_code: + commands += '; sh -c "exit $return_code"' + return commands def get_work_dir_outputs( self, job_wrapper ): 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 defining and building repository dependency relationships when installing tool shed repositories into Galaxy and fixes for handling Galaxy tool panel section selection when installing repository dependencies.
by commits-noreply＠bitbucket.org 09 Oct '13

09 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/50f5157b063f/ Changeset: 50f5157b063f User: greg Date: 2013-10-09 19:33:31 Summary: Code cleanup for defining and building repository dependency relationships when installing tool shed repositories into Galaxy and fixes for handling Galaxy tool panel section selection when installing repository dependencies. Affected #: 8 files diff -r 53d53422782c2b1837959d6192e81c9886e2d4eb -r 50f5157b063f5567fa2cea820d85bb4abd233f91 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -286,7 +286,6 @@ installation_dict = dict( install_repository_dependencies=install_repository_dependencies, new_tool_panel_section=new_tool_panel_section, no_changes_checked=False, - reinstalling=False, repo_info_dicts=repo_info_dicts, tool_panel_section=tool_panel_section, tool_path=tool_path, diff -r 53d53422782c2b1837959d6192e81c9886e2d4eb -r 50f5157b063f5567fa2cea820d85bb4abd233f91 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 @@ -854,7 +854,6 @@ installation_dict = dict( install_repository_dependencies=install_repository_dependencies, new_tool_panel_section=new_tool_panel_section, no_changes_checked=False, - reinstalling=False, repo_info_dicts=repo_info_dicts, tool_panel_section=tool_panel_section, tool_path=tool_path, @@ -1099,7 +1098,6 @@ tool_path=tool_path, tool_shed_url=tool_shed_url, repo_info_dicts=repo_info_dicts, - reinstalling=True, install_repository_dependencies=install_repository_dependencies, no_changes_checked=no_changes_checked, tool_panel_section=tool_panel_section, diff -r 53d53422782c2b1837959d6192e81c9886e2d4eb -r 50f5157b063f5567fa2cea820d85bb4abd233f91 lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -154,6 +154,10 @@ self.times_downloaded = times_downloaded self.deprecated = deprecated + def allow_push( self, app ): + repo = hg.repository( ui.ui(), self.repo_path( app ) ) + return repo.ui.config( 'web', 'allow_push' ) + def can_change_type( self, app ): # Allow changing the type only if the repository has no contents, has never been installed, or has never been changed from # the default type. @@ -172,12 +176,6 @@ return True return False - def to_dict( self, view='collection', value_mapper=None ): - rval = super( Repository, self ).to_dict( view=view, value_mapper=value_mapper ) - if 'user_id' in rval: - rval[ 'owner' ] = self.user.username - return rval - def get_changesets_for_setting_metadata( self, app ): type_class = self.get_type_class( app ) return type_class.get_changesets_for_setting_metadata( app, self ) @@ -185,6 +183,11 @@ def get_type_class( self, app ): return app.repository_types_registry.get_class_by_label( self.type ) + def is_new( self, app ): + repo = hg.repository( ui.ui(), self.repo_path( app ) ) + tip_ctx = repo.changectx( repo.changelog.tip() ) + return tip_ctx.rev() < 0 + def repo_path( self, app ): return app.hgweb_config_manager.get_entry( os.path.join( "repos", self.user.username, self.name ) ) @@ -193,19 +196,6 @@ tip_ctx = repo.changectx( repo.changelog.tip() ) return "%s:%s" % ( str( tip_ctx.rev() ), str( repo.changectx( repo.changelog.tip() ) ) ) - def tip( self, app ): - repo = hg.repository( ui.ui(), self.repo_path( app ) ) - return str( repo.changectx( repo.changelog.tip() ) ) - - def is_new( self, app ): - repo = hg.repository( ui.ui(), self.repo_path( app ) ) - tip_ctx = repo.changectx( repo.changelog.tip() ) - return tip_ctx.rev() < 0 - - def allow_push( self, app ): - repo = hg.repository( ui.ui(), self.repo_path( app ) ) - return repo.ui.config( 'web', 'allow_push' ) - def set_allow_push( self, app, usernames, remove_auth='' ): allow_push = util.listify( self.allow_push( app ) ) if remove_auth: @@ -227,6 +217,16 @@ fp.write( line ) fp.close() + def tip( self, app ): + repo = hg.repository( ui.ui(), self.repo_path( app ) ) + return str( repo.changectx( repo.changelog.tip() ) ) + + def to_dict( self, view='collection', value_mapper=None ): + rval = super( Repository, self ).to_dict( view=view, value_mapper=value_mapper ) + if 'user_id' in rval: + rval[ 'owner' ] = self.user.username + return rval + class RepositoryMetadata( object, Dictifiable ): dict_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'has_repository_dependencies', 'includes_datatypes', diff -r 53d53422782c2b1837959d6192e81c9886e2d4eb -r 50f5157b063f5567fa2cea820d85bb4abd233f91 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -430,7 +430,6 @@ install_repository_dependencies = installation_dict[ 'install_repository_dependencies' ] new_tool_panel_section = installation_dict[ 'new_tool_panel_section' ] no_changes_checked = installation_dict[ 'no_changes_checked' ] - reinstalling = installation_dict[ 'reinstalling' ] repo_info_dicts = installation_dict[ 'repo_info_dicts' ] tool_panel_section = installation_dict[ 'tool_panel_section' ] tool_path = installation_dict[ 'tool_path' ] @@ -440,7 +439,6 @@ tool_path=tool_path, tool_shed_url=tool_shed_url, repo_info_dicts=repo_info_dicts, - reinstalling=reinstalling, install_repository_dependencies=install_repository_dependencies, no_changes_checked=no_changes_checked, tool_panel_section=tool_panel_section, diff -r 53d53422782c2b1837959d6192e81c9886e2d4eb -r 50f5157b063f5567fa2cea820d85bb4abd233f91 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1240,10 +1240,14 @@ return repository_dependency_tup, is_valid, error_message repo = hg.repository( suc.get_configured_ui(), repository.repo_path( app ) ) # The received changeset_revision may be None since defining it in the dependency definition is optional. If this is the case, - # the default will be to set it's value to the repository dependency tip revision. - if changeset_revision is None: - changeset_revision = str( repo.changectx( repo.changelog.tip() ) ) + # the default will be to set it's value to the repository dependency tip revision. This probably occurs only when handling + # circular dependency definitions. + tip_ctx = repo.changectx( repo.changelog.tip() ) + # Make sure the repo.changlog includes at least 1 revision. + if changeset_revision is None and tip_ctx.rev() >= 0: + changeset_revision = str( tip_ctx ) repository_dependency_tup = [ toolshed, name, owner, changeset_revision, prior_installation_required, str( only_if_compiling_contained_td ) ] + return repository_dependency_tup, is_valid, error_message else: # Find the specified changeset revision in the repository's changelog to see if it's valid. found = False diff -r 53d53422782c2b1837959d6192e81c9886e2d4eb -r 50f5157b063f5567fa2cea820d85bb4abd233f91 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -95,155 +95,116 @@ return False return True -def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False, install_repository_dependencies=False, +def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, install_repository_dependencies=False, no_changes_checked=False, tool_panel_section=None, new_tool_panel_section=None ): """ Discover all repository dependencies and make sure all tool_shed_repository and associated repository_dependency records exist as well as - the dependency relationships between installed repositories. This method is called when new repositories are being installed into a Galaxy - instance and when uninstalled repositories are being reinstalled. + the dependency relationships between installed repositories. This method is called when uninstalled repositories are being reinstalled. + If the user elected to install repository dependencies, all items in the all_repo_info_dicts list will be processed. However, if repository + dependencies are not to be installed, only those items contained in the received repo_info_dicts list will be processed. """ - # The following list will be maintained within this method to contain all created or updated tool shed repositories, including repository dependencies - # that may not be installed. + # The following list will be maintained within this method to contain all created or updated tool shed repositories, including repository + # dependencies that may not be installed. all_created_or_updated_tool_shed_repositories = [] - # There will be a one-to-one mapping between items in 3 lists: created_or_updated_tool_shed_repositories, tool_panel_section_keys and filtered_repo_info_dicts. - # The 3 lists will filter out repository dependencies that are not to be installed. + # There will be a one-to-one mapping between items in 3 lists: created_or_updated_tool_shed_repositories, tool_panel_section_keys and + # filtered_repo_info_dicts. The 3 lists will filter out repository dependencies that are not to be installed. created_or_updated_tool_shed_repositories = [] tool_panel_section_keys = [] - # Repositories will be filtered (e.g., if already installed, if elected to not be installed, etc), so filter the associated repo_info_dicts accordingly. + # Repositories will be filtered (e.g., if already installed, if elected to not be installed, etc), so filter the associated repo_info_dicts + # accordingly. filtered_repo_info_dicts = [] - # Discover all repository dependencies and retrieve information for installing them. Even if the user elected to not install repository dependencies we have - # to make sure all repository dependency objects exist so that the appropriate repository dependency relationships can be built. + # Discover all repository dependencies and