January 2015 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: guerler: Api: Redirect deprecated ftp files api
by commits-noreply＠bitbucket.org 29 Jan '15

29 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/18aa57e52605/ Changeset: 18aa57e52605 User: guerler Date: 2015-01-29 17:18:03+00:00 Summary: Api: Redirect deprecated ftp files api Affected #: 1 file diff -r 4fcd087ac38c5ff89e715b969de0210fd3c395e0 -r 18aa57e52605ca18e6f0e4d1fcfcdff53b0664fa lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -179,6 +179,7 @@ webapp.mapper.resource( 'form', 'forms', path_prefix='/api' ) webapp.mapper.resource( 'request_type', 'request_types', path_prefix='/api' ) webapp.mapper.resource( 'role', 'roles', path_prefix='/api' ) + webapp.mapper.connect( '/api/ftp_files', controller='remote_files' ) webapp.mapper.resource( 'remote_file', 'remote_files', path_prefix='/api' ) webapp.mapper.resource( 'group', 'groups', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) 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: Api: Rename ftp_files to remote_files
by commits-noreply＠bitbucket.org 29 Jan '15

29 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4fcd087ac38c/ Changeset: 4fcd087ac38c User: guerler Date: 2015-01-29 16:56:56+00:00 Summary: Api: Rename ftp_files to remote_files Affected #: 9 files diff -r be28a5fda9ddbc05df0e545a3a85434630212433 -r 4fcd087ac38c5ff89e715b969de0210fd3c395e0 client/galaxy/scripts/mvc/library/library-model.js --- a/client/galaxy/scripts/mvc/library/library-model.js +++ b/client/galaxy/scripts/mvc/library/library-model.js @@ -199,7 +199,7 @@ */ var Jstree = Backbone.Model.extend({ - urlRoot: '/api/ftp_files' + urlRoot: '/api/remote_files' }); return { diff -r be28a5fda9ddbc05df0e545a3a85434630212433 -r 4fcd087ac38c5ff89e715b969de0210fd3c395e0 client/galaxy/scripts/mvc/upload/upload-ftp.js --- a/client/galaxy/scripts/mvc/upload/upload-ftp.js +++ b/client/galaxy/scripts/mvc/upload/upload-ftp.js @@ -26,7 +26,7 @@ // load extension Utils.get({ - url : galaxy_config.root + 'api/ftp_files', + url : galaxy_config.root + 'api/remote_files', success : function(ftp_files) { self._fill(ftp_files); }, error : function() { self._fill(); } }); diff -r be28a5fda9ddbc05df0e545a3a85434630212433 -r 4fcd087ac38c5ff89e715b969de0210fd3c395e0 lib/galaxy/webapps/galaxy/api/ftp_files.py --- a/lib/galaxy/webapps/galaxy/api/ftp_files.py +++ /dev/null @@ -1,147 +0,0 @@ -""" -API operations on remote files. -""" -import os -import time -import hashlib -from galaxy import web -from galaxy import exceptions -from galaxy.web import _future_expose_api as expose_api -from galaxy.util import jstree -from galaxy.web.base.controller import BaseAPIController, url_for -from operator import itemgetter - -import logging -log = logging.getLogger( __name__ ) - -class FTPFilesAPIController( BaseAPIController ): - - @expose_api - def index( self, trans, **kwd ): - """ - GET /api/ftp_files/ - - Displays remote files. - - :param target: target to load available datasets from, defaults to ftp - possible values: ftp, userdir - :type target: str - - :param format: requested format of data, defaults to flat - possible values: flat, jstree, ajax - - :returns: list of available files - :rtype: list - """ - target = kwd.get( 'target', None ) - format = kwd.get( 'format', None ) - - if target == 'userdir': - user_login = trans.user.email - user_base_dir = trans.app.config.user_library_import_dir - if user_base_dir is None: - raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from user directories.' ) - full_import_dir = os.path.join( user_base_dir, user_login ) - if full_import_dir is not None: - if format == 'jstree': - disable = kwd.get( 'disable', 'folders') - try: - userdir_jstree = self.__create_jstree( full_import_dir, disable ) - response = userdir_jstree.jsonData() - except Exception, exception: - log.debug( str( exception ) ) - raise exceptions.InternalServerError( 'Could not create tree representation of the given folder: ' + str( full_import_dir ) ) - elif format == 'ajax': - raise exceptions.NotImplemented( 'Not implemented yet. Sorry.' ) - else: - try: - response = self.__load_all_filenames( full_import_dir ) - except Exception, exception: - log.error( 'Could not get user import files: %s', str( exception ), exc_info=True ) - raise exceptions.InternalServerError( 'Could not get the files from your user directory folder.' ) - else: - raise exceptions.InternalServerError( 'Could not get the files from your user directory folder.' ) - elif target == 'importdir': - base_dir = trans.app.config.library_import_dir - if base_dir is None: - raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow usage of import directory.' ) - if format == 'jstree': - disable = kwd.get( 'disable', 'folders') - try: - importdir_jstree = self.__create_jstree( base_dir, disable ) - response = importdir_jstree.jsonData() - except Exception, exception: - log.debug( str( exception ) ) - raise exceptions.InternalServerError( 'Could not create tree representation of the given folder: ' + str( base_dir ) ) - elif format == 'ajax': - raise exceptions.NotImplemented( 'Not implemented yet. Sorry.' ) - else: - try: - response = self.__load_all_filenames( base_dir ) - except Exception, exception: - log.error( 'Could not get user import files: %s', str( exception ), exc_info=True ) - raise exceptions.InternalServerError( 'Could not get the files from your import directory folder.' ) - else: - user_ftp_base_dir = trans.app.config.ftp_upload_dir - if user_ftp_base_dir is None: - raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from FTP directories.' ) - try: - user_ftp_dir = None - identifier = trans.app.config.ftp_upload_dir_identifier - user_ftp_dir = os.path.join( user_ftp_base_dir, getattr(trans.user, identifier) ) - if user_ftp_dir is not None: - response = self.__load_all_filenames( user_ftp_dir ) - else: - raise exceptions.ConfigDoesNotAllowException( 'You do not have an FTP directory named as your login at this Galaxy instance.' ) - except Exception, exception: - log.error( 'Could not get ftp files: %s', str( exception ), exc_info=True ) - raise exceptions.InternalServerError( 'Could not get the files from your FTP folder.' ) - return response - - def __load_all_filenames( self, directory ): - """ - Loads recursively all files within the given folder and its - subfolders and returns a flat list. - """ - response = [] - if os.path.exists( directory ): - for ( dirpath, dirnames, filenames ) in os.walk( directory ): - for filename in filenames: - path = os.path.relpath( os.path.join( dirpath, filename ), directory ) - statinfo = os.lstat( os.path.join( dirpath, filename ) ) - response.append( dict( path = path, - size = statinfo.st_size, - ctime = time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) - else: - raise exceptions.ConfigDoesNotAllowException( 'The given directory does not exist.' ) - # sort by path - response = sorted(response, key=itemgetter("path")) - return response - - def __create_jstree( self, directory, disable='folders' ): - """ - Loads recursively all files and folders within the given folder - and its subfolders and returns jstree representation - of its structure. - """ - userdir_jstree = None - jstree_paths = [] - if os.path.exists( directory ): - for ( dirpath, dirnames, filenames ) in os.walk( directory ): - - for dirname in dirnames: - dir_path = os.path.relpath( os.path.join( dirpath, dirname ), directory ) - dir_path_hash = hashlib.sha1( dir_path ).hexdigest() - disabled = True if disable == 'folders' else False - jstree_paths.append( jstree.Path( dir_path, dir_path_hash, { 'type': 'folder', 'state': { 'disabled': disabled }, 'li_attr': { 'full_path': dir_path } } ) ) - - for filename in filenames: - file_path = os.path.relpath( os.path.join( dirpath, filename ), directory ) - file_path_hash = hashlib.sha1( file_path ).hexdigest() - disabled = True if disable == 'files' else False - jstree_paths.append( jstree.Path( file_path, file_path_hash, { 'type': 'file', 'state': { 'disabled': disabled }, 'li_attr': { 'full_path': file_path } } ) ) - else: - raise exceptions.ConfigDoesNotAllowException( 'The given directory does not exist.' ) - - userdir_jstree = jstree.JSTree( jstree_paths ) - return userdir_jstree diff -r be28a5fda9ddbc05df0e545a3a85434630212433 -r 4fcd087ac38c5ff89e715b969de0210fd3c395e0 lib/galaxy/webapps/galaxy/api/remote_files.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/remote_files.py @@ -0,0 +1,147 @@ +""" +API operations on remote files. +""" +import os +import time +import hashlib +from galaxy import web +from galaxy import exceptions +from galaxy.web import _future_expose_api as expose_api +from galaxy.util import jstree +from galaxy.web.base.controller import BaseAPIController, url_for +from operator import itemgetter + +import logging +log = logging.getLogger( __name__ ) + +class RemoteFilesAPIController( BaseAPIController ): + + @expose_api + def index( self, trans, **kwd ): + """ + GET /api/remote_files/ + + Displays remote files. + + :param target: target to load available datasets from, defaults to ftp + possible values: ftp, userdir + :type target: str + + :param format: requested format of data, defaults to flat + possible values: flat, jstree, ajax + + :returns: list of available files + :rtype: list + """ + target = kwd.get( 'target', None ) + format = kwd.get( 'format', None ) + + if target == 'userdir': + user_login = trans.user.email + user_base_dir = trans.app.config.user_library_import_dir + if user_base_dir is None: + raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from user directories.' ) + full_import_dir = os.path.join( user_base_dir, user_login ) + if full_import_dir is not None: + if format == 'jstree': + disable = kwd.get( 'disable', 'folders') + try: + userdir_jstree = self.__create_jstree( full_import_dir, disable ) + response = userdir_jstree.jsonData() + except Exception, exception: + log.debug( str( exception ) ) + raise exceptions.InternalServerError( 'Could not create tree representation of the given folder: ' + str( full_import_dir ) ) + elif format == 'ajax': + raise exceptions.NotImplemented( 'Not implemented yet. Sorry.' ) + else: + try: + response = self.__load_all_filenames( full_import_dir ) + except Exception, exception: + log.error( 'Could not get user import files: %s', str( exception ), exc_info=True ) + raise exceptions.InternalServerError( 'Could not get the files from your user directory folder.' ) + else: + raise exceptions.InternalServerError( 'Could not get the files from your user directory folder.' ) + elif target == 'importdir': + base_dir = trans.app.config.library_import_dir + if base_dir is None: + raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow usage of import directory.' ) + if format == 'jstree': + disable = kwd.get( 'disable', 'folders') + try: + importdir_jstree = self.__create_jstree( base_dir, disable ) + response = importdir_jstree.jsonData() + except Exception, exception: + log.debug( str( exception ) ) + raise exceptions.InternalServerError( 'Could not create tree representation of the given folder: ' + str( base_dir ) ) + elif format == 'ajax': + raise exceptions.NotImplemented( 'Not implemented yet. Sorry.' ) + else: + try: + response = self.__load_all_filenames( base_dir ) + except Exception, exception: + log.error( 'Could not get user import files: %s', str( exception ), exc_info=True ) + raise exceptions.InternalServerError( 'Could not get the files from your import directory folder.' ) + else: + user_ftp_base_dir = trans.app.config.ftp_upload_dir + if user_ftp_base_dir is None: + raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from FTP directories.' ) + try: + user_ftp_dir = None + identifier = trans.app.config.ftp_upload_dir_identifier + user_ftp_dir = os.path.join( user_ftp_base_dir, getattr(trans.user, identifier) ) + if user_ftp_dir is not None: + response = self.