retrieve information for installing them. Even if the user elected to not install repository + # dependencies we have to make sure all repository dependency objects exist so that the appropriate repository dependency relationships can + # be built. all_required_repo_info_dict = common_install_util.get_required_repo_info_dicts( trans, tool_shed_url, repo_info_dicts ) all_repo_info_dicts = all_required_repo_info_dict.get( 'all_repo_info_dicts', [] ) if not all_repo_info_dicts: # No repository dependencies were discovered so process the received repositories. all_repo_info_dicts = [ rid for rid in repo_info_dicts ] for repo_info_dict in all_repo_info_dicts: - for name, repo_info_tuple in repo_info_dict.items(): - description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ - suc.get_repo_info_tuple_contents( repo_info_tuple ) - # Make sure the repository was not already installed. - installed_tool_shed_repository, installed_changeset_revision = suc.repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple ) - if installed_tool_shed_repository: - tool_section, new_tool_panel_section, tool_panel_section_key = tool_util.handle_tool_panel_selection( trans=trans, - metadata=installed_tool_shed_repository.metadata, - no_changes_checked=no_changes_checked, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) - if reinstalling or install_repository_dependencies: - # If the user elected to install repository dependencies, all items in the all_repo_info_dicts list will be processed. However, if - # repository dependencies are not to be installed, only those items contained in the received repo_info_dicts list will be processed. - if is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ) or install_repository_dependencies: - if installed_tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR, - trans.model.ToolShedRepository.installation_status.NEW, - trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: + # If the user elected to install repository dependencies, all items in the all_repo_info_dicts list will be processed. However, if + # repository dependencies are not to be installed, only those items contained in the received repo_info_dicts list will be processed + # but the the all_repo_info_dicts list will be used to create all defined repository dependency relationships. + if is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ) or install_repository_dependencies: + for name, repo_info_tuple in repo_info_dict.items(): + can_update_db_record = False + description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ + suc.get_repo_info_tuple_contents( repo_info_tuple ) + # See if the repository has an existing record in the database. + repository_db_record, installed_changeset_revision = \ + suc.repository_was_previously_installed( trans, tool_shed_url, name, repo_info_tuple ) + if repository_db_record: + if repository_db_record.status in [ trans.model.ToolShedRepository.installation_status.INSTALLED, + trans.model.ToolShedRepository.installation_status.CLONING, + trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS, + trans.model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES, + trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES, + trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ]: + log.debug( "Skipping installation of tool_shed_repository '%s' because it's installation status is '%s'." % \ + ( str( repository_db_record.name ), str( repository_db_record.status ) ) ) + else: + if repository_db_record.status in [ trans.model.ToolShedRepository.installation_status.ERROR, + trans.model.ToolShedRepository.installation_status.NEW, + trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: # The current tool shed repository is not currently installed, so we can update it's record in the database. - can_update = True - name = installed_tool_shed_repository.name - description = installed_tool_shed_repository.description - installed_changeset_revision = installed_tool_shed_repository.installed_changeset_revision - metadata_dict = installed_tool_shed_repository.metadata - dist_to_shed = installed_tool_shed_repository.dist_to_shed - elif installed_tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.DEACTIVATED ]: + name = repository_db_record.name + installed_changeset_revision = repository_db_record.installed_changeset_revision + metadata_dict = repository_db_record.metadata + dist_to_shed = repository_db_record.dist_to_shed + can_update_db_record = True + elif repository_db_record.status in [ trans.model.ToolShedRepository.installation_status.DEACTIVATED ]: # The current tool shed repository is deactivated, so updating it's database record is not necessary - just activate it. - log.debug( "Reactivating deactivated tool_shed_repository '%s'." % str( installed_tool_shed_repository.name ) ) - common_install_util.activate_repository( trans, installed_tool_shed_repository ) - can_update = False - else: - # The tool shed repository currently being processed is already installed or is in the process of being installed, so it's record - # in the database cannot be updated. - if installed_tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.INSTALLED ]: - log.debug( "Skipping installation of tool_shed_repository '%s' because it is already installed." % \ - str( installed_tool_shed_repository.name ) ) - else: - log.debug( "Skipping installation of tool_shed_repository '%s' because it's installation status is '%s'." % \ - ( str( installed_tool_shed_repository.name ), str( installed_tool_shed_repository.status ) ) ) - can_update = False + log.debug( "Reactivating deactivated tool_shed_repository '%s'." % str( repository_db_record.name ) ) + common_install_util.activate_repository( trans, repository_db_record ) + # No additional updates to the database record are necessary. + can_update_db_record = False + elif repository_db_record.status not in [ trans.model.ToolShedRepository.installation_status.NEW ]: + # Set changeset_revision here so suc.create_or_update_tool_shed_repository will find the previously installed + # and uninstalled repository instead of creating a new record. + changeset_revision = repository_db_record.installed_changeset_revision + suc.reset_previously_installed_repository( trans, repository_db_record ) + can_update_db_record = True + else: + # No record exists in the database for the repository currently being processed. + installed_changeset_revision = changeset_revision + metadata_dict = {} + dist_to_shed = False + can_update_db_record = True + if can_update_db_record: + # The database record for the tool shed repository currently being processed can be updated. Get the repository metadata + # to see where it was previously located in the tool panel. + if repository_db_record and repository_db_record.metadata: + tool_section, new_tool_panel_section, tool_panel_section_key = \ + tool_util.handle_tool_panel_selection( trans=trans, + metadata=repository_db_record.metadata, + no_changes_checked=no_changes_checked, + tool_panel_section=tool_panel_section, + new_tool_panel_section=new_tool_panel_section ) else: - # This block will be reached only if reinstalling is True, install_repository_dependencies is False and is_in_repo_info_dicts is False. - # The tool shed repository currently being processed must be a repository dependency that the user elected to not install, so it's - # record in the database cannot be updated. - debug_msg = "Skipping installation of tool_shed_repository '%s' because it is likely a " % str( installed_tool_shed_repository.name ) - debug_msg += "repository dependency that was elected to not be installed." - log.debug( debug_msg ) - can_update = False - else: - # This block will be reached only if reinstalling is False and install_repository_dependencies is False. This implies that the tool shed - # repository currently being processed has already been installed. - if installed_tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.INSTALLED ]: - # Since the repository currently being processed is already in the INSTALLED state, skip it and process the next repository in the - # list if there is one. - log.debug( "Skipping installation of tool_shed_repository '%s' because it's installation status is '%s'." % \ - ( str( installed_tool_shed_repository.name ), str( installed_tool_shed_repository.status ) ) ) - can_update = False - else: - # The repository currently being processed is in some state other than INSTALLED, so reset it for installation. - debug_msg = "Resetting tool_shed_repository '%s' for installation.