__load_all_filenames( user_ftp_dir ) + else: + raise exceptions.ConfigDoesNotAllowException( 'You do not have an FTP directory named as your login at this Galaxy instance.' ) + except Exception, exception: + log.error( 'Could not get ftp files: %s', str( exception ), exc_info=True ) + raise exceptions.InternalServerError( 'Could not get the files from your FTP folder.' ) + return response + + def __load_all_filenames( self, directory ): + """ + Loads recursively all files within the given folder and its + subfolders and returns a flat list. + """ + response = [] + if os.path.exists( directory ): + for ( dirpath, dirnames, filenames ) in os.walk( directory ): + for filename in filenames: + path = os.path.relpath( os.path.join( dirpath, filename ), directory ) + statinfo = os.lstat( os.path.join( dirpath, filename ) ) + response.append( dict( path = path, + size = statinfo.st_size, + ctime = time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) + else: + raise exceptions.ConfigDoesNotAllowException( 'The given directory does not exist.' ) + # sort by path + response = sorted(response, key=itemgetter("path")) + return response + + def __create_jstree( self, directory, disable='folders' ): + """ + Loads recursively all files and folders within the given folder + and its subfolders and returns jstree representation + of its structure. + """ + userdir_jstree = None + jstree_paths = [] + if os.path.exists( directory ): + for ( dirpath, dirnames, filenames ) in os.walk( directory ): + + for dirname in dirnames: + dir_path = os.path.relpath( os.path.join( dirpath, dirname ), directory ) + dir_path_hash = hashlib.sha1( dir_path ).hexdigest() + disabled = True if disable == 'folders' else False + jstree_paths.append( jstree.Path( dir_path, dir_path_hash, { 'type': 'folder', 'state': { 'disabled': disabled }, 'li_attr': { 'full_path': dir_path } } ) ) + + for filename in filenames: + file_path = os.path.relpath( os.path.join( dirpath, filename ), directory ) + file_path_hash = hashlib.sha1( file_path ).hexdigest() + disabled = True if disable == 'files' else False + jstree_paths.append( jstree.Path( file_path, file_path_hash, { 'type': 'file', 'state': { 'disabled': disabled }, 'li_attr': { 'full_path': file_path } } ) ) + else: + raise exceptions.ConfigDoesNotAllowException( 'The given directory does not exist.' ) + + userdir_jstree = jstree.JSTree( jstree_paths ) + return userdir_jstree diff -r be28a5fda9ddbc05df0e545a3a85434630212433 -r 4fcd087ac38c5ff89e715b969de0210fd3c395e0 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -179,7 +179,7 @@ webapp.mapper.resource( 'form', 'forms', path_prefix='/api' ) webapp.mapper.resource( 'request_type', 'request_types', path_prefix='/api' ) webapp.mapper.resource( 'role', 'roles', path_prefix='/api' ) - webapp.mapper.resource( 'ftp_file', 'ftp_files', path_prefix='/api' ) + webapp.mapper.resource( 'remote_file', 'remote_files', path_prefix='/api' ) webapp.mapper.resource( 'group', 'groups', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) webapp.mapper.connect( '/api/tools/{id:.+?}/build', action='build', controller="tools" ) diff -r be28a5fda9ddbc05df0e545a3a85434630212433 -r 4fcd087ac38c5ff89e715b969de0210fd3c395e0 static/scripts/mvc/library/library-model.js --- a/static/scripts/mvc/library/library-model.js +++ b/static/scripts/mvc/library/library-model.js @@ -199,7 +199,7 @@ */ var Jstree = Backbone.Model.extend({ - urlRoot: '/api/ftp_files' + urlRoot: '/api/remote_files' }); return { diff -r be28a5fda9ddbc05df0e545a3a85434630212433 -r 4fcd087ac38c5ff89e715b969de0210fd3c395e0 static/scripts/mvc/upload/upload-ftp.js --- a/static/scripts/mvc/upload/upload-ftp.js +++ b/static/scripts/mvc/upload/upload-ftp.js @@ -26,7 +26,7 @@ // load extension Utils.get({ - url : galaxy_config.root + 'api/ftp_files', + url : galaxy_config.root + 'api/remote_files', success : function(ftp_files) { self._fill(ftp_files); }, error : function() { self._fill(); } }); diff -r be28a5fda9ddbc05df0e545a3a85434630212433 -r 4fcd087ac38c5ff89e715b969de0210fd3c395e0 static/scripts/packed/mvc/library/library-model.js --- a/static/scripts/packed/mvc/library/library-model.js +++ b/static/scripts/packed/mvc/library/library-model.js @@ -1,1 +1,1 @@ -define([],function(){var f=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(n){var m=true;if((!n)&&(this.get("deleted"))){m=false}return m}});var i=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,initialize:function(m){m=m||{}},getVisible:function(n,o){o=o||[];var m=new i(this.filter(function(p){return p.isVisible(n)}));return m},sortByNameAsc:function(){this.comparator=function(n,m){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return 1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return -1}return 0};this.sort();return this},sortByNameDesc:function(){this.comparator=function(n,m){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return -1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return 1}return 0};this.sort();return this}});var g=Backbone.Model.extend({urlRoot:"/api/libraries/datasets/"});var l=Backbone.Model.extend({urlRoot:"/api/libraries/datasets/"});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var c=Backbone.Collection.extend({model:g,sortByNameAsc:function(){this.comparator=function(n,m){if(n.get("type")===m.get("type")){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return 1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return -1}return 0}else{if(n.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this},sortByNameDesc:function(){this.comparator=function(n,m){if(n.get("type")===m.get("type")){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return -1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return 1}return 0}else{if(n.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this}});var e=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(m){this.get("folder").reset(m.folder_contents);return m}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var d=Backbone.Collection.extend({urlRoot:"/api/histories/",initialize:function(m){this.id=m.id},url:function(){return this.urlRoot+this.id+"/contents"},model:b});var h=Backbone.Model.extend({urlRoot:"/api/histories/"});var k=Backbone.Collection.extend({url:"/api/histories",model:h});var j=Backbone.Model.extend({urlRoot:"/api/ftp_files"});return{Library:f,FolderAsModel:a,Libraries:i,Item:g,Ldda:l,Folder:c,FolderContainer:e,HistoryItem:b,HistoryContents:d,GalaxyHistory:h,GalaxyHistories:k,Jstree:j}}); \ No newline at end of file +define([],function(){var f=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(n){var m=true;if((!n)&&(this.get("deleted"))){m=false}return m}});var i=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,initialize:function(m){m=m||{}},getVisible:function(n,o){o=o||[];var m=new i(this.filter(function(p){return p.isVisible(n)}));return m},sortByNameAsc:function(){this.comparator=function(n,m){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return 1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return -1}return 0};this.sort();return this},sortByNameDesc:function(){this.comparator=function(n,m){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return -1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return 1}return 0};this.sort();return this}});var g=Backbone.Model.extend({urlRoot:"/api/libraries/datasets/"});var l=Backbone.Model.extend({urlRoot:"/api/libraries/datasets/"});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var c=Backbone.Collection.extend({model:g,sortByNameAsc:function(){this.comparator=function(n,m){if(n.get("type")===m.get("type")){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return 1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return -1}return 0}else{if(n.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this},sortByNameDesc:function(){this.comparator=function(n,m){if(n.get("type")===m.get("type")){if(n.get("name").toLowerCase()>m.get("name").toLowerCase()){return -1}if(m.get("name").toLowerCase()>n.get("name").toLowerCase()){return 1}return 0}else{if(n.get("type")==="folder"){return -1}else{return 1}}};this.sort();return this}});var e=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(m){this.get("folder").reset(m.folder_contents);return m}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var d=Backbone.Collection.extend({urlRoot:"/api/histories/",initialize:function(m){this.id=m.id},url:function(){return this.urlRoot+this.id+"/contents"},model:b});var h=Backbone.Model.extend({urlRoot:"/api/histories/"});var k=Backbone.Collection.extend({url:"/api/histories",model:h});var j=Backbone.Model.extend({urlRoot:"/api/remote_files"});return{Library:f,FolderAsModel:a,Libraries:i,Item:g,Ldda:l,Folder:c,FolderContainer:e,HistoryItem:b,HistoryContents:d,GalaxyHistory:h,GalaxyHistories:k,Jstree:j}}); \ No newline at end of file diff -r be28a5fda9ddbc05df0e545a3a85434630212433 -r 4fcd087ac38c5ff89e715b969de0210fd3c395e0 static/scripts/packed/mvc/upload/upload-ftp.js --- a/static/scripts/packed/mvc/upload/upload-ftp.js +++ b/static/scripts/packed/mvc/upload/upload-ftp.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o",class_partial:"upload-icon-button fa fa-minus-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());this.rows=[];a.get({url:galaxy_config.root+"api/ftp_files",success:function(d){b._fill(d)},error:function(){b._fill()}})},events:{mousedown:function(b){b.preventDefault()}},_fill:function(d){if(d&&d.length>0){this.$el.find("#upload-ftp-content").html($(this._templateTable()));var c=0;for(key in d){this.rows.push(this._add(d[key]));c+=d[key].size}this.$el.find("#upload-ftp-number").html(d.length+" files");this.$el.find("#upload-ftp-disk").html(a.bytesToString(c,true));this.$select_all=$("#upload-selectall");this.$select_all.addClass(this.options.class_add);var b=this;this.$select_all.on("click",function(){var g=b.$select_all.hasClass(b.options.class_add);for(key in d){var f=d[key];var e=b._find(f);if(!e&&g||e&&!g){b.rows[key].trigger("click")}}});b._refresh()}else{this.$el.find("#upload-ftp-content").html($(this._templateInfo()))}this.$el.find("#upload-ftp-wait").hide()},_add:function(f){var d=this;var e=$(this._templateRow(f));var b=e.find(".icon");$(this.el).find("tbody").append(e);var c="";if(this._find(f)){c=this.options.class_remove}else{c=this.options.class_add}b.addClass(c);e.on("click",function(){var g=d._find(f);b.removeClass();if(!g){d.app.uploadbox.add([{mode:"ftp",name:f.path,size:f.size,path:f.path}]);b.addClass(d.options.class_remove)}else{d.app.collection.remove(g);b.addClass(d.options.class_add)}d._refresh()});return e},_refresh:function(){var b=this.app.collection.where({file_mode:"ftp"});this.$select_all.removeClass();if(b.length==0){this.$select_all.addClass(this.options.class_add)}else{if(b.length==this.rows.length){this.$select_all.addClass(this.options.class_remove)}else{this.$select_all.addClass(this.options.class_partial)}}},_find:function(c){var b=this.app.collection.findWhere({file_path:c.path,status:"init",file_mode:"ftp"});if(b){return b.get("id")}return null},_templateRow:function(b){return'<tr class="upload-ftp-row"><td><div class="icon"/></td><td class="label"><p>'+b.path+'</p></td><td class="nonlabel">'+a.bytesToString(b.size)+'</td><td class="nonlabel">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>  <span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th><div id="upload-selectall"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"></div><div>'}})}); \ No newline at end of file +define(["utils/utils"],function(a){return Backbone.View.extend({options:{class_add:"upload-icon-button fa fa-square-o",class_remove:"upload-icon-button fa fa-check-square-o",class_partial:"upload-icon-button fa fa-minus-square-o"},initialize:function(c){this.app=c;var b=this;this.setElement(this._template());this.rows=[];a.get({url:galaxy_config.root+"api/remote_files",success:function(d){b._fill(d)},error:function(){b._fill()}})},events:{mousedown:function(b){b.preventDefault()}},_fill:function(d){if(d&&d.length>0){this.$el.find("#upload-ftp-content").html($(this._templateTable()));var c=0;for(key in d){this.rows.push(this._add(d[key]));c+=d[key].size}this.$el.find("#upload-ftp-number").html(d.length+" files");this.$el.find("#upload-ftp-disk").html(a.bytesToString(c,true));this.$select_all=$("#upload-selectall");this.$select_all.addClass(this.options.class_add);var b=this;this.$select_all.on("click",function(){var g=b.$select_all.hasClass(b.options.class_add);for(key in d){var f=d[key];var e=b._find(f);if(!e&&g||e&&!g){b.rows[key].trigger("click")}}});b._refresh()}else{this.$el.find("#upload-ftp-content").html($(this._templateInfo()))}this.$el.find("#upload-ftp-wait").hide()},_add:function(f){var d=this;var e=$(this._templateRow(f));var b=e.find(".icon");$(this.el).find("tbody").append(e);var c="";if(this._find(f)){c=this.options.class_remove}else{c=this.options.class_add}b.addClass(c);e.on("click",function(){var g=d._find(f);b.removeClass();if(!g){d.app.uploadbox.add([{mode:"ftp",name:f.path,size:f.size,path:f.path}]);b.addClass(d.options.class_remove)}else{d.app.collection.remove(g);b.addClass(d.options.class_add)}d._refresh()});return e},_refresh:function(){var b=this.app.collection.where({file_mode:"ftp"});this.$select_all.removeClass();if(b.length==0){this.$select_all.addClass(this.options.class_add)}else{if(b.length==this.rows.length){this.$select_all.addClass(this.options.class_remove)}else{this.$select_all.addClass(this.options.class_partial)}}},_find:function(c){var b=this.app.collection.findWhere({file_path:c.path,status:"init",file_mode:"ftp"});if(b){return b.get("id")}return null},_templateRow:function(b){return'<tr class="upload-ftp-row"><td><div class="icon"/></td><td class="label"><p>'+b.path+'</p></td><td class="nonlabel">'+a.bytesToString(b.size)+'</td><td class="nonlabel">'+b.ctime+"</td></tr>"},_templateTable:function(){return'<span style="whitespace: nowrap; float: left;">Available files: </span><span style="whitespace: nowrap; float: right;"><span class="upload-icon fa fa-file-text-o"/><span id="upload-ftp-number"/>  <span class="upload-icon fa fa-hdd-o"/><span id="upload-ftp-disk"/></span><table class="grid" style="float: left;"><thead><tr><th><div id="upload-selectall"></th><th>Name</th><th>Size</th><th>Created</th></tr></thead><tbody></tbody></table>'},_templateInfo:function(){return'<div class="upload-ftp-warning warningmessage">Your FTP directory does not contain any files.</div>'},_template:function(){return'<div class="upload-ftp"><div id="upload-ftp-wait" class="upload-ftp-wait fa fa-spinner fa-spin"/><div class="upload-ftp-help">This Galaxy server allows you to upload files via FTP. To upload some files, log in to the FTP server at <strong>'+this.app.options.ftp_upload_site+'</strong> using your Galaxy credentials (email address and password).</div><div id="upload-ftp-content"></div><div>'}})}); \ No newline at end of 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.