\n" % str( installed_tool_shed_repository.name ) - debug_msg += "The current state of the tool_shed_repository is:\n" - debug_msg += "deleted: %s\n" % str( installed_tool_shed_repository.deleted ) - debug_msg += "tool_shed_status: %s\n" % str( installed_tool_shed_repository.tool_shed_status ) - debug_msg += "uninstalled: %s\n" % str( installed_tool_shed_repository.uninstalled ) - debug_msg += "status: %s\n" % str( installed_tool_shed_repository.status ) - debug_msg += "error_message: %s\n" % str( installed_tool_shed_repository.error_message ) - log.debug( debug_msg ) - suc.reset_previously_installed_repository( trans, installed_tool_shed_repository ) - can_update = True - reinstalling = True - # Set changeset_revision here so suc.create_or_update_tool_shed_repository will find the previously installed - # and uninstalled repository instead of creating a new record. - changeset_revision = installed_tool_shed_repository.installed_changeset_revision - else: - # A tool shed repository is being installed into a Galaxy instance for the first time, or we're attempting to install it or reinstall it resulted - # in an error. In the latter case, the repository record in the database has no metadata and it's status has been set to 'New'. In either case, - # the repository's database record may be updated. - can_update = True - installed_changeset_revision = changeset_revision - metadata_dict = {} - dist_to_shed = False - if can_update: - # The database record for the tool shed repository currently being processed can be updated. - if reinstalling or install_repository_dependencies: - # Get the repository metadata to see where it was previously located in the tool panel. - if installed_tool_shed_repository: - # The tool shed repository status is one of 'New', 'Uninstalled', or 'Error'. - tool_section, new_tool_panel_section, tool_panel_section_key = tool_util.handle_tool_panel_selection( trans=trans, - metadata=installed_tool_shed_repository.metadata, - no_changes_checked=no_changes_checked, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) - else: - # We're installing a new tool shed repository that does not yet have a database record. This repository is a repository dependency - # of a different repository being installed. + # We're installing a new tool shed repository that does not yet have a database record. tool_panel_section_key, tool_section = tool_util.handle_tool_panel_section( trans, tool_panel_section=tool_panel_section, new_tool_panel_section=new_tool_panel_section ) - - else: - # We're installing a new tool shed repository that does not yet have a database record. - tool_panel_section_key, tool_section = tool_util.handle_tool_panel_section( trans, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) - tool_shed_repository = suc.create_or_update_tool_shed_repository( app=trans.app, - name=name, - description=description, - installed_changeset_revision=changeset_revision, - ctx_rev=ctx_rev, - repository_clone_url=repository_clone_url, - metadata_dict={}, - status=trans.model.ToolShedRepository.installation_status.NEW, - current_changeset_revision=changeset_revision, - owner=repository_owner, - dist_to_shed=False ) - if tool_shed_repository not in all_created_or_updated_tool_shed_repositories: - # Add the processed tool shed repository to the list of all processed repositories maintained within this method. - all_created_or_updated_tool_shed_repositories.append( tool_shed_repository ) - # Only append the tool shed repository to the list of created_or_updated_tool_shed_repositories if it is supposed to be installed. - if install_repository_dependencies or is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ): - if tool_shed_repository not in created_or_updated_tool_shed_repositories: - # Keep the one-to-one mapping between items in 3 lists. - created_or_updated_tool_shed_repositories.append( tool_shed_repository ) - tool_panel_section_keys.append( tool_panel_section_key ) - filtered_repo_info_dicts.append( repo_info_dict ) + tool_shed_repository = suc.create_or_update_tool_shed_repository( app=trans.app, + name=name, + description=description, + installed_changeset_revision=changeset_revision, + ctx_rev=ctx_rev, + repository_clone_url=repository_clone_url, + metadata_dict={}, + status=trans.model.ToolShedRepository.installation_status.NEW, + current_changeset_revision=changeset_revision, + owner=repository_owner, + dist_to_shed=False ) + if tool_shed_repository not in all_created_or_updated_tool_shed_repositories: + all_created_or_updated_tool_shed_repositories.append( tool_shed_repository ) + # Only append the tool shed repository to the list of created_or_updated_tool_shed_repositories if it is supposed to be installed. + if install_repository_dependencies or is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ): + if tool_shed_repository not in created_or_updated_tool_shed_repositories: + # Keep the one-to-one mapping between items in 3 lists. + created_or_updated_tool_shed_repositories.append( tool_shed_repository ) + tool_panel_section_keys.append( tool_panel_section_key ) + filtered_repo_info_dicts.append( repo_info_dict ) # Build repository dependency relationships even if the user chose to not install repository dependencies. build_repository_dependency_relationships( trans, all_repo_info_dicts, all_created_or_updated_tool_shed_repositories ) return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts diff -r 53d53422782c2b1837959d6192e81c9886e2d4eb -r 50f5157b063f5567fa2cea820d85bb4abd233f91 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 @@ -1467,9 +1467,17 @@ def reset_previously_installed_repository( trans, repository ): """ - Reset the atrributes of a tool_shed_repository that was previsouly installed. The repository will be in some state other than with a - status of INSTALLED, so all atributes will be set to the default NEW state. This will enable the repository to be freshly installed. + Reset the atrributes of a tool_shed_repository that was previsouly installed. The repository will be in some state other than INSTALLED, + so all atributes will be set to the default NEW state. This will enable the repository to be freshly installed. """ + debug_msg = "Resetting tool_shed_repository '%s' for installation.\n" % str( repository.name ) + debug_msg += "The current state of the tool_shed_repository is:\n" + debug_msg += "deleted: %s\n" % str( repository.deleted ) + debug_msg += "tool_shed_status: %s\n" % str( repository.tool_shed_status ) + debug_msg += "uninstalled: %s\n" % str( repository.uninstalled ) + debug_msg += "status: %s\n" % str( repository.status ) + debug_msg += "error_message: %s\n" % str( repository.error_message ) + log.debug( debug_msg ) repository.deleted = False repository.tool_shed_status = None repository.uninstalled = False diff -r 53d53422782c2b1837959d6192e81c9886e2d4eb -r 50f5157b063f5567fa2cea820d85bb4abd233f91 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -745,7 +745,8 @@ else: elems.append( elem ) else: - log.debug( "The '%s' data table file was not found, but was expected to be copied from '%s' during repository installation.", tool_data_table_conf_filename, TOOL_DATA_TABLE_FILE_SAMPLE_NAME ) + log.debug( "The '%s' data table file was not found, but was expected to be copied from '%s' during repository installation.", + tool_data_table_conf_filename, TOOL_DATA_TABLE_FILE_SAMPLE_NAME ) for elem in elems: if elem.tag == 'table': for file_elem in elem.findall( 'file' ): 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 and enhance admin/view_tool_data_tables.
by commits-noreply＠bitbucket.org 09 Oct '13

09 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/53d53422782c/ Changeset: 53d53422782c User: dan Date: 2013-10-09 18:01:54 Summary: Fix and enhance admin/view_tool_data_tables. Affected #: 2 files diff -r affd8fe24fc149b354fa3b603d205f4539e0804d -r 53d53422782c2b1837959d6192e81c9886e2d4eb lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -43,6 +43,9 @@ except KeyError: return default + def get_tables( self ): + return self.data_tables + def load_from_config_file( self, config_filename, tool_data_path, from_shed_config=False ): """ This method is called under 3 conditions: diff -r affd8fe24fc149b354fa3b603d205f4539e0804d -r 53d53422782c2b1837959d6192e81c9886e2d4eb templates/admin/view_data_tables_registry.mako --- a/templates/admin/view_data_tables_registry.mako +++ b/templates/admin/view_data_tables_registry.mako @@ -7,34 +7,39 @@ <% ctr = 0 - data_tables = trans.app.tool_data_tables - sorted_data_table_elem_names = sorted( trans.app.tool_data_tables.data_table_elem_names ) + sorted_data_tables = sorted( trans.app.tool_data_tables.get_tables().items() ) %><div class="toolForm"> - <div class="toolFormTitle">Current data table registry contains ${len( sorted_data_table_elem_names )} data tables</div> + <div class="toolFormTitle">Current data table registry contains ${len( sorted_data_tables )} data tables</div><div class="toolFormBody"><table class="manage-table colored" border="0" cellspacing="0" cellpadding="0" width="100%"><tr><th bgcolor="#D8D8D8">Name</th> + <th bgcolor="#D8D8D8">Filename</th><th bgcolor="#D8D8D8">Tool data path</th><th bgcolor="#D8D8D8">Missing index file</th></tr> - %for data_table_elem_name in sorted_data_table_elem_names: - <% data_table = data_tables[ data_table_elem_name ] %> + %for data_table_elem_name, data_table in sorted_data_tables: %if ctr % 2 == 1: <tr class="odd_row"> %else: <tr class="tr"> %endif <td>${data_table.name}</td> - <td>${data_table.tool_data_path}</td> - <td> - %if data_table.missing_index_file: - ${data_table.missing_index_file} + %for i, ( filename, file_dict ) in enumerate( data_table.filenames.iteritems() ): + %if i > 0: + <tr><td></td> %endif - </td> - </tr> + <td>${ filename | h }</td> + <td>${ file_dict.get( 'tool_data_path' ) | h }</td> + <td> + %if not file_dict.get( 'found' ): + missing + %endif + </td> + </tr> + %endfor <% ctr += 1 %> %endfor </table> 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 lib/galaxy/datatypes/converters/fastq_to_fqtoc.py
by commits-noreply＠bitbucket.org 09 Oct '13

09 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/affd8fe24fc1/ Changeset: affd8fe24fc1 User: dan Date: 2013-10-09 16:52:36 Summary: Fix for lib/galaxy/datatypes/converters/fastq_to_fqtoc.py Affected #: 1 file diff -r 9741409d89322b3da25e13be8a65a062a688f823 -r affd8fe24fc149b354fa3b603d205f4539e0804d lib/galaxy/datatypes/converters/fastq_to_fqtoc.py --- a/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py +++ b/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py @@ -28,7 +28,7 @@ lines_per_chunk = 4*sequences chunk_begin = 0 - in_file = open(input_name) + in_file = open(input_fname) out_file.write('{"sections" : ['); 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 references to g2.trac.bx.psu.edu. Several references still exist in rgenetics converter tools and rgenetics test-data.