1 0

commit/galaxy-central: martenson: found a known Whoosh bug, trying to avoid it
by commits-noreply＠bitbucket.org 29 Jan '15

29 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/be28a5fda9dd/ Changeset: be28a5fda9dd User: martenson Date: 2015-01-29 16:43:29+00:00 Summary: found a known Whoosh bug, trying to avoid it https://bitbucket.org/mchaput/whoosh/issue/386/keyerror-1l Affected #: 2 files diff -r e3196615d5faf9c0b713933664150e9cc1ef1e21 -r be28a5fda9ddbc05df0e545a3a85434630212433 lib/galaxy/webapps/tool_shed/search/repo_search.py --- a/lib/galaxy/webapps/tool_shed/search/repo_search.py +++ b/lib/galaxy/webapps/tool_shed/search/repo_search.py @@ -49,7 +49,12 @@ # Arbitrary for now reasonable_hits = 100.0 - times_downloaded = int( searcher.stored_fields( docnum )[ "times_downloaded" ] ) + + stored_times_downloaded = searcher.stored_fields( docnum )[ "times_downloaded" ] + if not isinstance( stored_times_downloaded, ( int, long ) ): + times_downloaded = int( stored_times_downloaded ) + else: + times_downloaded = stored_times_downloaded # Add 1 to prevent 0 being divided if times_downloaded == 0: times_downloaded = 1 diff -r e3196615d5faf9c0b713933664150e9cc1ef1e21 -r be28a5fda9ddbc05df0e545a3a85434630212433 scripts/tool_shed/build_ts_whoosh_index.py --- a/scripts/tool_shed/build_ts_whoosh_index.py +++ b/scripts/tool_shed/build_ts_whoosh_index.py @@ -93,7 +93,10 @@ long_description = repo.long_description homepage_url = repo.homepage_url remote_repository_url = repo.remote_repository_url + times_downloaded = repo.times_downloaded + if not isinstance( times_downloaded, ( int, long ) ): + times_downloaded = 0 repo_owner_username = '' if repo.user_id is not None: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: Fix to 68f0ed3: remove old import
by commits-noreply＠bitbucket.org 29 Jan '15

29 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e3196615d5fa/ Changeset: e3196615d5fa User: carlfeberhard Date: 2015-01-29 16:35:39+00:00 Summary: Fix to 68f0ed3: remove old import Affected #: 1 file diff -r 89ea937034b80e7cad24005ffb018f2b1c4f5f65 -r e3196615d5faf9c0b713933664150e9cc1ef1e21 lib/galaxy/managers/base.py --- a/lib/galaxy/managers/base.py +++ b/lib/galaxy/managers/base.py @@ -32,7 +32,6 @@ from galaxy import exceptions from galaxy import model from galaxy.model import tool_shed_install -from galaxy.managers import filters as filter_parser import logging log = logging.getLogger( __name__ ) 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.