by commits-noreply＠bitbucket.org 09 Oct '13

09 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9741409d8932/ Changeset: 9741409d8932 User: dan Date: 2013-10-09 16:50:05 Summary: Remove references to g2.trac.bx.psu.edu. Several references still exist in rgenetics converter tools and rgenetics test-data. Affected #: 3 files diff -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a -r 9741409d89322b3da25e13be8a65a062a688f823 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -192,7 +192,7 @@ self.message_box_content = kwargs.get( 'message_box_content', None ) self.message_box_class = kwargs.get( 'message_box_class', 'info' ) self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' ) - self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' ) + self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.galaxyproject.org/' ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.library_import_dir = kwargs.get( 'library_import_dir', None ) diff -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a -r 9741409d89322b3da25e13be8a65a062a688f823 templates/webapps/galaxy/admin/center.mako --- a/templates/webapps/galaxy/admin/center.mako +++ b/templates/webapps/galaxy/admin/center.mako @@ -106,7 +106,7 @@ <p><strong>Data Security and Data Libraries</strong></p><p/><strong>Security</strong> - Data security in Galaxy is a new feature, so familiarize yourself with the details which can be found - here or in our <a href="http://g2.trac.bx.psu.edu/wiki/SecurityFeatures" target="_blank">data security page</a>. The data security + here or in our <a href="http://wiki.galaxyproject.org/Learn/Security%20Features" target="_blank">data security page</a>. The data security process incorporates users, groups and roles, and enables the application of certain permissions on datasets, specifically "access" and "manage permissions". By default, the "manage permissions" permission is associated with the dataset owner's private role, and the "access" permission is not set, making the dataset public. With these default permissions, users should not see any difference diff -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a -r 9741409d89322b3da25e13be8a65a062a688f823 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -368,7 +368,7 @@ #logo_url = / # The URL linked by the "Galaxy Wiki" link in the "Help" menu. -#wiki_url = http://wiki.g2.bx.psu.edu/ +#wiki_url = http://wiki.galaxyproject.org/ # The URL linked by the "Support" link in the "Help" menu. #support_url = http://wiki.g2.bx.psu.edu/Support 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: Dave Bouvier: Prevent duplicate lines from being written to an env.sh file when installing a tool dependency or re-running a tool migration script with tool dependencies specified to be installed.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8af9e0ac6d2a/ Changeset: 8af9e0ac6d2a User: Dave Bouvier Date: 2013-10-08 22:48:05 Summary: Prevent duplicate lines from being written to an env.sh file when installing a tool dependency or re-running a tool migration script with tool dependencies specified to be installed. Affected #: 3 files diff -r b61927f340f30a636204ec560522acf9b76fd262 -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a 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 @@ -19,12 +19,41 @@ 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 ): + ''' + 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. + ''' + 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 ) + return_code = 0 + # Convert the contents to a list, in order to support adding one or more lines to env.sh. + 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. + line = line.replace( "'", r"'\\''" ) + return_code = local( "echo '%s' >> %s" % ( line, env_shell_file ) ).return_code + return return_code + def check_fabric_version(): version = env.version if int( version.split( "." )[ 0 ] ) < 1: @@ -301,8 +330,8 @@ for env_var_dict in env_var_dicts: # 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_command = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) - return_code = handle_command( app, tool_dependency, install_dir, env_command ) + 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 ) if return_code: return elif action_type == 'set_environment_for_install': @@ -344,13 +373,13 @@ 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 ) - modify_env_command = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict ) - return_code = handle_command( app, tool_dependency, install_dir, modify_env_command ) + 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 ) if return_code: return modify_env_command_dict = dict( name="PATH", action="prepend_to", value=os.path.join( venv_directory, "bin" ) ) - modify_env_command = td_common_util.create_or_update_env_shell_file( install_dir, modify_env_command_dict ) - return_code = handle_command( app, tool_dependency, install_dir, modify_env_command ) + 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 ) if return_code: return elif action_type == 'shell_command': diff -r b61927f340f30a636204ec560522acf9b76fd262 -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a 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 @@ -820,10 +820,10 @@ type='set_environment', status=app.model.ToolDependency.installation_status.INSTALLING, set_status=True ) - cmd = td_common_util.create_or_update_env_shell_file( install_dir, env_var_dict ) + 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.handle_command( app, tool_dependency, install_dir, cmd ) + fabric_util.add_to_env_shell_file( env_entry, env_file ) sa_session.refresh( tool_dependency ) if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR: tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED diff -r b61927f340f30a636204ec560522acf9b76fd262 -r 8af9e0ac6d2a5fba8e69bd7fb5ae980d7ba1614a lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -1,5 +1,6 @@ import logging import os +import re import shutil import sys import tarfile @@ -170,26 +171,9 @@ changed_value = '%s' % env_var_value elif env_var_action == 'append_to': changed_value = '$%s:%s' % ( env_var_name, env_var_value ) - line = "%s=%s; export %s" % (env_var_name, changed_value, env_var_name) - return create_or_update_env_shell_file_with_command(install_dir, line) - - -def create_or_update_env_shell_file_with_command( install_dir, command ): - """ - Return a shell expression which when executed will create or update - a Galaxy env.sh dependency file in the specified install_dir containing - the supplied command. - """ - env_shell_file_path = '%s/env.sh' % install_dir - if os.path.exists( env_shell_file_path ): - write_action = '>>' - else: - write_action = '>' - cmd = "echo %s %s %s;chmod +x %s" % ( __shellquote(command), - write_action, - __shellquote(env_shell_file_path), - __shellquote(env_shell_file_path)) - return cmd + line = "%s=%s; export %s" % ( env_var_name, changed_value, env_var_name ) + env_shell_file_path = os.path.join( install_dir, 'env.sh' ) + return line, env_shell_file_path def download_binary( url, work_dir ): ''' @@ -199,6 +183,17 @@ dir = url_download( work_dir, downloaded_filename, url, extract=False ) return downloaded_filename +def egrep_escape( text ): + """Escape ``text`` to allow literal matching using egrep.""" + regex = re.escape( text ) + # Seems like double escaping is needed for \ + regex = regex.replace( '\\\\', '\\\\\\' ) + # Triple-escaping seems to be required for $ signs + regex = regex.replace( r'\$', r'\\\$' ) + # Whereas single quotes should not be escaped + regex = regex.replace( r"\'", "'" ) + return regex + def format_traceback(): ex_type, ex, tb = sys.exc_info() return ''.join( traceback.format_tb( tb ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Fixes for 82b1789: (a) incorporate default values correctly and (b) use Backbone-style gets to access config values.