1 0

commit/galaxy-central: davebgx: Set time to epoch instead of throwing server error if repository_metadata.time_last_tested is unset.
by commits-noreply＠bitbucket.org 29 Jan '15

29 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/89ea937034b8/ Changeset: 89ea937034b8 User: davebgx Date: 2015-01-29 16:23:35+00:00 Summary: Set time to epoch instead of throwing server error if repository_metadata.time_last_tested is unset. Affected #: 1 file diff -r c805913c4646238890e727a5f1c203058c6413b6 -r 89ea937034b80e7cad24005ffb018f2b1c4f5f65 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1696,7 +1696,10 @@ description_lines = [] # Per the RSS 2.0 specification, all dates in RSS feeds must be formatted as specified in RFC 822 # section 5.1, e.g. Sat, 07 Sep 2002 00:00:01 UT - time_tested = repository_metadata.time_last_tested.strftime( '%a, %d %b %Y %H:%M:%S UT' ) + if repository_metadata.time_last_tested is None: + time_tested = 'Thu, 01 Jan 1970 00:00:00 UT' + else: + time_tested = repository_metadata.time_last_tested.strftime( '%a, %d %b %Y %H:%M:%S UT' ) # Generate a citable URL for this repository with owner and changeset revision. repository_citable_url = common_util.url_join( tool_shed_url, 'view', 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.

1 0

commit/galaxy-central: carlfeberhard: History API: update documentation
by commits-noreply＠bitbucket.org 29 Jan '15

29 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c805913c4646/ Changeset: c805913c4646 User: carlfeberhard Date: 2015-01-29 16:13:28+00:00 Summary: History API: update documentation Affected #: 2 files diff -r e0441a0f85307fb9caf854fd10133f71cc3852d3 -r c805913c4646238890e727a5f1c203058c6413b6 lib/galaxy/managers/histories.py --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -384,12 +384,12 @@ #TODO: I'm not entirely convinced this (or tags) are a good idea for filters since they involve a/the user self.fn_filter_parsers.update({ #TODO: add this in annotatable mixin - 'annotation' : { 'op': { 'in' : self.filter_annotation_contains, } }, + 'annotation' : { 'op': { 'has' : self.filter_annotation_contains, } }, #TODO: add this in taggable mixin 'tag' : { 'op': { 'eq' : self.filter_has_tag, - 'in' : self.filter_has_partial_tag, + 'has': self.filter_has_partial_tag, } } }) diff -r e0441a0f85307fb9caf854fd10133f71cc3852d3 -r c805913c4646238890e727a5f1c203058c6413b6 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -56,6 +56,44 @@ :rtype: list :returns: list of dictionaries containing summary history information + + The following are optional parameters: + view: string, one of ('summary','detailed'), defaults to 'summary' + controls which set of properties to return + keys: comma separated strings, unused by default + keys/names of individual properties to return + + If neither keys or views are sent, the default view (set of keys) is returned. + If both a view and keys are sent, the key list and the view's keys are + combined. + If keys are send and no view, only those properties in keys are returned. + + For which properties are available see: + galaxy/managers/histories/HistorySerializer + + The list returned can be filtered by using two optional parameters: + q: string, generally a property name to filter by followed + by an (often optional) hyphen and operator string. + qv: string, the value to filter by + + ..example: + To filter the list to only those created after 2015-01-29, + the query string would look like: + '?q=create_time-gt&qv=2015-01-29' + + Multiple filters can be sent in using multiple q/qv pairs: + '?q=create_time-gt&qv=2015-01-29&q=tag-has&qv=experiment-1' + + The list returned can be paginated using two optional parameters: + limit: integer, defaults to no value and no limit (return all) + how many items to return + offset: integer, defaults to 0 and starts at the beginning + skip the first ( offset - 1 ) items and begin returning + at the Nth item + + ..example: + limit and offset can be combined. Skip the first two and return five: + '?limit=5&offset=3' """ serialization_params = self._parse_serialization_params( kwd, 'summary' ) limit, offset = self.parse_limit_offset( kwd ) @@ -126,6 +164,9 @@ :type deleted: boolean :param deleted: if True, allow information on a deleted history to be shown. + :param keys: same as the use of `keys` in the `index` function above + :param view: same as the use of `view` in the `index` function above + :rtype: dictionary :returns: detailed history information """ @@ -172,6 +213,9 @@ * archive_source: the url that will generate the archive to import * archive_type: 'url' (default) + :param keys: same as the use of `keys` in the `index` function above + :param view: same as the use of `view` in the `index` function above + :rtype: dict :returns: element view of new history """ @@ -220,6 +264,9 @@ * payload: a dictionary itself containing: * purge: if True, purge the history and all of its HDAs + :param keys: same as the use of `keys` in the `index` function above + :param view: same as the use of `view` in the `index` function above + :rtype: dict :returns: an error object if an error occurred or a dictionary containing: * id: the encoded id of the history, @@ -250,6 +297,9 @@ :type id: str :param id: the encoded id of the history to undelete + :param keys: same as the use of `keys` in the `index` function above + :param view: same as the use of `view` in the `index` function above + :rtype: str :returns: 'OK' if the history was undeleted """ @@ -275,6 +325,9 @@ * annotation: an annotation for the history + :param keys: same as the use of `keys` in the `index` function above + :param view: same as the use of `view` in the `index` function above + :rtype: dict :returns: an error object if an error occurred or a dictionary containing any values that were different from the original and, therefore, updated 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.

1 0

commit/galaxy-central: guerler: Workflow: Revise action form
by commits-noreply＠bitbucket.org 29 Jan '15

29 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e0441a0f8530/ Changeset: e0441a0f8530 User: guerler Date: 2015-01-29 15:56:15+00:00 Summary: Workflow: Revise action form Affected #: 9 files diff -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 -r e0441a0f85307fb9caf854fd10133f71cc3852d3 client/galaxy/scripts/mvc/tools/tools-form-workflow.js --- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js @@ -9,27 +9,29 @@ initialize: function(options) { // link with node representation in workflow module this.node = workflow.active_node; - if (!this.node) { console.debug('FAILED - tools-form-workflow:initialize() - Node not found in workflow.'); return; } - + + // link actions + this.post_job_actions = this.node.post_job_actions || {}; + // initialize parameters this.options = options; - + // set labels this.options.text_enable = 'In Advance'; this.options.text_disable = 'At Runtime'; this.options.use_defaults = true; - + // declare fields as optional Utils.deepeach(options.inputs, function(item) { if (item.type) { item.optional = (['data', 'data_hidden', 'hidden', 'drill_down', 'repeat', 'conditional']).indexOf(item.type) == -1; } }); - + // declare conditional fields as not optional Utils.deepeach(options.inputs, function(item) { if (item.type) { @@ -51,32 +53,53 @@ } }); }, - + /** Builds all sub sections */ _makeSections: function(inputs){ // for annotation inputs[Utils.uuid()] = { - label : 'Edit Step Attributes', - type : 'section', - expand : this.node.annotation, - inputs : [{ - label : 'Annotation / Notes', - name : 'annotation', - type : 'text', - area : true, - help : 'Add an annotation or notes to this step; annotations are available when a workflow is viewed.', - value : this.node.annotation - }] + label : 'Annotation / Notes', + name : 'annotation', + type : 'text', + area : true, + help : 'Add an annotation or note for this step. It will be shown with the workflow.', + value : this.node.annotation } - - // for actions - this.post_job_actions = this.node.post_job_actions; - for (var i in this.node.output_terminals) { - inputs[Utils.uuid()] = this._makeSection(i); + + // get first output id + var output_id = this.node.output_terminals && Object.keys(this.node.output_terminals)[0]; + if (output_id) { + // send email on job completion + inputs[Utils.uuid()] = { + name : 'pja__' + output_id + '__EmailAction', + label : 'Email notification', + type : 'boolean', + value : String(Boolean(this.post_job_actions['EmailAction' + output_id])), + ignore : 'false', + help : 'An email notification will be send when the job has completed.', + payload : { + 'host' : window.location.host + } + }; + + // delete non-output files + inputs[Utils.uuid()] = { + name : 'pja__' + output_id + '__DeleteIntermediatesAction', + label : 'Output cleanup', + type : 'boolean', + value : String(Boolean(this.post_job_actions['DeleteIntermediatesAction' + output_id])), + ignore : 'false', + help : 'Delete intermediate outputs if they are not used as input for another job.' + }; + + // add output specific actions + for (var i in this.node.output_terminals) { + inputs[Utils.uuid()] = this._makeSection(i); + } } }, - + /** Builds sub section with step actions/annotation */ _makeSection: function(output_id){ @@ -88,12 +111,12 @@ 1 : this.datatypes[key] }); } - + // sort extensions extensions.sort(function(a, b) { return a.label > b.label ? 1 : a.label < b.label ? -1 : 0; }); - + // add additional options extensions.unshift({ 0 : 'Sequences', @@ -105,12 +128,12 @@ }); extensions.unshift({ 0 : 'Leave unchanged', - 1 : 'None' + 1 : '' }); - + // create custom sub section var input_config = { - label : 'Edit Step Action: \'' + output_id + '\'', + label : 'Add Actions: \'' + output_id + '\'', type : 'section', inputs : [{ action : 'RenameDatasetAction', @@ -125,7 +148,7 @@ argument : 'newtype', label : 'Change datatype', type : 'select', - ignore : 'None', + ignore : '', options : extensions, help : 'This action will change the datatype of the output to the indicated value.' },{ @@ -143,59 +166,42 @@ action : 'ColumnSetAction', argument : 'chromCol', label : 'Chrom column', - type : 'text', + type : 'integer', value : '', ignore : '' },{ action : 'ColumnSetAction', argument : 'startCol', label : 'Start column', - type : 'text', + type : 'integer', value : '', ignore : '' },{ action : 'ColumnSetAction', argument : 'endCol', label : 'End column', - type : 'text', + type : 'integer', value : '', ignore : '' },{ action : 'ColumnSetAction', argument : 'strandCol', label : 'Strand column', - type : 'text', + type : 'integer', value : '', ignore : '' },{ action : 'ColumnSetAction', argument : 'nameCol', label : 'Name column', - type : 'text', + type : 'integer', value : '', ignore : '' }], help : 'This action will set column assignments in the output dataset. Blank fields are ignored.' - },{ - action : 'EmailAction', - label : 'Email notification', - type : 'boolean', - value : 'false', - ignore : 'false', - help : 'This action will send an email notifying you when the job is done.', - payload : { - 'host' : window.location.host - } - },{ - action : 'DeleteIntermediatesAction', - label : 'Delete non-outputs', - type : 'boolean', - value : 'false', - ignore : 'false', - help : 'All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect.' }] }; - + // visit input nodes and enrich by name/value pairs from server data var self = this; function visit (head, head_list) { @@ -209,7 +215,7 @@ if (input.argument) { input.name += '__' + input.argument; } - + // modify names of payload arguments if (input.payload) { for (var p_id in input.payload) { @@ -218,7 +224,7 @@ delete p; } } - + // access/verify existence of value var d = self.post_job_actions[input.action + output_id]; if (d) { @@ -242,11 +248,11 @@ } } visit(input_config); - + // return final configuration return input_config; }, - + /** Builds a new model through api call and recreates the entire form */ _buildModel: function() { @@ -260,24 +266,24 @@ } }); }, - + /** Request a new model for an already created tool form and updates the form inputs */ _updateModel: function() { // create the request dictionary var self = this; var current_state = this.tree.finalize(); - + // log tool state console.debug('tools-form-workflow::_refreshForm() - Refreshing states.'); console.debug(current_state); - + // register process var process_id = this.deferred.register(); // build model url for request var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False'; - + // post job Utils.request({ type : 'GET', diff -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 -r e0441a0f85307fb9caf854fd10133f71cc3852d3 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -275,6 +275,7 @@ } }); portlet.append(sub_section.$el); + portlet.append($('<div/>').addClass('ui-table-form-info').html(input_def.help)); // add event handler visibility button var visible = false; diff -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 -r e0441a0f85307fb9caf854fd10133f71cc3852d3 client/galaxy/scripts/mvc/ui/ui-slider.js --- a/client/galaxy/scripts/mvc/ui/ui-slider.js +++ b/client/galaxy/scripts/mvc/ui/ui-slider.js @@ -54,7 +54,7 @@ } // add text field event - this.$text.on('change', function () { + this.$text.on('input', function () { self.value($(this).val()); }); diff -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 -r e0441a0f85307fb9caf854fd10133f71cc3852d3 static/scripts/mvc/tools/tools-form-workflow.js --- a/static/scripts/mvc/tools/tools-form-workflow.js +++ b/static/scripts/mvc/tools/tools-form-workflow.js @@ -9,27 +9,29 @@ initialize: function(options) { // link with node representation in workflow module this.node = workflow.active_node; - if (!this.node) { console.debug('FAILED - tools-form-workflow:initialize() - Node not found in workflow.'); return; } - + + // link actions + this.post_job_actions = this.node.post_job_actions || {}; + // initialize parameters this.options = options; - + // set labels this.options.text_enable = 'In Advance'; this.options.text_disable = 'At Runtime'; this.options.use_defaults = true; - + // declare fields as optional Utils.deepeach(options.inputs, function(item) { if (item.type) { item.optional = (['data', 'data_hidden', 'hidden', 'drill_down', 'repeat', 'conditional']).indexOf(item.type) == -1; } }); - + // declare conditional fields as not optional Utils.deepeach(options.inputs, function(item) { if (item.type) { @@ -51,32 +53,53 @@ } }); }, - + /** Builds all sub sections */ _makeSections: function(inputs){ // for annotation inputs[Utils.uuid()] = { - label : 'Edit Step Attributes', - type : 'section', - expand : this.node.annotation, - inputs : [{ - label : 'Annotation / Notes', - name : 'annotation', - type : 'text', - area : true, - help : 'Add an annotation or notes to this step; annotations are available when a workflow is viewed.', - value : this.node.annotation - }] + label : 'Annotation / Notes', + name : 'annotation', + type : 'text', + area : true, + help : 'Add an annotation or note for this step. It will be shown with the workflow.', + value : this.node.annotation } - - // for actions - this.post_job_actions = this.node.post_job_actions; - for (var i in this.node.output_terminals) { - inputs[Utils.uuid()] = this._makeSection(i); + + // get first output id + var output_id = this.node.output_terminals && Object.keys(this.node.output_terminals)[0]; + if (output_id) { + // send email on job completion + inputs[Utils.uuid()] = { + name : 'pja__' + output_id + '__EmailAction', + label : 'Email notification', + type : 'boolean', + value : String(Boolean(this.post_job_actions['EmailAction' + output_id])), + ignore : 'false', + help : 'An email notification will be send when the job has completed.', + payload : { + 'host' : window.location.host + } + }; + + // delete non-output files + inputs[Utils.uuid()] = { + name : 'pja__' + output_id + '__DeleteIntermediatesAction', + label : 'Output cleanup', + type : 'boolean', + value : String(Boolean(this.post_job_actions['DeleteIntermediatesAction' + output_id])), + ignore : 'false', + help : 'Delete intermediate outputs if they are not used as input for another job.' + }; + + // add output specific actions + for (var i in this.node.output_terminals) { + inputs[Utils.uuid()] = this._makeSection(i); + } } }, - + /** Builds sub section with step actions/annotation */ _makeSection: function(output_id){ @@ -88,12 +111,12 @@ 1 : this.datatypes[key] }); } - + // sort extensions extensions.sort(function(a, b) { return a.label > b.label ? 1 : a.label < b.label ? -1 : 0; }); - + // add additional options extensions.unshift({ 0 : 'Sequences', @@ -105,12 +128,12 @@ }); extensions.unshift({ 0 : 'Leave unchanged', - 1 : 'None' + 1 : '' }); - + // create custom sub section var input_config = { - label : 'Edit Step Action: \'' + output_id + '\'', + label : 'Add Actions: \'' + output_id + '\'', type : 'section', inputs : [{ action : 'RenameDatasetAction', @@ -125,7 +148,7 @@ argument : 'newtype', label : 'Change datatype', type : 'select', - ignore : 'None', + ignore : '', options : extensions, help : 'This action will change the datatype of the output to the indicated value.' },{ @@ -143,59 +166,42 @@ action : 'ColumnSetAction', argument : 'chromCol', label : 'Chrom column', - type : 'text', + type : 'integer', value : '', ignore : '' },{ action : 'ColumnSetAction', argument : 'startCol', label : 'Start column', - type : 'text', + type : 'integer', value : '', ignore : '' },{ action : 'ColumnSetAction', argument : 'endCol', label : 'End column', - type : 'text', + type : 'integer', value : '', ignore : '' },{ action : 'ColumnSetAction', argument : 'strandCol', label : 'Strand column', - type : 'text', + type : 'integer', value : '', ignore : '' },{ action : 'ColumnSetAction', argument : 'nameCol', label : 'Name column', - type : 'text', + type : 'integer', value : '', ignore : '' }], help : 'This action will set column assignments in the output dataset. Blank fields are ignored.' - },{ - action : 'EmailAction', - label : 'Email notification', - type : 'boolean', - value : 'false', - ignore : 'false', - help : 'This action will send an email notifying you when the job is done.', - payload : { - 'host' : window.location.host - } - },{ - action : 'DeleteIntermediatesAction', - label : 'Delete non-outputs', - type : 'boolean', - value : 'false', - ignore : 'false', - help : 'All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect.' }] }; - + // visit input nodes and enrich by name/value pairs from server data var self = this; function visit (head, head_list) { @@ -209,7 +215,7 @@ if (input.argument) { input.name += '__' + input.argument; } - + // modify names of payload arguments if (input.payload) { for (var p_id in input.payload) { @@ -218,7 +224,7 @@ delete p; } } - + // access/verify existence of value var d = self.post_job_actions[input.action + output_id]; if (d) { @@ -242,11 +248,11 @@ } } visit(input_config); - + // return final configuration return input_config; }, - + /** Builds a new model through api call and recreates the entire form */ _buildModel: function() { @@ -260,24 +266,24 @@ } }); }, - + /** Request a new model for an already created tool form and updates the form inputs */ _updateModel: function() { // create the request dictionary var self = this; var current_state = this.tree.finalize(); - + // log tool state console.debug('tools-form-workflow::_refreshForm() - Refreshing states.'); console.debug(current_state); - + // register process var process_id = this.deferred.register(); // build model url for request var model_url = galaxy_config.root + 'workflow/editor_form_post?tool_id=' + this.options.id + '&__is_dynamic__=False'; - + // post job Utils.request({ type : 'GET', diff -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 -r e0441a0f85307fb9caf854fd10133f71cc3852d3 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -275,6 +275,7 @@ } }); portlet.append(sub_section.$el); + portlet.append($('<div/>').addClass('ui-table-form-info').html(input_def.help)); // add event handler visibility button var visible = false; diff -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 -r e0441a0f85307fb9caf854fd10133f71cc3852d3 static/scripts/mvc/ui/ui-slider.js --- a/static/scripts/mvc/ui/ui-slider.js +++ b/static/scripts/mvc/ui/ui-slider.js @@ -54,7 +54,7 @@ } // add text field event - this.$text.on('change', function () { + this.$text.on('input', function () { self.value($(this).val()); }); diff -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 -r e0441a0f85307fb9caf854fd10133f71cc3852d3 static/scripts/packed/mvc/tools/tools-form-workflow.js --- a/static/scripts/packed/mvc/tools/tools-form-workflow.js +++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.use_defaults=true;b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Edit Step Attributes",type:"section",expand:this.node.annotation,inputs:[{label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or notes to this step; annotations are available when a workflow is viewed.",value:this.node.annotation}]};this.post_job_actions=this.node.post_job_actions;for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:"None"});var f={label:"Edit Step Action: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"None",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"text",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"text",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."},{action:"EmailAction",label:"Email notification",type:"boolean",value:"false",ignore:"false",help:"This action will send an email notifying you when the job is done.",payload:{host:window.location.host}},{action:"DeleteIntermediatesAction",label:"Delete non-outputs",type:"boolean",value:"false",ignore:"false",help:"All non-output steps of this workflow will have datasets deleted if they are no longer being used as job inputs when the job this action is attached to is finished. You *must* be using workflow outputs (the snowflake) in your workflow for this to have any effect."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.use_defaults=true;b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e=this.tree.finalize();console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"workflow/editor_form_post?tool_id="+this.options.id+"&__is_dynamic__=False";b.request({type:"GET",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}}); \ No newline at end of file diff -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 -r e0441a0f85307fb9caf854fd10133f71cc3852d3 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls="ui-table-plain";i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/ui/ui-portlet","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(e,b,h,d,c,a,f){var g=Backbone.View.extend({initialize:function(j,i){this.app=j;this.inputs=i.inputs;i.cls="ui-table-plain";i.cls_tr="section-row";this.table=new b.View(i);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var j in this.inputs){this.add(this.inputs[j])}},add:function(k){var j=this;var i=jQuery.extend(true,{},k);i.id=k.id=e.uuid();this.app.input_list[i.id]=i;var l=i.type;switch(l){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(j){var k=this;j.test_param.id=j.id;var n=this._addRow(j.test_param);n.options.onchange=function(w){var v=k.app.tree.matchCase(j,w);for(var u in j.cases){var q=j.cases[u];var t=j.id+"-section-"+u;var p=k.table.get(t);var s=false;for(var r in q.inputs){if(!q.inputs[r].hidden){s=true;break}}if(u==v&&s){p.fadeIn("fast")}else{p.hide()}}k.app.trigger("refresh")};for(var m in j.cases){var l=j.id+"-section-"+m;var o=new g(this.app,{inputs:j.cases[m].inputs});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(l)}n.trigger("change")},_addRepeat:function(p){var s=this;var q=0;function n(i,u){var t=p.id+"-section-"+(q++);var v=null;if(u){v=function(){l.del(t);l.retitle(p.title);s.app.trigger("refresh")}}var w=new g(s.app,{inputs:i});l.add({id:t,title:p.title,$el:w.$el,ondel:v});l.retitle(p.title)}var l=new c.View({title_new:p.title,max:p.max,onnew:function(){n(p.inputs,true);s.app.trigger("refresh")}});var j=p.min;var r=_.size(p.cache);for(var m=0;m<Math.max(r,j);m++){var o=null;if(m<r){o=p.cache[m]}else{o=p.inputs}n(o,m>=j)}var k=new f(this.app,{label:p.title,help:p.help,field:l});k.$el.addClass("ui-table-form-section");this.table.add(k.$el);this.table.append(p.id)},_addSection:function(i){var j=this;var n=new g(j.app,{inputs:i.inputs});var m=new h.ButtonIcon({icon:"fa-eye-slash",tooltip:"Show/hide section",cls:"ui-button-icon-plain"});var l=new d.View({title:i.label,cls:"ui-portlet-section",operations:{button_visible:m}});l.append(n.$el);l.append($("<div/>").addClass("ui-table-form-info").html(i.help));var k=false;l.$content.hide();l.$header.css("cursor","pointer");l.$header.on("click",function(){if(k){k=false;l.$content.hide();m.setIcon("fa-eye-slash")}else{k=true;l.$content.fadeIn("fast");m.setIcon("fa-eye")}});if(i.expand){l.$header.trigger("click")}this.table.add(l.$el);this.table.append(i.id)},_addRow:function(i){var l=i.id;var j=this._createField(i);this.app.field_list[l]=j;var k=new f(this.app,{label:i.label,default_value:i.default_value,optional:i.optional,help:i.help,field:j});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);if(i.hidden){this.table.get(l).hide()}return j},_createField:function(i){var j=null;switch(i.type){case"text":j=this._fieldText(i);break;case"select":j=this._fieldSelect(i);break;case"data":j=this._fieldData(i);break;case"data_collection":j=this._fieldData(i);break;case"data_column":i.error_text="Missing columns in referenced dataset.";j=this._fieldSelect(i);break;case"hidden":j=this._fieldHidden(i);break;case"hidden_data":j=this._fieldHidden(i);break;case"integer":j=this._fieldSlider(i);break;case"float":j=this._fieldSlider(i);break;case"boolean":j=this._fieldBoolean(i);break;case"genomebuild":i.searchable=true;j=this._fieldSelect(i);break;case"drill_down":j=this._fieldDrilldown(i);break;case"baseurl":j=this._fieldHidden(i);break;default:this.app.incompatible=true;if(i.options){j=this._fieldSelect(i)}else{j=this._fieldText(i)}console.debug("tools-form::_addRow() : Auto matched field type ("+i.type+").")}if(i.value!==undefined){j.value(i.value)}return j},_fieldData:function(i){if(!this.app.options.is_dynamic){i.info="Data input '"+i.name+"' ("+e.textify(i.extensions.toString())+")";i.value=null;return this._fieldHidden(i)}var j=this;return new a.View(this.app,{id:"field-"+i.id,extensions:i.extensions,optional:i.optional,multiple:i.multiple,type:i.type,data:i.options,onchange:function(){j.app.trigger("refresh")}})},_fieldSelect:function(j){if(!this.app.options.is_dynamic&&j.is_dynamic){return this._fieldText(j)}var l=[];for(var m in j.options){var n=j.options[m];l.push({label:n[0],value:n[1]})}var o=h.Select;switch(j.display){case"checkboxes":o=h.Checkbox;break;case"radio":o=h.Radio;break}var k=this;return new o.View({id:"field-"+j.id,data:l,error_text:j.error_text||"No options available",multiple:j.multiple,searchable:j.searchable,onchange:function(){k.app.trigger("refresh")}})},_fieldDrilldown:function(i){if(!this.app.options.is_dynamic&&i.is_dynamic){return this._fieldText(i)}var j=this;return new h.Drilldown.View({id:"field-"+i.id,data:i.options,display:i.display,onchange:function(){j.app.trigger("refresh")}})},_fieldText:function(i){if(i.options){i.area=i.multiple;if(!e.validate(i.value)){i.value=""}else{if(i.value instanceof Array){i.value=value.toString()}else{i.value=String(i.value).replace(/[\[\]'"\s]/g,"");if(i.multiple){i.value=i.value.replace(/,/g,"\n")}}}}var j=this;return new h.Input({id:"field-"+i.id,area:i.area,onchange:function(){j.app.trigger("refresh")}})},_fieldSlider:function(i){var j=this;return new h.Slider.View({id:"field-"+i.id,precise:i.type=="float",min:i.min,max:i.max,onchange:function(){j.app.trigger("refresh")}})},_fieldHidden:function(i){return new h.Hidden({id:"field-"+i.id,info:i.info})},_fieldBoolean:function(i){var j=this;return new h.RadioButton.View({id:"field-"+i.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}],onchange:function(){j.app.trigger("refresh")}})}});return{View:g}}); \ No newline at end of file diff -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 -r e0441a0f85307fb9caf854fd10133f71cc3852d3 static/scripts/packed/mvc/ui/ui-slider.js --- a/static/scripts/packed/mvc/ui/ui-slider.js +++ b/static/scripts/packed/mvc/ui/ui-slider.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{min:null,max:null,step:null,precise:false,split:10000},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min;if(this.options.step===null){this.options.step=1;if(this.options.precise&&this.useslider){this.options.step=(this.options.max-this.options.min)/this.options.split}}if(this.useslider){this.$slider=this.$el.find("#slider");this.$slider.slider(this.options);this.$slider.on("slide",function(f,g){c.value(g.value)})}else{this.$el.find(".ui-form-slider-text").css("width","100%")}this.$text=this.$el.find("#text");if(this.options.value!==undefined){this.value(this.options.value)}this.$text.on("change",function(){c.value($(this).val())});var e=[];this.$text.on("keyup",function(f){e[f.which]=false});this.$text.on("keydown",function(g){var f=g.which;e[f]=true;if(!(f==8||f==9||f==13||f==37||f==39||(f>=48&&f<=57)||(f==190&&$(this).val().indexOf(".")==-1&&c.options.precise)||(f==189&&$(this).val().indexOf("-")==-1)||e[91]||e[17])){event.preventDefault()}})},value:function(c){if(c!==undefined){if(isNaN(c)){c=0}if(this.options.max!==null){c=Math.min(c,this.options.max)}if(this.options.min!==null){c=Math.max(c,this.options.min)}if(this.options.onchange){this.options.onchange(c)}this.$slider&&this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{min:null,max:null,step:null,precise:false,split:10000},initialize:function(d){var c=this;this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.useslider=this.options.max!==null&&this.options.min!==null&&this.options.max>this.options.min;if(this.options.step===null){this.options.step=1;if(this.options.precise&&this.useslider){this.options.step=(this.options.max-this.options.min)/this.options.split}}if(this.useslider){this.$slider=this.$el.find("#slider");this.$slider.slider(this.options);this.$slider.on("slide",function(f,g){c.value(g.value)})}else{this.$el.find(".ui-form-slider-text").css("width","100%")}this.$text=this.$el.find("#text");if(this.options.value!==undefined){this.value(this.options.value)}this.$text.on("input",function(){c.value($(this).val())});var e=[];this.$text.on("keyup",function(f){e[f.which]=false});this.$text.on("keydown",function(g){var f=g.which;e[f]=true;if(!(f==8||f==9||f==13||f==37||f==39||(f>=48&&f<=57)||(f==190&&$(this).val().indexOf(".")==-1&&c.options.precise)||(f==189&&$(this).val().indexOf("-")==-1)||e[91]||e[17])){event.preventDefault()}})},value:function(c){if(c!==undefined){if(isNaN(c)){c=0}if(this.options.max!==null){c=Math.min(c,this.options.max)}if(this.options.min!==null){c=Math.max(c,this.options.min)}if(this.options.onchange){this.options.onchange(c)}this.$slider&&this.$slider.slider("value",c);this.$text.val(c)}return this.$text.val()},_template:function(c){return'<div id="'+c.id+'" class="ui-form-slider"><input id="text" type="text" class="ui-form-slider-text"/><div id="slider" class="ui-form-slider-element"/></div>'}});return{View:b}}); \ 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: carlfeberhard: History API: allow filtering, limit, and offset in index params; Implement managers/base.FilterParser to configure how models can be filtered; Change ModelManager.list to allow limit, offset, and post-query (functional) filters; Add user filter, limit, and offset parsers to BaseController; Add tests for previous; Remove some UserManager functions; Continue filling out Annotatable mixin
by commits-noreply＠bitbucket.org 29 Jan '15