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b61927f340f3/ Changeset: b61927f340f3 User: jgoecks Date: 2013-10-08 18:25:10 Summary: Fixes for 82b1789: (a) incorporate default values correctly and (b) use Backbone-style gets to access config values. Affected #: 1 file diff -r 5d5729d40b4f394dc6884d22daa39e3696842b80 -r b61927f340f30a636204ec560522acf9b76fd262 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -222,7 +222,7 @@ ], saved_values: obj_dict.prefs, onchange: function() { - this.track.set_name(this.track.config.values.name); + this.track.set_name(this.track.config.get('values').name); } }); this.prefs = this.config.get('values'); @@ -1136,7 +1136,7 @@ }, get_base_color: function(base) { - return this.config.values[ base.toLowerCase() + '_color' ] || this.config.values[ 'n_color' ]; + return this.config.get('values')[ base.toLowerCase() + '_color' ] || this.config.get('values')[ 'n_color' ]; } }); @@ -1893,16 +1893,29 @@ */ var Config = Backbone.Model.extend({ initialize: function(options) { - // values is a simple param_key -- value dictionary shared with drawables. - this.set('values', {}); + // values is a simple param_key-to-value dictionary used to store + // param values. + var values = {}; + + // Set default values. + _.each(options.params, function(p) { + values[p.key] = p.default_value; + }); // Restore saved values. if (options.saved_values) { - this.restore_values(options.saved_values); + _.each( this.get('params'), function(p) { + if (p.key in options.saved_values) { + values[p.key] = options.saved_values[p.key]; + } + }); } + + this.set('values', values); + + // HACK: to make onchange work as written, attach track at the + // top level of model and call onchange on custom event. if (options.onchange) { - // HACK: to make onchange work as written, attach track at the - // top level of model and call onchange on custom event. this.track = options.track; this.on('change:values', options.onchange, this); } @@ -1955,18 +1968,7 @@ else { return false; } - }, - - /** - * Restore config values from a dictionary. - */ - restore_values: function( values ) { - var self = this; - _.each( this.get('params'), function(param) { - self.set_param_value(param.key, values[param.key] || param.default_value); - }); - }, - + } }); var ConfigView = Backbone.View.extend({ @@ -2563,7 +2565,7 @@ track.tile_cache.clear(); in_drag = false; if (!in_handle) { drag_control.hide(); } - track.config.values.height = track.visible_height_px; + track.config.get('values').height = track.visible_height_px; track.changed(); }).appendTo(track.container_div); }, @@ -2575,8 +2577,8 @@ // Set modes, init mode. this.display_modes = new_modes; this.mode = (init_mode ? init_mode : - (this.config && this.config.values['mode'] ? - this.config.values['mode'] : this.display_modes[0]) + (this.config && this.config.get('values')['mode'] ? + this.config.get('values')['mode'] : this.display_modes[0]) ); this.action_icons.mode_icon.attr("title", "Set display mode (now: " + this.mode + ")"); @@ -2926,7 +2928,7 @@ var track = this; // TODO: is it necessary to store the mode in two places (.mode and track_config)? track.mode = new_mode; - track.config.values['mode'] = new_mode; + track.config.get('values')['mode'] = new_mode; // FIXME: find a better way to get Auto data w/o clearing cache; using mode in the // data manager would work if Auto data were checked for compatibility when a specific // mode is chosen. @@ -3955,7 +3957,7 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, { set_painter_from_config: function() { - if ( this.config.values['connector_style'] === 'arcs' ) { + if ( this.config.get('values')['connector_style'] === 'arcs' ) { this.painter = painters.ArcLinkedFeaturePainter; } else { this.painter = painters.LinkedFeaturePainter; 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: guerler: Update modal and upload
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5d5729d40b4f/ Changeset: 5d5729d40b4f User: guerler Date: 2013-10-08 18:12:48 Summary: Update modal and upload Affected #: 2 files diff -r 125a7cafb851d9b70195466389acf08dd9b98fd6 -r 5d5729d40b4f394dc6884d22daa39e3696842b80 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -12,9 +12,10 @@ elMain: '#everything', // defaults inputs - optionsDefaults: { - title : "galaxy-modal", - body : "No content available." + optionsDefault: { + title : "galaxy-modal", + body : "", + backdrop : true }, // initialize @@ -30,8 +31,16 @@ this.initialize(options); // fix height - var body = (this.$el).find('.modal-body'); - body.css('max-height', $(document).height() / 2); + this.$body.css('max-height', $(document).height() / 2); + + // set max-height so that modal does not exceed window size and is in middle of page. + /*/ TODO: this could perhaps be handled better using CSS. + this.$body.css( "max-height", + $(window).height() - + this.$footer.outerHeight() - + this.$header.outerHeight() - + parseInt( this.$dialog.css( "padding-top" ), 10 ) - + parseInt( this.$dialog.css( "padding-bottom" ), 10 ));*/ // show if (this.visible) @@ -39,7 +48,7 @@ else this.$el.fadeIn('fast'); - // set visibility flag + // set flag this.visible = true; }, @@ -47,8 +56,8 @@ hide: function(){ // fade out this.$el.fadeOut('fast'); - - // set visibility flag + + // set flag this.visible = false; }, @@ -56,11 +65,11 @@ create: function(options) { // configure options 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>'; - + 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.$el.remove(); @@ -69,45 +78,54 @@ this.setElement(this.template(options.title)); // link elements - var body = (this.$el).find('.modal-body'); - var footer = (this.$el).find('.modal-footer'); - var buttons = (this.$el).find('.buttons'); + this.$body = (this.$el).find('.modal-body'); + this.$footer = (this.$el).find('.modal-footer'); + this.$buttons = (this.$el).find('.buttons'); + this.$backdrop = (this.$el).find('.modal-backdrop'); // append body - body.append($(options.body)); - + this.$body.html(options.body); + // fix height if available if (options.height) - body.css('height', options.height); + this.$body.css('height', options.height); + // fix min-width so that modal cannot shrink considerably if new content is loaded. + this.$body.css('min-width', this.$body.width()); + + // configure background + if (!options.backdrop) + this.$backdrop.removeClass('in'); + // append buttons if (options.buttons) { // link functions + var self = this; $.each(options.buttons, function(name, value) { - buttons.append($('<button id="' + String(name).toLowerCase() + '"></button>').text(name).click(value)).append(" "); + self.$buttons.append($('<button id="' + String(name).toLowerCase() + '"></button>').text(name).click(value)).append(" "); }); } else // hide footer - footer.hide(); + this.$footer.hide(); // append to main element $(this.elMain).append($(this.el)); }, // enable buttons - enable: function(name) { - $(this.el).find('#' + String(name).toLowerCase()).prop('disabled', false); + enableButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', false); }, // disable buttons - disable: function(name) { - $(this.el).find('#' + String(name).toLowerCase()).prop('disabled', true); + disableButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', true); }, // returns scroll top for body element scrollTop: function() { - return $(this.el).find('.modal-body').scrollTop(); + return this.$body.scrollTop(); }, /* @@ -116,12 +134,13 @@ // fill regular modal template template: function(title) { - return '<div class="modal in">' + - '<div class="modal-backdrop in" style="z-index: -1;"></div>' + + return '<div class="modal">' + + '<div class="modal-backdrop fade in" style="z-index: -1;"></div>' + '<div class="modal-dialog">' + '<div class="modal-content">' + '<div class="modal-header">' + - '<span><h3 class="title">' + title + '</h3></span>' + + '<button type="button" class="close" style="display: none;">×</button>' + + '<h4 class="title">' + title + '</h4>' + '</div>' + '<div class="modal-body"></div>' + '<div class="modal-footer">' + diff -r 125a7cafb851d9b70195466389acf08dd9b98fd6 -r 5d5729d40b4f394dc6884d22daa39e3696842b80 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -426,21 +426,21 @@ // update reset button if (this.counter.running == 0 && this.counter.announce + this.counter.success + this.counter.error > 0) - this.modal.enable('Reset'); + this.modal.enableButton('Reset'); else - this.modal.disable('Reset'); + this.modal.disableButton('Reset'); // update upload button if (this.counter.running == 0 && this.counter.announce > 0) - this.modal.enable('Upload'); + this.modal.enableButton('Upload'); else - this.modal.disable('Upload'); + this.modal.disableButton('Upload'); // select upload button if (this.counter.running == 0) - this.modal.enable('Select'); + this.modal.enableButton('Select'); else - this.modal.disable('Select'); + this.modal.disableButton('Select'); }, // load html template Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for automatically populating the changeset revision in a repository_dependencies..xml file for defined dependencies that are circular.