29 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/68f0ed37e089/ Changeset: 68f0ed37e089 User: carlfeberhard Date: 2015-01-29 15:42:54+00:00 Summary: History API: allow filtering, limit, and offset in index params; Implement managers/base.FilterParser to configure how models can be filtered; Change ModelManager.list to allow limit, offset, and post-query (functional) filters; Add user filter, limit, and offset parsers to BaseController; Add tests for previous; Remove some UserManager functions; Continue filling out Annotatable mixin Affected #: 13 files diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 lib/galaxy/managers/annotatable.py --- a/lib/galaxy/managers/annotatable.py +++ b/lib/galaxy/managers/annotatable.py @@ -11,6 +11,26 @@ annotation_assoc = None # TODO: most of this seems to be covered by item_attrs.UsesAnnotations + # TODO: use these below (serializer/deserializer) + def user_annotation( self, trans, item, user ): + return item.get_item_annotation_str( self.app.model.context, user, item ) + + def owner_annotation( self, trans, item ): + return self.user_annotation( trans, item, item.user ) + + def delete_annotation( self, trans, item, user ): + return item.delete_item_annotation( self.app.model.context, user, item ) + + def annotate( self, trans, item, user, annotation ): + if annotation is None: + self.delete_annotation( self, trans, item, user ) + return None + + annotation_obj = item.add_item_annotation( self.app.model.context, user, item, annotation ) + return annotation_obj.annotation + + #def by_user( self, trans, user, **kwargs ): + # pass class AnnotatableSerializer( object ): diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 lib/galaxy/managers/base.py --- a/lib/galaxy/managers/base.py +++ b/lib/galaxy/managers/base.py @@ -32,6 +32,7 @@ from galaxy import exceptions from galaxy import model from galaxy.model import tool_shed_install +from galaxy.managers import filters as filter_parser import logging log = logging.getLogger( __name__ ) @@ -159,12 +160,7 @@ def __init__( self, app ): self.app = app - def _default_order_by( self ): - """ - Returns a tuple of columns for the default order when getting multiple models. - """ - return ( self.model_class.create_time, ) - + # .... query foundation wrapper def query( self, trans, eagerloads=True, filters=None, order_by=None, limit=None, offset=None, **kwargs ): """ Return a basic query from model_class, filters, order_by, and limit and offset. @@ -172,17 +168,17 @@ Set eagerloads to False to disable them for this query. """ query = trans.sa_session.query( self.model_class ) - # joined table loading if eagerloads is False: query = query.enable_eagerloads( False ) - # TODO: if non-orm filters are the only option, here is where they'd go - query = self._apply_filters( query, filters ) - query = self._apply_order_by_limit_offset( query, order_by, limit, offset ) + query = self._apply_orm_filters( query, filters ) + query = self._apply_order_by( query, order_by ) + query = self._apply_orm_limit_offset( query, limit, offset ) return query - def _apply_filters( self, query, filters ): + # .... filters + def _apply_orm_filters( self, query, filters ): """ Add any filters to the given query. """ @@ -213,13 +209,7 @@ filtersB = [ filtersB ] return filtersA + filtersB - def _apply_order_by_limit_offset( self, query, order_by, limit, offset ): - """ - Return the query after adding the order_by, limit, and offset clauses. - """ - query = self._apply_order_by( query, order_by ) - return self._apply_limit_offset( query, limit, offset ) - + # .... order, limit, and offset def _apply_order_by( self, query, order_by ): """ Return the query after adding the order_by clauses. @@ -233,7 +223,13 @@ return query.order_by( *order_by ) return query.order_by( order_by ) - def _apply_limit_offset( self, query, limit, offset ): + def _default_order_by( self ): + """ + Returns a tuple of columns for the default order when getting multiple models. + """ + return ( self.model_class.create_time, ) + + def _apply_orm_limit_offset( self, query, limit, offset ): """ Return the query after applying the given limit and offset (if not None). """ @@ -243,6 +239,7 @@ query = query.offset( offset ) return query + # .... query resolution def one( self, trans, **kwargs ): """ Sends kwargs to build the query and returns one and only one model. @@ -284,25 +281,94 @@ id_filter = self.model_class.id == id return self.one( trans, filters=id_filter, **kwargs ) - def list( self, trans, query=None, **kwargs ): + # .... multirow queries + def _orm_list( self, trans, query=None, **kwargs ): """ Sends kwargs to build the query return all models found. """ query = query or self.query( trans, **kwargs ) return query.all() - def _query_by_ids( self, trans, ids, filters=None, **kwargs ): + #def list( self, trans, query=None, filters=None, order_by=None, limit=None, offset=None, **kwargs ): + def list( self, trans, filters=None, order_by=None, limit=None, offset=None, **kwargs ): """ - Builds a query to find a list of models with the given list of `ids`. + Returns all objects matching the given filters """ - ids_filter = self.model_class.id.in_( ids ) - return self.query( trans, filters=self._munge_filters( ids_filter, filters ), **kwargs ) + orm_filters, fn_filters = self._split_filters( filters ) + if not fn_filters: + # if no fn_filtering required, we can use the 'all orm' version with limit offset + return self._orm_list( trans, filters=orm_filters, order_by=order_by, limit=limit, offset=offset, **kwargs ) - def by_ids( self, trans, ids, **kwargs ): + # fn filters will change the number of items returnable by limit/offset - remove them here from the orm query + query = self.query( trans, filters=orm_filters, order_by=order_by, limit=None, offset=None, **kwargs ) + items = query.all() + + # apply limit, offset after SQL filtering + items = self._apply_fn_filters_gen( items, fn_filters ) + return list( self._apply_fn_limit_offset_gen( items, limit, offset ) ) + + def _split_filters( self, filters ): + """ + Splits `filters` into a tuple of two lists: + a list of filters to be added to the SQL query + and a list of functional filters to be applied after the SQL query. + """ + orm_filters, fn_filters = ( [], [] ) + if filters is None: + return ( orm_filters, fn_filters ) + if not isinstance( filters, list ): + filters = [ filters ] + for filter_ in filters: + if self._is_fn_filter( filter_ ): + fn_filters.append( filter_ ) + else: + orm_filters.append( filter_ ) + return ( orm_filters, fn_filters ) + + def _is_fn_filter( self, filter_ ): + """ + Returns True if `filter_` is a functional filter to be applied after the SQL query. + """ + return callable( filter_ ) + + def _apply_fn_filters_gen( self, items, filters ): + """ + If all the filter functions in `filters` return True for an item in `items`, + yield that item. + """ + #cpu-expensive + for item in items: + filter_results = map( lambda f: f( item ), filters ) + if all( filter_results ): + yield item + + def _apply_fn_limit_offset_gen( self, items, limit, offset ): + """ + Iterate over `items` and begin yielding items after + `offset` number of items and stop when we've yielded + `limit` number of items. + """ + # change negative limit, offset to None + if limit is not None and limit < 0: + limit = None + if offset is not None and offset < 0: + offset = None + + yielded = 0 + for i, item in enumerate( items ): + if offset is not None and i < offset: + continue + if limit is not None and yielded >= limit: + break + yield item + yielded += 1 + + def by_ids( self, trans, ids, filters=None, **kwargs ): """ Returns an in-order list of models with the matching ids in `ids`. """ - found = self._query_by_ids( trans, ids, **kwargs ).all() + ids_filter = self.model_class.id.in_( ids ) + found = self.list( trans, filters=self._munge_filters( ids_filter, filters ), **kwargs ) # TODO: this does not order by the original 'ids' array # ...could use get (supposedly since found are in the session, the db won't be hit twice) @@ -607,6 +673,9 @@ val = self.validate.int_range( key, val, min, max ) return self.default_deserializer( trans, item, key, val ) + #def deserialize_date( self, trans, item, key, val ): + # #TODO: parse isoformat date into date object + # ... common deserializers for Galaxy def deserialize_genome_build( self, trans, item, key, val ): """ @@ -691,6 +760,229 @@ # pass +# ==== Building query filters based on model data +class FilterParser( object ): + """ + Converts string tuples (partially converted query string params) of + attr, op, val into either: + - ORM based filters (filters that can be applied by the ORM at the SQL + level) or + - functional filters (filters that use derived values or values not + within the SQL tables) + These filters can then be applied to queries. + + This abstraction allows 'smarter' application of limit and offset at either the + SQL level or the generator/list level based on the presence of functional + filters. In other words, if no functional filters are present, limit and offset + may be applied at the SQL level. If functional filters are present, limit and + offset need to applied at the list level. + + These might be safely be replaced in the future by creating SQLAlchemy + hybrid properties or more thoroughly mapping derived values. + """ + #??: this class kindof 'lives' in both the world of the controllers/param-parsing and to models/orm + # (as the model informs how the filter params are parsed) + # I have no great idea where this 'belongs', so it's here for now + + #: model class + model_class = None + + def __init__( self, app ): + """ + Set up serializer map, any additional serializable keys, and views here. + """ + self.app = app + + #: dictionary containing parsing data for ORM/SQLAlchemy-based filters + #..note: although kind of a pain in the ass and verbose, opt-in/whitelisting allows more control + #: over potentially expensive queries + self.orm_filter_parsers = {} + + #: dictionary containing parsing data for functional filters - applied after a query is made + self.fn_filter_parsers = {} + + # set up both of the above + self._add_parsers() + + def _add_parsers( self ): + """ + Set up, extend, or alter `orm_filter_parsers` and `fn_filter_parsers`. + """ + pass + + def parse_filters( self, filter_tuple_list ): + """ + Parse string 3-tuples (attr, op, val) into orm or functional filters. + """ + parsed = [] + for ( attr, op, val ) in filter_tuple_list: + filter_ = self.parse_filter( attr, op, val ) + parsed.append( filter_ ) + return parsed + + def parse_filter( self, attr, op, val ): + """ + Attempt to parse filter as a custom/fn filter, then an orm filter, and + if neither work - raise an error. + + :raises exceptions.RequestParameterInvalidException: if no functional or orm + filter can be parsed. + """ + try: + # check for a custom filter + fn_filter = self._parse_fn_filter( attr, op, val ) + if fn_filter is not None: + return fn_filter + + # if no custom filter found, try to make an ORM filter + #note: have to use explicit is None here, bool( sqlalx.filter ) == False + orm_filter = self._parse_orm_filter( attr, op, val ) + if orm_filter is not None: + return orm_filter + + # by convention, assume most val parsers raise ValueError + except ValueError, val_err: + raise exceptions.RequestParameterInvalidException( 'unparsable value for filter', + column=attr, operation=op, value=val ) + + # if neither of the above work, raise an error with how-to info + #TODO: send back all valid filter keys in exception for added user help + raise exceptions.RequestParameterInvalidException( 'bad filter', column=attr, operation=op ) + + # ---- fn filters + def _parse_fn_filter( self, attr, op, val ): + """ + """ + # fn_filter_list is a dict: fn_filter_list[ attr ] = { 'opname1' : opfn1, 'opname2' : opfn2, etc. } + + # attr, op is a nested dictionary pointing to the filter fn + attr_map = self.fn_filter_parsers.get( attr, None ) + if not attr_map: + return None + allowed_ops = attr_map.get( 'op' ) + # allowed ops is a map here, op => fn + filter_fn = allowed_ops.get( op, None ) + if not filter_fn: + return None + # parse the val from string using the 'val' parser if present (otherwise, leave as string) + val_parser = attr_map.get( 'val', None ) + if val_parser: + val = val_parser( val ) + + # curry/partial and fold the val in there now + return lambda i: filter_fn( i, val ) + + # ---- ORM filters + def _parse_orm_filter( self, attr, op, val ): + """ + """ + # orm_filter_list is a dict: orm_filter_list[ attr ] = <list of allowed ops> + # attr must be a whitelisted column + column = self.model_class.table.columns.get( attr ) + column_map = self.orm_filter_parsers.get( attr, None ) + if column is None or not column_map: + return None + # op must be whitelisted: contained in the list orm_filter_list[ attr ][ 'op' ] + allowed_ops = column_map.get( 'op' ) + if op not in allowed_ops: + return None + op = self._convert_op_string_to_fn( column, op ) + # parse the val from string using the 'val' parser if present (otherwise, leave as string) + val_parser = column_map.get( 'val', None ) + if val_parser: + val = val_parser( val ) + + orm_filter = op( val ) + return orm_filter + + #: these are the easier/shorter string equivalents to the python operator fn names that need '__' around them + UNDERSCORED_OPS = ( 'lt', 'le', 'eq', 'ne', 'ge', 'gt' ) + #UNCHANGED_OPS = ( 'like' ) + def _convert_op_string_to_fn( self, column, op_string ): + """ + """ + # correct op_string to usable function key + fn_name = op_string + if op_string in self.UNDERSCORED_OPS: + fn_name = '__' + op_string + '__' + elif op_string == 'in': + fn_name = 'in_' + + # get the column fn using the op_string and error if not a callable attr + #TODO: special case 'not in' - or disallow? + op_fn = getattr( column, fn_name, None ) + if not op_fn or not callable( op_fn ): + return None + return op_fn + + # --- more parsers! yay! +#TODO: These should go somewhere central - we've got ~6 parser modules/sections now + #TODO: to annotatable + def _owner_annotation( self, item ): + """ + Get the annotation by the item's owner. + """ + if not item.user: + return None + for annotation in item.annotations: + if annotation.user == item.user: + return annotation.annotation + return None + + def filter_annotation_contains( self, item, val ): + """ + Test whether `val` is in the owner's annotation. + """ + owner_annotation = self._owner_annotation( item ) + if owner_annotation is None: + return False + return val in owner_annotation + + #TODO: to taggable + def _filter_tags( self, item, val, fn_name='__eq__' ): + """ + Test whether the string version of any tag `fn_name`s (__eq__, contains) + `val`. + """ + #TODO: which user is this? all? + for tag in item.tags: + tag_str = tag.user_tname + if tag.value is not None: + tag_str += ":" + tag.user_value + if tag_str[ fn_name ]( val ): + return True + return False + + def filter_has_partial_tag( self, item, val ): + """ + Return True if any tag partially contains `val`. + """ + return self._filter_tags( item, val, fn_name='contains' ) + + def filter_has_tag( self, item, val ): + """ + Return True if any tag exactly equals `val`. + """ + return self._filter_tags( item, val, fn_name='__eq__' ) + + def parse_bool( self, bool_string ): + """ + Parse a boolean from a string. + """ + #Be strict here to remove complexity of options. + if bool_string in ( 'True', True ): + return True + if bool_string in ( 'False', False ): + return False + raise ValueError( 'invalid boolean: ' + str( bool_string ) ) + + def parse_id_list( self, id_list_string, sep=',' ): + """ + Split `id_list_string` at `sep`. + """ + return id_list_string.split( sep ) + + # ==== Security Mixins class AccessibleModelInterface( object ): """ @@ -794,8 +1086,9 @@ :raises exceptions.ItemAccessibilityException: """ + raise exceptions.NotImplemented( "Abstract Interface Method" ) # just alias to by_user (easier/same thing) - return self.by_user( trans, user, **kwargs ) + #return self.by_user( trans, user, **kwargs ) def filter_owned( self, trans, user, **kwargs ): """ diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 lib/galaxy/managers/histories.py --- a/lib/galaxy/managers/histories.py +++ b/lib/galaxy/managers/histories.py @@ -63,7 +63,7 @@ return super( HistoryManager, self ).is_owner( trans, history, user ) #TODO: possibly to sharable - def most_recent( self, trans, user, **kwargs ): + def most_recent( self, trans, user, filters=None, **kwargs ): """ Return the most recently update history for the user. """ @@ -71,7 +71,8 @@ if not user: return None if trans.history.deleted else trans.history desc_update_time = self.model_class.table.c.update_time - return self._query_by_user( trans, user, order_by=desc_update_time, limit=1, **kwargs ).first() + filters = self._munge_filters( filters, self.model_class.user_id == user.id ) + return self.query( trans, filters=filters, order_by=desc_update_time, limit=1, **kwargs ).first() # .... purgable def purge( self, trans, history, flush=True, **kwargs ): @@ -109,7 +110,7 @@ return self.set_current( trans, self.by_id( trans, history_id ) ) # .... serialization - #TODO: move to serializer (i.e. history with contents attr) +#TODO: move to serializer (i.e. history with contents attr) def _get_history_data( self, trans, history ): """ Returns a dictionary containing ``history`` and ``contents``, serialized @@ -342,7 +343,6 @@ super( HistoryDeserializer, self ).__init__( app ) self.history_manager = self.manager - #assumes: incoming from json.loads and sanitized def add_deserializers( self ): super( HistoryDeserializer, self ).add_deserializers() base.PurgableModelDeserializer.add_deserializers( self ) @@ -351,3 +351,45 @@ 'name' : self.deserialize_basestring, 'genome_build' : self.deserialize_genome_build, }) + + +class HistoryFilters( base.FilterParser ): + model_class = model.History + + def _add_parsers( self ): + super( HistoryFilters, self )._add_parsers() + self.orm_filter_parsers.update({ + #TODO: these three are (prob.) applicable to all models + 'id' : { 'op': ( 'in' ), 'val': self.parse_id_list }, + # dates can be directly passed through the orm into a filter (no need to parse into datetime object) + 'create_time' : { 'op': ( 'le', 'ge' ) }, + 'update_time' : { 'op': ( 'le', 'ge' ) }, + + # history specific + 'name' : { 'op': ( 'eq', 'contains', 'like' ) }, + 'genome_build' : { 'op': ( 'eq', 'contains', 'like' ) }, + + #TODO: purgable + 'deleted' : { 'op': ( 'eq' ), 'val': self.parse_bool }, + 'purged' : { 'op': ( 'eq' ), 'val': self.parse_bool }, + + #TODO: sharable + 'importable' : { 'op': ( 'eq' ), 'val': self.parse_bool }, + 'published' : { 'op': ( 'eq' ), 'val': self.parse_bool }, + 'slug' : { 'op': ( 'eq', 'contains', 'like' ) }, + # chose by user should prob. only be available for admin? (most often we'll only need trans.user) + #'user' : { 'op': ( 'eq' ), 'val': self.parse_id_list }, + }) + + #TODO: I'm not entirely convinced this (or tags) are a good idea for filters since they involve a/the user + self.fn_filter_parsers.update({ + #TODO: add this in annotatable mixin + 'annotation' : { 'op': { 'in' : self.filter_annotation_contains, } }, + #TODO: add this in taggable mixin + 'tag' : { + 'op': { + 'eq' : self.filter_has_tag, + 'in' : self.filter_has_partial_tag, + } + } + }) diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 lib/galaxy/managers/ratable.py --- a/lib/galaxy/managers/ratable.py +++ b/lib/galaxy/managers/ratable.py @@ -16,6 +16,9 @@ #TODO: most of this seems to be covered by item_attrs.UsesItemRatings + #def by_user( self, trans, user, **kwargs ): + # pass + class RatableSerializer( object ): @@ -33,6 +36,7 @@ """ pass + class RatableDeserializer( object ): def add_deserializers( self ): diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 lib/galaxy/managers/sharable.py --- a/lib/galaxy/managers/sharable.py +++ b/lib/galaxy/managers/sharable.py @@ -41,22 +41,14 @@ self.user_manager = users.UserManager( app ) # .... has a user - def _query_by_user( self, trans, user, filters=None, **kwargs ): + def by_user( self, trans, user, filters=None, **kwargs ): """ - Return query for all items (of model_class type) associated with the given + Return list for all items (of model_class type) associated with the given `user`. """ user_filter = self.model_class.user_id == user.id filters=self._munge_filters( user_filter, filters ) - return self.query( trans, filters=filters, **kwargs ) - - def by_user( self, trans, user, **kwargs ): - """ - Return list for all items (of model_class type) associated with the given - `user`. - """ - query = self._query_by_user( trans, user, **kwargs ) - return self.list( trans, query=query, **kwargs ) + return self.list( trans, filters=filters, **kwargs ) # .... owned model interface def is_owner( self, trans, item, user ): diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 lib/galaxy/managers/taggable.py --- a/lib/galaxy/managers/taggable.py +++ b/lib/galaxy/managers/taggable.py @@ -15,6 +15,9 @@ #TODO: most of this can be done by delegating to the TagManager? + #def by_user( self, trans, user, **kwargs ): + # pass + class TaggableSerializer( object ): diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 lib/galaxy/managers/users.py --- a/lib/galaxy/managers/users.py +++ b/lib/galaxy/managers/users.py @@ -145,37 +145,9 @@ return user # ---- current - def is_current_user( self, trans, user ): - """ - Return True if this user is the trans' current user. - """ + def current_user( self, trans ): # define here for single point of change and make more readable - return user == trans.user - - def is_current_user_anonymous( self, trans ): - """ - Return True if the current user is anonymous. - """ - return self.is_anonymous( trans.user ) - - def is_current_user_admin( self, trans ): - """ - Return True if the current user is admin. - """ - return self.is_admin( trans, trans.user ) - - # ---- User-created notes/metadata on other models - #def tags( self, trans, user, **kwargs ): - # """ - # Return all tags created by this user. - # """ - # pass - - #def annotations( self, trans, user, **kwargs ): - # """ - # Return all annotations created by this user. - # """ - # pass + return trans.user # ---- api keys def create_api_key( self, trans, user ): diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -100,6 +100,7 @@ def get_role( self, trans, id, check_ownership=False, check_accessible=False, deleted=None ): return self.get_object( trans, id, 'Role', check_ownership=False, check_accessible=False, deleted=deleted ) + # ---- parsing query params def decode_id( self, id ): try: return self.app.security.decode_id( id ) @@ -115,6 +116,53 @@ """ return trans.security.encode_all_ids( rval, recursive=recursive ) + def parse_filter_params( self, qdict, filter_attr_key='q', filter_value_key='qv', attr_op_split_char='-' ): + """ + """ + #TODO: import DEFAULT_OP from FilterParser + DEFAULT_OP = 'eq' + if filter_attr_key not in qdict: + return [] + #precondition: attrs/value pairs are in-order in the qstring + attrs = qdict.get( filter_attr_key ) + if not isinstance( attrs, list ): + attrs = [ attrs ] + # ops are strings placed after the attr strings and separated by a split char (e.g. 