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/125a7cafb851/ Changeset: 125a7cafb851 User: greg Date: 2013-10-08 17:56:00 Summary: Fix for automatically populating the changeset revision in a repository_dependencies..xml file for defined dependencies that are circular. Affected #: 1 file diff -r 36577eb9f7a4c48211b1947d8aeb053512f5fccd -r 125a7cafb851d9b70195466389acf08dd9b98fd6 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1238,21 +1238,27 @@ log.debug( error_message ) is_valid = False return repository_dependency_tup, is_valid, error_message - # Find the specified changeset revision in the repository's changelog to see if it's valid. - found = False repo = hg.repository( suc.get_configured_ui(), repository.repo_path( app ) ) - for changeset in repo.changelog: - changeset_hash = str( repo.changectx( changeset ) ) - if changeset_hash == changeset_revision: - found = True - break - if not found: - error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, changeset revision %s "% \ - ( toolshed, name, owner, changeset_revision ) - error_message += "because the changeset revision is invalid. " - log.debug( error_message ) - is_valid = False - return repository_dependency_tup, is_valid, error_message + # The received changeset_revision may be None since defining it in the dependency definition is optional. If this is the case, + # the default will be to set it's value to the repository dependency tip revision. + if changeset_revision is None: + changeset_revision = str( repo.changectx( repo.changelog.tip() ) ) + repository_dependency_tup = [ toolshed, name, owner, changeset_revision, prior_installation_required, str( only_if_compiling_contained_td ) ] + else: + # Find the specified changeset revision in the repository's changelog to see if it's valid. + found = False + for changeset in repo.changelog: + changeset_hash = str( repo.changectx( changeset ) ) + if changeset_hash == changeset_revision: + found = True + break + if not found: + error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, changeset revision %s "% \ + ( toolshed, name, owner, changeset_revision ) + error_message += "because the changeset revision is invalid. " + log.debug( error_message ) + is_valid = False + return repository_dependency_tup, is_valid, error_message else: # Repository dependencies are currently supported within a single tool shed. error_message = "Repository dependencies are currently supported only within the same tool shed. Ignoring repository dependency definition " 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: small fixes for calculating tile height.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/36577eb9f7a4/ Changeset: 36577eb9f7a4 User: jgoecks Date: 2013-10-08 17:45:49 Summary: Trackster: small fixes for calculating tile height. Affected #: 1 file diff -r c0f049223e27a3984dab6b018afa1fce440e6288 -r 36577eb9f7a4c48211b1947d8aeb053512f5fccd static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2128,9 +2128,9 @@ this.low = region.get('start'); this.high = region.get('end'); this.w_scale = w_scale; - // Wrap element in div for background and explicitly set height. Use canvas - // height attribute because canvas may not have height if it is not in document yet. - this.html_elt = $("<div class='track-tile'/>").append(canvas).height( $(canvas).attr("height") ); + this.canvas = canvas; + // Wrap element in div for background and to provide container for tile-specific elements. + this.html_elt = $("<div class='track-tile'/>").append(canvas); this.data = data; this.stale = false; }; @@ -3371,14 +3371,11 @@ // -- Update track, tile heights based on new tile. -- - // Clear any previous height settings for tile. - tile.html_elt.height('auto'); - - // Update max height based on current tile. - this.max_height_px = Math.max(this.max_height_px, tile.html_elt.height()); + // Update max height based on current tile's canvas. + this.max_height_px = Math.max(this.max_height_px, $(tile.canvas).height()); // Update height for all tiles based on max height. - tile.html_elt.parent().children().css("height", this.max_height_px + "px"); + tile_element.parent().children().css("height", this.max_height_px + "px"); // Update track height based on max height and visible height. var track_height = this.max_height_px; 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: Dave Bouvier: Fix for a bug introduced with the rename_to option for the move_file action.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c0f049223e27/ Changeset: c0f049223e27 User: Dave Bouvier Date: 2013-10-08 17:12:10 Summary: Fix for a bug introduced with the rename_to option for the move_file action. Affected #: 1 file diff -r 82b1789621244bd81bf68c28fbe42a29931efee1 -r c0f049223e27a3984dab6b018afa1fce440e6288 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -316,7 +316,8 @@ shutil.move( source_file, destination_file ) def move_file( current_dir, source, destination, rename_to=None ): - source_file = os.path.abspath( os.path.join( current_dir, source ) ) + source_path = os.path.abspath( os.path.join( current_dir, source ) ) + source_file = os.path.basename( source_path ) if rename_to is not None: destination_file = rename_to destination_directory = os.path.join( destination ) @@ -326,7 +327,7 @@ destination_path = os.path.join( destination_directory, source_file ) if not os.path.exists( destination_directory ): os.makedirs( destination_directory ) - shutil.move( source_file, destination_path ) + shutil.move( source_path, destination_path ) def parse_package_elem( package_elem, platform_info_dict=None, include_after_install_actions=True ): """ 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: make DrawableConfig into a Backbone model and consolidate rendering into a Backbone view.
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/82b178962124/ Changeset: 82b178962124 User: jgoecks Date: 2013-10-08 16:55:43 Summary: Trackster: make DrawableConfig into a Backbone model and consolidate rendering into a Backbone view. Affected #: 1 file diff -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 -r 82b1789621244bd81bf68c28fbe42a29931efee1 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -215,7 +215,7 @@ this.name = obj_dict.name; this.view = view; this.container = container; - this.config = new DrawableConfig({ + this.config = new Config({ track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name } @@ -225,7 +225,7 @@ this.track.set_name(this.track.config.values.name); } }); - this.prefs = this.config.values; + this.prefs = this.config.get('values'); this.drag_handle_class = obj_dict.drag_handle_class; this.is_overview = false; this.action_icons = {}; @@ -285,24 +285,10 @@ title: "Edit settings", css_class: "settings-icon", on_click_fn: function(drawable) { - var cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, - ok_fn = function() { - drawable.config.update_from_form( $(Galaxy.modal.el) ); - Galaxy.modal.hide(); - $(window).unbind("keypress.check_enter_esc"); - }, - check_enter_esc = function(e) { - if ((e.keyCode || e.which) === 27) { // Escape key - cancel_fn(); - } else if ((e.keyCode || e.which) === 13) { // Enter key - ok_fn(); - } - }; - - $(window).bind("keypress.check_enter_esc", check_enter_esc); - - // show dialog - Galaxy.modal.show({title: "Configure", body: drawable.config.build_form(), buttons : {'Cancel' : cancel_fn, 'Ok' : ok_fn } }); + var view = new ConfigView({ + model: drawable.config + }); + view.render(); } }, // Remove. @@ -911,7 +897,7 @@ this.reset(); // Define track configuration - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'a_color', label: 'A Color', type: 'color', default_value: "#FF0000" }, @@ -1903,22 +1889,30 @@ }; /** - * Container for Drawable configuration data. + * Configuration object. */ -var DrawableConfig = function( options ) { - this.track = options.track; - this.params = options.params; - this.values = {}; - this.restore_values( (options.saved_values ? options.saved_values : {}) ); - this.onchange = options.onchange; -}; - -extend(DrawableConfig.prototype, { +var Config = Backbone.Model.extend({ + initialize: function(options) { + // values is a simple param_key -- value dictionary shared with drawables. + this.set('values', {}); + + // Restore saved values. + if (options.saved_values) { + this.restore_values(options.saved_values); + } + if (options.onchange) { + // HACK: to make onchange work as written, attach track at the + // top level of model and call onchange on custom event. + this.track = options.track; + this.on('change:values', options.onchange, this); + } + }, + /** * Set default value for parameter. */ set_param_default_value: function(key, default_value) { - var param = _.find(this.params, function(p) { + var param = _.find(this.get('params'), function(p) { return p.key === key; }); @@ -1932,7 +1926,7 @@ */ set_param_value: function(key, value) { // Find param. - var param = _.find(this.params, function(p) { + var param = _.find(this.get('params'), function(p) { return p.key === key; }); @@ -1952,8 +1946,10 @@ } // Set value and return true if changed, false otherwise. - if (this.values[key] !== value) { - this.values[key] = value; + if (this.get('values')[key] !