'create_time-lt') + # ops are optional and default to 'eq' + reparsed_attrs = [] + ops = [] + for attr in attrs: + op = DEFAULT_OP + if attr_op_split_char in attr: + #note: only split the last (e.g. q=community-tags-in&qv=rna yields ( 'community-tags', 'in', 'rna' ) + attr, op = attr.rsplit( attr_op_split_char, 1 ) + ops.append( op ) + reparsed_attrs.append( attr ) + attrs = reparsed_attrs + + values = qdict.get( filter_value_key, [] ) + if not isinstance( values, list ): + values = [ values ] + #TODO: it may be more helpful to the consumer if we error on incomplete 3-tuples + # (instead of relying on zip to shorten) + return zip( attrs, ops, values ) + + def parse_limit_offset( self, qdict ): + """ + """ + def _parse_pos_int( i ): + try: + new_val = int( i ) + if new_val >= 0: + return new_val + except ( TypeError, ValueError ): + pass + return None + + limit = _parse_pos_int( qdict.get( 'limit', None ) ) + offset = _parse_pos_int( qdict.get( 'offset', None ) ) + return ( limit, offset ) + Root = BaseController diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -19,7 +19,7 @@ from galaxy.web.base.controller import ExportsHistoryMixin from galaxy.web.base.controller import ImportsHistoryMixin -from galaxy.managers import histories, citations +from galaxy.managers import histories, citations, users from galaxy import util from galaxy.util import string_as_bool @@ -35,9 +35,11 @@ def __init__( self, app ): super( HistoriesController, self ).__init__( app ) self.citations_manager = citations.CitationsManager( app ) + self.user_manager = users.UserManager( app ) self.history_manager = histories.HistoryManager( app ) self.history_serializer = histories.HistorySerializer( app ) self.history_deserializer = histories.HistoryDeserializer( app ) + self.history_filters = histories.HistoryFilters( app ) @expose_api_anonymous def index( self, trans, deleted='False', **kwd ): @@ -55,21 +57,58 @@ :rtype: list :returns: list of dictionaries containing summary history information """ + serialization_params = self._parse_serialization_params( kwd, 'summary' ) + limit, offset = self.parse_limit_offset( kwd ) + filter_params = self.parse_filter_params( kwd ) + + # bail early with current history if user is anonymous + current_user = self.user_manager.current_user( trans ) + if self.user_manager.is_anonymous( current_user ): + current_history = self.history_manager.get_current( trans ) + #note: ignores filters, limit, offset + return [ self.history_serializer.serialize_to_view( trans, current_history, **serialization_params ) ] + + filters = [] + # support the old default of not-returning/filtering-out deleted histories + filters += self._get_deleted_filter( deleted, filter_params ) + # users are limited to requesting only their own histories (here) + filters += [ self.app.model.History.user == current_user ] + # and any sent in from the query string + filters += self.history_filters.parse_filters( filter_params ) + + #TODO: eventually make order_by a param as well + order_by = sqlalchemy.desc( self.app.model.History.create_time ) + histories = self.history_manager.list( trans, filters=filters, order_by=order_by, limit=limit, offset=offset ) + rval = [] - serialization_params = self._parse_serialization_params( kwd, 'summary' ) - - deleted_filter = ( self.app.model.History.deleted == False ) - if string_as_bool( deleted ): - deleted_filter = ( self.app.model.History.deleted == True ) - - #TODO: create time? is this right? - order_by = sqlalchemy.desc( self.app.model.History.create_time ) - histories = self.history_manager.by_user( trans, user=trans.user, filters=deleted_filter, order_by=order_by ) for history in histories: history_dict = self.history_serializer.serialize_to_view( trans, history, **serialization_params ) rval.append( history_dict ) + return rval - return rval + def _get_deleted_filter( self, deleted, filter_params ): + #TODO: this should all be removed (along with the default) in v2 + # support the old default of not-returning/filtering-out deleted histories + try: + # the consumer must explicitly ask for both deleted and non-deleted + # but pull it from the parsed params (as the filter system will error on None) + deleted_filter_index = filter_params.index( ( 'deleted', 'eq', 'None' ) ) + filter_params.pop( deleted_filter_index ) + return [] + except ValueError: + pass + + # the deleted string bool was also used as an 'include deleted' flag + if deleted in ( 'True', 'true' ): + return [ self.app.model.History.deleted == True ] + + # the third option not handled here is 'return only deleted' + # if this is passed in (in the form below), simply return and let the filter system handle it + if ( 'deleted', 'eq', 'True' ) in filter_params: + return [] + + # otherwise, do the default filter of removing the deleted histories + return [ self.app.model.History.deleted == False ] @expose_api_anonymous def show( self, trans, id, deleted='False', **kwd ): diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 test/unit/managers/mock.py --- a/test/unit/managers/mock.py +++ b/test/unit/managers/mock.py @@ -18,6 +18,9 @@ # ============================================================================= +class OpenObject( object ): + pass + class MockAppConfig( Bunch ): def __init__( self, **kwargs ): Bunch.__init__( self, **kwargs ) diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 test/unit/managers/test_HistoryManager.py --- a/test/unit/managers/test_HistoryManager.py +++ b/test/unit/managers/test_HistoryManager.py @@ -20,6 +20,7 @@ import mock from test_ModelManager import BaseTestCase from galaxy.managers.histories import HistoryManager +from galaxy.managers.histories import HistoryFilters # ============================================================================= @@ -92,9 +93,6 @@ user_histories = self.history_mgr.by_user( self.trans, owner ) self.assertEqual( user_histories, [ item1, item2 ] ) - query = self.history_mgr._query_by_user( self.trans, owner ) - self.assertEqual( query.all(), user_histories ) - def test_ownable( self ): owner = self.user_mgr.create( self.trans, **user2_data ) non_owner = self.user_mgr.create( self.trans, **user3_data ) @@ -307,6 +305,239 @@ self.assertEqual( self.history_mgr.get_current( self.trans ), history1 ) + # ---- functional and orm filter splitting and resolution + def test_parse_filters( self ): + filter_parser = HistoryFilters( self.app ) + filters = filter_parser.parse_filters([ + ( 'name', 'eq', 'wot' ), + ( 'deleted', 'eq', 'True' ), + ( 'annotation', 'in', 'hrrmm' ) + ]) + self.log( 'both orm and fn filters should be parsed and returned' ) + self.assertEqual( len( filters ), 3 ) + + self.log( 'values should be parsed' ) + self.assertEqual( filters[1].right.value, True ) + + def test_parse_filters_invalid_filters( self ): + filter_parser = HistoryFilters( self.app ) + self.log( 'should error on non-column attr') + self.assertRaises( exceptions.RequestParameterInvalidException, filter_parser.parse_filters, [ + ( 'merp', 'eq', 'wot' ), + ]) + self.log( 'should error on non-whitelisted attr') + self.assertRaises( exceptions.RequestParameterInvalidException, filter_parser.parse_filters, [ + ( 'user_id', 'eq', 'wot' ), + ]) + self.log( 'should error on non-whitelisted op') + self.assertRaises( exceptions.RequestParameterInvalidException, filter_parser.parse_filters, [ + ( 'name', 'lt', 'wot' ), + ]) + self.log( 'should error on non-listed fn op') + self.assertRaises( exceptions.RequestParameterInvalidException, filter_parser.parse_filters, [ + ( 'annotation', 'like', 'wot' ), + ]) + self.log( 'should error on val parsing error') + self.assertRaises( exceptions.RequestParameterInvalidException, filter_parser.parse_filters, [ + ( 'deleted', 'eq', 'true' ), + ]) + + def test_orm_filter_parsing( self ): + filter_parser = HistoryFilters( self.app ) + user2 = self.user_mgr.create( self.trans, **user2_data ) + history1 = self.history_mgr.create( self.trans, name='history1', user=user2 ) + history2 = self.history_mgr.create( self.trans, name='history2', user=user2 ) + history3 = self.history_mgr.create( self.trans, name='history3', user=user2 ) + + filters = filter_parser.parse_filters([ + ( 'name', 'like', 'history%' ), + ]) + histories = self.history_mgr.list( self.trans, filters=filters ) + #for h in histories: + # print h.name + self.assertEqual( histories, [ history1, history2, history3 ]) + + filters = filter_parser.parse_filters([ ( 'name', 'like', '%2' ), ]) + self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history2 ]) + + filters = filter_parser.parse_filters([ ( 'name', 'eq', 'history2' ), ]) + self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history2 ]) + + self.history_mgr.update( self.trans, history1, dict( deleted=True ) ) + filters = filter_parser.parse_filters([ ( 'deleted', 'eq', 'True' ), ]) + self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history1 ]) + filters = filter_parser.parse_filters([ ( 'deleted', 'eq', 'False' ), ]) + self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history2, history3 ]) + self.assertEqual( self.history_mgr.list( self.trans ), [ history1, history2, history3 ]) + + self.history_mgr.update( self.trans, history3, dict( deleted=True ) ) + self.history_mgr.update( self.trans, history1, dict( importable=True ) ) + self.history_mgr.update( self.trans, history2, dict( importable=True ) ) + filters = filter_parser.parse_filters([ + ( 'deleted', 'eq', 'True' ), + ( 'importable', 'eq', 'True' ), + ]) + self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history1 ]) + self.assertEqual( self.history_mgr.list( self.trans ), [ history1, history2, history3 ]) + + def test_fn_filter_parsing( self ): + filter_parser = HistoryFilters( self.app ) + user2 = self.user_mgr.create( self.trans, **user2_data ) + history1 = self.history_mgr.create( self.trans, name='history1', user=user2 ) + history2 = self.history_mgr.create( self.trans, name='history2', user=user2 ) + history3 = self.history_mgr.create( self.trans, name='history3', user=user2 ) + + filters = filter_parser.parse_filters([ ( 'annotation', 'in', 'no play' ), ]) + anno_filter = filters[0] + + history3.add_item_annotation( self.trans.sa_session, user2, history3, "All work and no play" ) + self.trans.sa_session.flush() + + self.assertTrue( anno_filter( history3 ) ) + self.assertFalse( anno_filter( history2 ) ) + + self.assertEqual( self.history_mgr.list( self.trans, filters=filters ), [ history3 ]) + + self.log( 'should allow combinations of orm and fn filters' ) + self.history_mgr.update( self.trans, history3, dict( importable=True ) ) + self.history_mgr.update( self.trans, history2, dict( importable=True ) ) + history1.add_item_annotation( self.trans.sa_session, user2, history1, "All work and no play" ) + self.trans.sa_session.flush() + + shining_examples = self.history_mgr.list( self.trans, filters=filter_parser.parse_filters([ + ( 'importable', 'eq', 'True' ), + ( 'annotation', 'in', 'no play' ), + ])) + self.assertEqual( shining_examples, [ history3 ]) + + def test_fn_filter_currying( self ): + filter_parser = HistoryFilters( self.app ) + filter_parser.fn_filter_parsers = { + 'name_len' : { 'op': { 'lt' : lambda i, v: len( i.name ) < v }, 'val': int } + } + self.log( 'should be 2 filters now' ) + self.assertEqual( len( filter_parser.fn_filter_parsers ), 1 ) + filters = filter_parser.parse_filters([ + ( 'name_len', 'lt', '4' ) + ]) + self.log( 'should have parsed out a single filter' ) + self.assertEqual( len( filters ), 1 ) + + filter_ = filters[0] + fake = mock.OpenObject() + fake.name = '123' + self.log( '123 should return true through the filter' ) + self.assertTrue( filter_( fake ) ) + fake.name = '1234' + self.log( '1234 should return false through the filter' ) + self.assertFalse( filter_( fake ) ) + + def test_list( self ): + """ + Test limit and offset in conjunction with both orm and fn filtering. + """ + filter_parser = HistoryFilters( self.app ) + user2 = self.user_mgr.create( self.trans, **user2_data ) + history1 = self.history_mgr.create( self.trans, name='history1', user=user2 ) + history2 = self.history_mgr.create( self.trans, name='history2', user=user2 ) + history3 = self.history_mgr.create( self.trans, name='history3', user=user2 ) + history4 = self.history_mgr.create( self.trans, name='history4', user=user2 ) + + self.history_mgr.delete( self.trans, history1 ) + self.history_mgr.delete( self.trans, history2 ) + self.history_mgr.delete( self.trans, history3 ) + + test_annotation = "testing" + history2.add_item_annotation( self.trans.sa_session, user2, history2, test_annotation ) + self.trans.sa_session.flush() + history3.add_item_annotation( self.trans.sa_session, user2, history3, test_annotation ) + self.trans.sa_session.flush() + history3.add_item_annotation( self.trans.sa_session, user2, history4, test_annotation ) + self.trans.sa_session.flush() + + all_histories = [ history1, history2, history3, history4 ] + deleted_and_annotated = [ history2, history3 ] + + self.log( "no offset, no limit should work" ) + self.assertEqual( self.history_mgr.list( self.trans, offset=None, limit=None ), all_histories ) + self.assertEqual( self.history_mgr.list( self.trans ), all_histories ) + self.log( "no offset, limit should work" ) + self.assertEqual( self.history_mgr.list( self.trans, limit=2 ), [ history1, history2 ] ) + self.log( "offset, no limit should work" ) + self.assertEqual( self.history_mgr.list( self.trans, offset=1 ), [ history2, history3, history4 ] ) + self.log( "offset, limit should work" ) + self.assertEqual( self.history_mgr.list( self.trans, offset=1, limit=1 ), [ history2 ] ) + + self.log( "zero limit should return empty list" ) + self.assertEqual( self.history_mgr.list( self.trans, limit=0 ), [] ) + self.log( "past len offset should return empty list" ) + self.assertEqual( self.history_mgr.list( self.trans, offset=len( all_histories ) ), [] ) + self.log( "negative limit should return full list" ) + self.assertEqual( self.history_mgr.list( self.trans, limit=-1 ), all_histories ) + self.log( "negative offset should return full list" ) + self.assertEqual( self.history_mgr.list( self.trans, offset=-1 ), all_histories ) + + filters = [ model.History.deleted == True ] + self.log( "orm filtered, no offset, no limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters ) + self.assertEqual( found, [ history1, history2, history3 ] ) + self.log( "orm filtered, no offset, limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters, limit=2 ) + self.assertEqual( found, [ history1, history2 ] ) + self.log( "orm filtered, offset, no limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters, offset=1 ) + self.assertEqual( found, [ history2, history3 ] ) + self.log( "orm filtered, offset, limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters, offset=1, limit=1 ) + self.assertEqual( found, [ history2 ] ) + + filters = filter_parser.parse_filters([ ( 'annotation', 'in', test_annotation ) ]) + self.log( "fn filtered, no offset, no limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters ) + self.assertEqual( found, [ history2, history3, history4 ] ) + self.log( "fn filtered, no offset, limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters, limit=2 ) + self.assertEqual( found, [ history2, history3 ] ) + self.log( "fn filtered, offset, no limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters, offset=1 ) + self.assertEqual( found, [ history3, history4 ] ) + self.log( "fn filtered, offset, limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters, offset=1, limit=1 ) + self.assertEqual( found, [ history3 ] ) + + filters = filter_parser.parse_filters([ + ( 'deleted', 'eq', 'True' ), + ( 'annotation', 'in', test_annotation ) + ]) + self.log( "orm and fn filtered, no offset, no limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters ) + self.assertEqual( found, [ history2, history3 ] ) + self.log( "orm and fn filtered, no offset, limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters, limit=1 ) + self.assertEqual( found, [ history2 ] ) + self.log( "orm and fn filtered, offset, no limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters, offset=1 ) + self.assertEqual( found, [ history3 ] ) + self.log( "orm and fn filtered, offset, limit should work" ) + found = self.history_mgr.list( self.trans, filters=filters, offset=1, limit=1 ) + self.assertEqual( found, [ history3 ] ) + + self.log( "orm and fn filtered, zero limit should return empty list" ) + found = self.history_mgr.list( self.trans, filters=filters, limit=0 ) + self.assertEqual( found, [] ) + self.log( "orm and fn filtered, past len offset should return empty list" ) + found = self.history_mgr.list( self.trans, filters=filters, offset=len( deleted_and_annotated ) ) + self.assertEqual( found, [] ) + self.log( "orm and fn filtered, negative limit should return full list" ) + found = self.history_mgr.list( self.trans, filters=filters, limit=-1 ) + self.assertEqual( found, deleted_and_annotated ) + self.log( "orm and fn filtered, negative offset should return full list" ) + found = self.history_mgr.list( self.trans, filters=filters, offset=-1 ) + self.assertEqual( found, deleted_and_annotated ) + + + + # ============================================================================= if __name__ == '__main__': # or more generally, nosetests test_resourcemanagers.py -s -v diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 test/unit/managers/test_ModelManager.py --- a/test/unit/managers/test_ModelManager.py +++ b/test/unit/managers/test_ModelManager.py @@ -22,6 +22,7 @@ import mock from galaxy.managers.users import UserManager +from galaxy.managers import base # ============================================================================= admin_email = 'admin(a)admin.admin' diff -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee -r 68f0ed37e08942acb1bb84b63911b22d7d4b6f65 test/unit/managers/test_UserManager.py --- a/test/unit/managers/test_UserManager.py +++ b/test/unit/managers/test_UserManager.py @@ -110,8 +110,8 @@ user3 = self.user_mgr.create( self.trans, **user3_data ) self.log( "should be able to tell if a user is the current (trans) user" ) - self.assertTrue( self.user_mgr.is_current_user( self.trans, self.admin_user ) ) - self.assertFalse( self.user_mgr.is_current_user( self.trans, user2 ) ) + self.assertEqual( self.user_mgr.current_user( self.trans ), self.admin_user ) + self.assertNotEqual( self.user_mgr.current_user( self.trans ), user2 ) def test_api_keys( self ): user2 = self.user_mgr.create( self.trans, **user2_data ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 29 Jan '15