== value) { + this.get('values')[key] = value; + // HACK: custom event trigger needed to indicate that values were updated. + this.trigger('change:values'); return true; } else { @@ -1965,21 +1961,25 @@ * Restore config values from a dictionary. */ restore_values: function( values ) { - var track_config = this; - $.each( this.params, function( index, param ) { - if ( values[ param.key ] !== undefined ) { - track_config.values[ param.key ] = values[ param.key ]; - } else { - track_config.values[ param.key ] = param.default_value; - } + var self = this; + _.each( this.get('params'), function(param) { + self.set_param_value(param.key, values[param.key] || param.default_value); }); }, +}); + +var ConfigView = Backbone.View.extend({ + /** - * Build form for modifying parameters. + * Build and show form for modifying configuration. Currently uses Galaxy modals. */ - build_form: function() { - var track_config = this; + render: function() { + // + // Build config selection UI. + // + + var track_config = this.model; var container = $("<div />"); var param; // Function to process parameters recursively @@ -1990,17 +1990,19 @@ if ( param.hidden ) { continue; } // Build row for param var id = 'param_' + index; - var value = track_config.values[ param.key ]; + var value = track_config.get('values')[ param.key ]; var row = $("<div class='form-row' />").appendTo( container ); row.append( $('<label />').attr("for", id ).text( param.label + ":" ) ); // Draw parameter as checkbox if ( param.type === 'bool' ) { row.append( $('<input type="checkbox" />').attr("id", id ).attr("name", id ).attr( 'checked', value ) ); // Draw parameter as textbox - } else if ( param.type === 'text' ) { + } + else if ( param.type === 'text' ) { row.append( $('<input type="text"/>').attr("id", id ).val(value).click( function() { $(this).select(); })); // Draw paramter as select area - } else if ( param.type === 'select' ) { + } + else if ( param.type === 'select' ) { var select = $('<select />').attr("id", id); for ( var i = 0; i < param.options.length; i++ ) { $("<option/>").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select ); @@ -2008,7 +2010,8 @@ select.val( value ); row.append( select ); // Draw parameter as color picker - } else if ( param.type === 'color' ) { + } + else if ( param.type === 'color' ) { var container_div = $("<div/>").appendTo(row), input = $('<input />').attr("id", id ).attr("name", id ).val( value ).css("float", "left") @@ -2071,32 +2074,48 @@ } } // Handle top level parameters in order - handle_params( this.params, container ); - // Return element containing constructed form - return container; + handle_params( track_config.get('params'), container ); + + // + // Use Galaxy modal to display config. + // + + var self = this, + cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, + ok_fn = function() { + self.update_from_form( $(Galaxy.modal.el) ); + Galaxy.modal.hide(); + $(window).unbind("keypress.check_enter_esc"); + }, + check_enter_esc = function(e) { + if ((e.keyCode || e.which) === 27) { // Escape key + cancel_fn(); + } else if ((e.keyCode || e.which) === 13) { // Enter key + ok_fn(); + } + }; + + $(window).bind("keypress.check_enter_esc", check_enter_esc); + Galaxy.modal.show({title: "Configure", body: container, buttons : {'Cancel' : cancel_fn, 'Ok' : ok_fn } }); }, /** * Update configuration from form. */ update_from_form: function( container ) { - var track_config = this; + var model = this.model; var changed = false; - $.each( this.params, function( index, param ) { - if ( ! param.hidden ) { + _.each(model.get('params'), function(param, index) { + if ( !param.hidden ) { // Get value from form element. var id = 'param_' + index; var value = container.find( '#' + id ).val(); if ( param.type === 'bool' ) { value = container.find( '#' + id ).is( ':checked' ); } - changed = track_config.set_param_value(param.key, value) || changed; + changed = model.set_param_value(param.key, value) || changed; } }); - if ( changed ) { - this.onchange(); - this.track.changed(); - } } }); @@ -3785,7 +3804,7 @@ TiledTrack.call(this, view, container, obj_dict); // Define track configuration - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -3793,7 +3812,7 @@ { key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined }, { key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, - { key: 'height', type: 'int', default_value: 32, hidden: true } + { key: 'height', type: 'int', default_value: 30, hidden: true } ], saved_values: obj_dict.prefs, onchange: function() { @@ -3802,8 +3821,8 @@ } }); - this.prefs = this.config.values; - this.visible_height_px = this.config.values.height; + this.prefs = this.config.get('values'); + this.visible_height_px = this.prefs.height; }; extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, { @@ -3844,7 +3863,7 @@ TiledTrack.call(this, view, container, obj_dict); // Define track configuration - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -3862,8 +3881,8 @@ } }); - this.prefs = this.config.values; - this.visible_height_px = this.config.values.height; + this.prefs = this.config.get('values'); + this.visible_height_px = this.prefs.height; }; extend(DiagonalHeatmapTrack.prototype, Drawable.prototype, TiledTrack.prototype, { /** @@ -3899,7 +3918,7 @@ var block_color = util.get_random_color(), reverse_strand_color = util.get_random_color( [ block_color, "#FFFFFF" ] ); - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -3922,8 +3941,8 @@ track.request_draw({ clear_tile_cache: true }); } }); - this.prefs = this.config.values; - this.visible_height_px = this.config.values.height; + this.prefs = this.config.get('values'); + this.visible_height_px = this.prefs.height; this.container_div.addClass( "feature-track" ); this.show_labels_scale = 0.001; @@ -4207,7 +4226,7 @@ this.display_modes = ["Auto", "Coverage", "Dense", "Squish", "Pack"]; TiledTrack.call(this, view, container, obj_dict); - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -4223,7 +4242,7 @@ this.track.request_draw({ clear_tile_cache: true }); } }); - this.prefs = this.config.values; + this.prefs = this.config.get('values'); this.painter = painters.VariantPainter; this.summary_draw_height = 30; @@ -4363,7 +4382,7 @@ var block_color = util.get_random_color(), reverse_strand_color = util.get_random_color( [ block_color, "#ffffff" ] ); - this.config = new DrawableConfig( { + this.config = new Config( { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: this.name }, @@ -4383,8 +4402,8 @@ this.track.request_draw({ clear_tile_cache: true }); } }); - this.prefs = this.config.values; - + this.prefs = this.config.get('values'); + // Choose painter based on whether there is reference data. this.painter = (view.reference_track ? painters.RefBasedReadPainter : painters.ReadPainter); 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: carlfeberhard: History panel: better reconciling of hda states within history and hda collection
by commits-noreply＠bitbucket.org 08 Oct '13

08 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/402c90f647b6/ Changeset: 402c90f647b6 User: carlfeberhard Date: 2013-10-08 16:47:43 Summary: History panel: better reconciling of hda states within history and hda collection Affected #: 3 files diff -r c8b55344e779e8be93bae5d66f52128addd83003 -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -48,7 +48,7 @@ /** HDACollection of the HDAs contained in this history. */ this.hdas = new HDACollection(); - + /** the setTimeout id for any updater currently set */ this.updateTimeoutId = null; // if we've got hdas passed in the constructor, load them and set up updates if needed @@ -57,10 +57,14 @@ this.checkForUpdates(); //TODO: don't call if force_history_refresh if( this.hdas.length > 0 ){ - this.updateDisplayApplications(); + this.fetchDisplayApplications(); } } + this.setHdaEventHandlers(); + this.setOwnEventHandlers(); + }, + setHdaEventHandlers : function(){ // if an hda moves into the ready state and has the force_history_refresh flag (often via tool.xml) // then: refresh the panel this.hdas.bind( 'state:ready', function( hda, newState, oldState ){ @@ -68,7 +72,9 @@ this.updateAfterDelay(); } }, this ); + }, + setOwnEventHandlers : function(){ if( this.logger ){ this.bind( 'all', function( event ){ this.log( this + '', arguments ); @@ -88,84 +94,86 @@ updateAfterDelay : function(){ var history = this; this.updateTimeoutId = setTimeout( function(){ + history.updateTimeoutId = null; history.stateUpdater(); }, History.UPDATE_DELAY ); return this.updateTimeoutId; }, - // get the history's state from it's cummulative ds states, delay + update if needed - // events: ready + isRunning : function(){ + var historyState = this.get( 'state' ); + // set up to keep pulling if this history in run/queue state + //note: the state strings btwn history & hda are shared on the server (or a subset of) + return ( ( historyState === HistoryDatasetAssociation.STATES.RUNNING ) + ||( historyState === HistoryDatasetAssociation.STATES.QUEUED ) ); + }, + + isReady : function(){ + return !this.isRunning(); + }, + checkForUpdates : function(){ - // get overall History state from collection, run updater if History has running/queued hdas - // boiling it down on the client to running/not - if( this.hdas.running().length ){ + // set up to keep pulling if this history in run/queue state + if( this.isRunning() ){ this.updateAfterDelay(); + // otherwise, we're now in a 'ready' state (no hdas running) } else { this.trigger( 'ready' ); } return this; }, - // update this history, find any hda's running/queued, update ONLY those that have changed states, - // set up to run this again in some interval of time + findHdasToUpdate : function(){ + var history = this, + state_ids = history.get( 'state_ids' ), + changedIds = []; + + // get a list of hda ids for hdas we need to get more info on + _.each( state_ids, function( list, stateAccrdToHistory ){ + _.each( list, function( id ){ + var hda = history.hdas.get( id ); + // if the id is not in the current hda list + // or the state doesn't match the state rpt. by the history - save that id + if( !hda || hda.get( 'state' ) !== stateAccrdToHistory ){ + changedIds.push( id ); + } + }); + }); + return changedIds; + }, + + // fetch new data for this history, + // compare the state_ids from that with the current list and fetch updates for new or changed hdas + // if the history still has non-ready hdas, set up to run this again in some interval of time // events: ready stateUpdater : function(){ //TODO: we need to get states from one location: history_contents (right now it's both history and contents) var history = this, oldState = this.get( 'state' ), - // state ids is a map of every possible hda state, each containing a list of ids for hdas in that state - oldStateIds = this.get( 'state_ids' ); + historyXhr = this.fetch(); // pull from the history api - //TODO: fetch? - jQuery.ajax( 'api/histories/' + this.get( 'id' ) - - ).success( function( response ){ + historyXhr.done( function( newHistoryModel ){ //this.log( 'historyApiRequest, response:', response ); - history.set( response ); - history.log( 'current history state:', history.get( 'state' ), - '(was)', oldState, + history.set( newHistoryModel ); + history.log( 'current history state:', history.get( 'state' ), '(was)', oldState, 'new size:', history.get( 'nice_size' ) ); - //TODO: revisit this - seems too elaborate, need something straightforward - // for each state, check for the difference between old dataset states and new - // the goal here is to check ONLY those datasets that have changed states (not all datasets) - var changedIds = []; - _.each( _.keys( response.state_ids ), function( state ){ - var diffIds = _.difference( response.state_ids[ state ], oldStateIds[ state ] ); - // aggregate those changed ids - changedIds = changedIds.concat( diffIds ); - }); - // send the changed ids (if any) to dataset collection to have them fetch their own model changes - if( changedIds.length ){ - history.fetchHdaUpdates( changedIds ) - .done( function(){ - furtherUpdatesOrReady( history ); + var hdaIdsToUpdate = history.findHdasToUpdate(); + if( hdaIdsToUpdate.length ){ + // simplify with empty promise when no ids + history.fetchHdaUpdates( hdaIdsToUpdate ) + .done( function( models ){ + history.checkForUpdates(); }); } else { - furtherUpdatesOrReady( history ); + history.checkForUpdates(); } - function furtherUpdatesOrReady( history ){ - var timeout; - // set up to keep pulling if this history in run/queue state - if( ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.RUNNING ) - || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.QUEUED ) - || ( history.get( 'state' ) === HistoryDatasetAssociation.STATES.SETTING_METADATA )){ - //|| ( history.hdas.running() ) ){ - timeout = history.updateAfterDelay(); - - // otherwise, we're now in a 'ready' state (no hdas running) - } else { - this.updateTimeoutId = null; - history.trigger( 'ready' ); - } - return timeout; - } - - }).error( function( xhr, status, error ){ + }); + historyXhr.fail( function( xhr, status, error ){ //TODO: use ajax.status handlers here // keep rolling on a bad gateway - server restart if( xhr.status === 502 ){ @@ -197,9 +205,7 @@ xhr = jQuery.ajax({ url : this.url() + '/contents?' + jQuery.param({ ids : hdaIds.join(',') }), - /** - * @inner - */ + /** @inner */ error : function( xhr, status, error ){ if( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ){ return; } @@ -286,11 +292,10 @@ * @param {String[]} ids an array of hda ids to update (optional, defaults to all hdas) * @returns {HistoryDatasetAssociation[]} hda models that were updated */ - updateDisplayApplications : function( ids ){ - this.log( this + 'updateDisplayApplications:', ids ); + fetchDisplayApplications : function( ids ){ + this.log( this + '.fetchDisplayApplications:', ids ); var history = this, - // data = { id: this.get( 'id' ) }; - //if( ids && _.isArray( ids ) ){ data.hda_ids = ids.join( ',' ); } + // if any ids passed place them in the query string data data = ( ids && _.isArray( ids ) )?({ hda_ids : ids.join( ',' ) }):({}); //TODO: hardcoded diff -r c8b55344e779e8be93bae5d66f52128addd83003 -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.updateDisplayApplications()}}this.hdas.bind("state:ready",function(e,f,d){if(e.get("force_history_refresh")){this.updateAfterDelay()}},this);if(this.logger){this.bind("all",function(d){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},checkForUpdates:function(){if(this.hdas.running().length){this.updateAfterDelay()}else{this.trigger("ready")}return this},stateUpdater:function(){var c=this,a=this.get("state"),b=this.get("state_ids");jQuery.ajax("api/histories/"+this.get("id")).success(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var f=[];_.each(_.keys(d.state_ids),function(h){var g=_.difference(d.state_ids[h],b[h]);f=f.concat(g)});if(f.length){c.fetchHdaUpdates(f).done(function(){e(c)})}else{e(c)}function e(h){var g;if((h.get("state")===HistoryDatasetAssociation.STATES.RUNNING)||(h.get("state")===HistoryDatasetAssociation.STATES.QUEUED)||(h.get("state")===HistoryDatasetAssociation.STATES.SETTING_METADATA)){g=h.updateAfterDelay()}else{this.updateTimeoutId=null;h.trigger("ready")}return g}}).error(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},updateDisplayApplications:function(a){this.log(this+"updateDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.fetchDisplayApplications()}}this.setHdaEventHandlers();this.setOwnEventHandlers()},setHdaEventHandlers:function(){this.hdas.bind("state:ready",function(b,c,a){if(b.get("force_history_refresh")){this.updateAfterDelay()}},this)},setOwnEventHandlers:function(){if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.updateTimeoutId=null;a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},isRunning:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.RUNNING)||(a===HistoryDatasetAssociation.STATES.QUEUED))},isReady:function(){return !this.isRunning()},checkForUpdates:function(){if(this.isRunning()){this.updateAfterDelay()}else{this.trigger("ready")}return this},findHdasToUpdate:function(){var c=this,a=c.get("state_ids"),b=[];_.each(a,function(d,e){_.each(d,function(g){var f=c.hdas.get(g);if(!f||f.get("state")!==e){b.push(g)}})});return b},stateUpdater:function(){var c=this,a=this.get("state"),b=this.fetch();b.done(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=c.findHdasToUpdate();if(e.length){c.fetchHdaUpdates(e).done(function(f){c.checkForUpdates()})}else{c.checkForUpdates()}});b.fail(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},fetchDisplayApplications:function(a){this.log(this+".fetchDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r c8b55344e779e8be93bae5d66f52128addd83003 -r 402c90f647b678688cba952e8a6a9b4f4b1cb320 templates/webapps/galaxy/root/history.mako --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -198,8 +198,11 @@ // 2. from console: new PersistentStorage( '__history_panel' ).set( 'debugging', true ) // -> history panel and hdas will display console logs in console var debugging = false; - if( jQuery.jStorage.get( '__history_panel' ) ){ + if( sessionStorage.getItem( '__history_panel' ) ){ debugging = new PersistentStorage( '__history_panel' ).get( 'debugging' ); + if( debugging ){ + console.debug( '(debugging)' ); + } } // get the current user (either from the top frame's Galaxy or if in tab via the bootstrap) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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