29 Jan '15

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/156321d8d23b/ Changeset: 156321d8d23b User: nsoranzo Date: 2015-01-29 13:52:19+00:00 Summary: Fix INTEGRATED_TOOL_PANEL_DESCRIPTION . Affected #: 1 file diff -r 2171bcc223ca38613f50bba79df7739aefeb701b -r 156321d8d23bb777be1b5dde6b89c1bb776b9ddd lib/galaxy/tools/toolbox/base.py --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -38,13 +38,17 @@ INTEGRATED_TOOL_PANEL_DESCRIPTION = """ -This is Galaxy's integrated tool panel and probably should not be modified -directly. It will be regenerated each time Galaxy starts up. To modify locally -managed tools (e.g. from tool_conf.xml) modify that file directly and restart -Galaxy. Whenever possible Tool Shed managed tools (e.g. from shed_tool_conf.xml) -should be managed from within the Galaxy interface of via is UI - but if changes -are nessecary (such as to hide a tool or re-assign its section) modify that file -and restart Galaxy. +This is Galaxy's integrated tool panel and should be modified directly only for +reordering tools inside a section. Each time Galaxy starts up, this file is +synchronized with the various tool config files: tools, sections and labels +added to one of these files, will be added also here in the appropriate place, +while elements removed from the tool config files will be correspondingly +deleted from this file. +To modify locally managed tools (e.g. from tool_conf.xml) modify that file +directly and restart Galaxy. Whenever possible Tool Shed managed tools (e.g. +from shed_tool_conf.xml) should be managed from within the Galaxy interface or +via its API - but if changes are necessary (such as to hide a tool or re-assign +its section) modify that file and restart Galaxy. """ https://bitbucket.org/galaxy/galaxy-central/commits/d55ccd0bd71e/ Changeset: d55ccd0bd71e User: nsoranzo Date: 2015-01-29 14:43:59+00:00 Summary: Enhancements for galaxy.ini documentation Affected #: 1 file diff -r 156321d8d23bb777be1b5dde6b89c1bb776b9ddd -r d55ccd0bd71e688c69753edf15cbff2f6a2b82ba config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -42,7 +42,8 @@ # Number of threads in the web server thread pool. #threadpool_workers = 10 -# Set the number of seconds a thread can work before you should kill it (assuming it will never finish) to 3 hours. +# Set the number of seconds a thread can work before you should kill it +# (assuming it will never finish) to 3 hours. Default is 600 (10 minutes). threadpool_kill_thread_limit = 10800 # ---- Filters -------------------------------------------------------------- @@ -172,10 +173,11 @@ # install from in the admin interface (.sample used if default does not exist). #tool_sheds_config_file = config/tool_sheds_conf.xml -# If the following option is set to True - Galaxy will monitor individual tools -# and tool directories specified in tool_conf.xml for changes and reload these -# tools. Watchdog must be installed and available to Galaxy to use this option. -# See https://pypi.python.org/pypi/watchdog. +# Enable monitoring of tools and tool directories listed in any tool config file +# specified in tool_config_file option. If changes are found, tools are +# automatically reloaded. +# Watchdog ( https://pypi.python.org/pypi/watchdog ) must be installed and +# available to Galaxy to use this option. #watch_tools = False # Enable automatic polling of relative tool sheds to see if any updates @@ -685,6 +687,8 @@ # used by the algorithm that encodes and decodes these values. It can be any # string. If left unchanged, anyone could construct a cookie that would grant # them access to others' sessions. +# One simple way to generate a value for this is with the shell command: +# python -c 'import time; print time.time()' | md5sum | cut -f 1 -d ' ' #id_secret = USING THE DEFAULT IS NOT SECURE! # User authentication can be delegated to an upstream proxy server (usually https://bitbucket.org/galaxy/galaxy-central/commits/8a234cd86e8a/ Changeset: 8a234cd86e8a User: nsoranzo Date: 2015-01-29 14:47:47+00:00 Summary: Whitespace fixes. 80 character limit. Small rewordings. Affected #: 1 file diff -r d55ccd0bd71e688c69753edf15cbff2f6a2b82ba -r 8a234cd86e8a972a43f0e13617c9f09ae1216fee config/galaxy.ini.sample --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -8,7 +8,7 @@ # Throughout this sample configuration file, except where stated otherwise, # uncommented values override the default if left unset, whereas commented -# values are set to the default value. Relative paths are relative to the root +# values are set to the default value. Relative paths are relative to the root # Galaxy directory. # # Examples of many of these options are explained in more detail in the wiki: @@ -118,10 +118,10 @@ #database_query_profiling_proxy = False # By default, Galaxy will use the same database to track user data and -# tool shed install data. There are many situtations in which it is +# tool shed install data. There are many situtations in which it is # valuable to seperate these - for instance bootstrapping fresh Galaxy -# instances with pretested installs. The following optin can be used to -# separate the tool shed install database (all other options listed above +# instances with pretested installs. The following optin can be used to +# separate the tool shed install database (all other options listed above # but prefixed with install_ are also available). #install_database_connection = sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE @@ -139,14 +139,16 @@ # config/tool_conf.xml does not exist). #tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml -# Enable / disable checking if any tools defined in the above non-shed tool_config_files -# (i.e., tool_conf.xml) have been migrated from the Galaxy code distribution to the Tool -# Shed. This setting should generally be set to False only for development Galaxy environments -# that are often rebuilt from scratch where migrated tools do not need to be available in the -# Galaxy tool panel. If the following setting remains commented, the default setting will be True. +# Enable / disable checking if any tools defined in the above non-shed +# tool_config_files (i.e., tool_conf.xml) have been migrated from the Galaxy +# code distribution to the Tool Shed. This setting should generally be set to +# False only for development Galaxy environments that are often rebuilt from +# scratch where migrated tools do not need to be available in the Galaxy tool +# panel. If the following setting remains commented, the default setting will +# be True. #check_migrate_tools = True -# Tool config maintained by tool migration scripts. If you use the migration +# Tool config maintained by tool migration scripts. If you use the migration # scripts to install tools that have been migrated to the tool shed upon a new # release, they will be added to this tool config file. #migrated_tools_config = config/migrated_tools_conf.xml @@ -154,11 +156,12 @@ # File that contains the XML section and tool tags from all tool panel config # files integrated into a single file that defines the tool panel layout. This # file can be changed by the Galaxy administrator to alter the layout of the -# tool panel. If not present, Galaxy will create it. +# tool panel. If not present, Galaxy will create it. #integrated_tool_panel_config = integrated_tool_panel.xml # Default path to the directory containing the tools defined in tool_conf.xml. -# Other tool config files must include the tool_path as an attribute in the <toolbox> tag. +# Other tool config files must include the tool_path as an attribute in the +# <toolbox> tag. #tool_path = tools # Path to the directory in which tool dependencies are placed. This is used by @@ -181,26 +184,28 @@ #watch_tools = False # Enable automatic polling of relative tool sheds to see if any updates -# are available for installed repositories. Ideally only one Galaxy +# are available for installed repositories. Ideally only one Galaxy # server process should be able to check for repository updates. The # setting for hours_between_check should be an integer between 1 and 24. #enable_tool_shed_check = False #hours_between_check = 12 -# Enable use of an in-memory registry with bi-directional relationships -# between repositories (i.e., in addition to lists of dependencies for a -# repository, keep an in-memory registry of dependent items for each repository. +# Enable use of an in-memory registry with bi-directional relationships between +# repositories (i.e., in addition to lists of dependencies for a repository, +# keep an in-memory registry of dependent items for each repository. #manage_dependency_relationships = False # XML config file that contains data table entries for the -# ToolDataTableManager. This file is manually # maintained by the Galaxy +# ToolDataTableManager. This file is manually # maintained by the Galaxy # administrator (.sample used if default does not exist). #tool_data_table_config_path = config/tool_data_table_conf.xml -# XML config file that contains additional data table entries for the ToolDataTableManager. This file -# is automatically generated based on the current installed tool shed repositories that contain valid -# tool_data_table_conf.xml.sample files. At the time of installation, these entries are automatically -# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up. +# XML config file that contains additional data table entries for the +# ToolDataTableManager. This file is automatically generated based on the +# current installed tool shed repositories that contain valid +# tool_data_table_conf.xml.sample files. At the time of installation, these +# entries are automatically added to the following file, which is parsed and +# applied to the ToolDataTableManager at server start up. #shed_tool_data_table_config = config/shed_tool_data_table_conf.xml # Directory where data used by tools is located, see the samples in that @@ -215,24 +220,26 @@ #len_file_path = tool-data/shared/ucsc/chrom # Datatypes config file(s), defines what data (file) types are available in -# Galaxy (.sample is used if default does not exist). If a datatype appears in -# multiple files - the last definition is used (though the first sniffer is used +# Galaxy (.sample is used if default does not exist). If a datatype appears in +# multiple files, the last definition is used (though the first sniffer is used # so limit sniffer definitions to one file). #datatypes_config_file = config/datatypes_conf.xml # Disable the 'Auto-detect' option for file uploads #datatypes_disable_auto = False -# Visualizations config directory: where to look for individual visualization plugins. -# The path is relative to the Galaxy root dir. To use an absolute path begin the path -# with '/'. This is a comma separated list. Defaults to "config/plugins/visualizations". +# Visualizations config directory: where to look for individual visualization +# plugins. The path is relative to the Galaxy root dir. To use an absolute +# path begin the path with '/'. This is a comma separated list. +# Defaults to "config/plugins/visualizations". #visualization_plugins_directory = config/plugins/visualizations -# Interactive environment plugins root directory: where to look for interactive environment -# plugins. By default none will be loaded. Set to config/plugins/interactive_environments -# to load Galaxy's stock plugins (currently just IPython). These will require Docker -# to be configured and have security considerations so proceed with caution. -#interactive_environment_plugins_directory = +# Interactive environment plugins root directory: where to look for interactive +# environment plugins. By default none will be loaded. Set to +# config/plugins/interactive_environments to load Galaxy's stock plugins +# (currently just IPython). These will require Docker to be configured and +# have security considerations, so proceed with caution. +#interactive_environment_plugins_directory = # Each job is given a unique empty directory as its current working directory. # This option defines in what parent directory those directories will be @@ -247,18 +254,20 @@ # used for the cache #template_cache_path = database/compiled_templates -# Citation related caching. Tool citations information maybe fetched from -# external sources such as http://dx.doi.org/ by Galaxy - the following parameters -# can be used to control the caching used to store this information. +# Citation related caching. Tool citations information maybe fetched from +# external sources such as http://dx.doi.org/ by Galaxy - the following +# parameters can be used to control the caching used to store this information. #citation_cache_type = file #citation_cache_data_dir = database/citations/data #citation_cache_lock_dir = database/citations/lock -# External service types config file, defines what types of external_services configurations -# are available in Galaxy (.sample is used if default does not exist). +# External service types config file, defining what types of external_services +# configurations are available in Galaxy (.sample is used if default does not +# exist). #external_service_type_config_file = config/external_service_types_conf.xml -# Path to the directory containing the external_service_types defined in the config. +# Path to the directory containing the external_service_types defined in the +# config. #external_service_type_path = external_service_types # Tools with a number of outputs not known until runtime can write these @@ -316,10 +325,11 @@ # -- Mail and notification -# Galaxy sends mail for various things: Subscribing users to the mailing list -# if they request it, emailing password resets, notification from the Galaxy -# Sample Tracking system, reporting dataset errors, and sending activation emails. -# To do this, it needs to send mail through an SMTP server, which you may define here (host:port). +# Galaxy sends mail for various things: subscribing users to the mailing list +# if they request it, password resets, notifications from the Galaxy Sample +# Tracking system, reporting dataset errors, and sending activation emails. +# To do this, it needs to send mail through an SMTP server, which you may +# define here (host:port). # Galaxy will automatically try STARTTLS but will continue upon failure. #smtp_server = None @@ -337,37 +347,44 @@ #mailing_join_addr = galaxy-announce-join(a)bx.psu.edu # Datasets in an error state include a link to report the error. Those reports -# will be sent to this address. Error reports are disabled if no address is set. -# Also this email is shown as a contact to user in case of Galaxy misconfiguration and other events user may encounter. +# will be sent to this address. Error reports are disabled if no address is +# set. Also this email is shown as a contact to user in case of Galaxy +# misconfiguration and other events user may encounter. #error_email_to = None -# Activation email is used as a sender ('from' field) for the account activation mail. -# We recommend using string in the following format: Galaxy Project <galaxy-no-reply(a)example.com> +# Activation email is used as a sender ('from' field) for the account +# activation mail. We recommend using string in the following format: +# Galaxy Project <galaxy-no-reply(a)example.com> #activation_email = None -# URL of the support resource for the galaxy instance. Used in activation emails. +# URL of the support resource for the galaxy instance. Used in activation +# emails. #instance_resource_url = http://wiki.galaxyproject.org/ -# E-mail domains blacklist is used for filtering out users that are using disposable email address -# during the registration. If their address domain matches any domain in the BL they are refused the registration. +# E-mail domains blacklist is used for filtering out users that are using +# disposable email address during the registration. If their address domain +# matches any domain in the blacklist, they are refused the registration. #blacklist_file = config/disposable_email_blacklist.conf -# Registration warning message is used to discourage people from registering multiple accounts. Applies mostly for the main Galaxy instance. +# Registration warning message is used to discourage people from registering +# multiple accounts. Applies mostly for the main Galaxy instance. # If no message specified the warning box will not be shown. #registration_warning_message = Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion. # -- Account activation -# This is user account activation feature global flag. If set to "False" the rest of the Account -# activation configuration is ignored and user activation is disabled (a.k.a. accounts are active since registration). -# Note the activation is also not working in case the smtp server is not defined. +# User account activation feature global flag. If set to "False", the rest of +# the Account activation configuration is ignored and user activation is +# disabled (i.e. accounts are active since registration). +# The activation is also not working in case the SMTP server is not defined. #user_activation_on = False -# Activation grace period. Activation is not forced (login is not disabled) until -# grace period has passed. Users under grace period can't run jobs (see inactivity_box_content). -# In hours. Default is 3. Enter 0 to disable grace period. -# Users with OpenID logins have grace period forever. +# Activation grace period (in hours). Activation is not forced (login is not +# disabled) until grace period has passed. Users under grace period can't run +# jobs (see inactivity_box_content). Default is 3. Enter 0 to disable grace +# period. +# Users with OpenID logins have grace period forever. #activation_grace_period = 0 # Used for warning box for inactive accounts (unable to run jobs). @@ -378,7 +395,7 @@ # -- Analytics # You can enter tracking code here to track visitor's behavior -# through your Google Analytics account. Example: UA-XXXXXXXX-Y +# through your Google Analytics account. Example: UA-XXXXXXXX-Y #ga_code = None # -- Display sites @@ -401,17 +418,19 @@ # them). #display_servers = hgw1.cse.ucsc.edu,hgw2.cse.ucsc.edu,hgw3.cse.ucsc.edu,hgw4.cse.ucsc.edu,hgw… -# To disable the old-style display applications that are hardcoded into datatype classes, -# set enable_old_display_applications = False. -# This may be desirable due to using the new-style, XML-defined, display applications that -# have been defined for many of the datatypes that have the old-style. +# To disable the old-style display applications that are hardcoded into +# datatype classes, set enable_old_display_applications = False. +# This may be desirable due to using the new-style, XML-defined, display +# applications that have been defined for many of the datatypes that have the +# old-style. # There is also a potential security concern with the old-style applications, -# where a malicious party could provide a link that appears to reference the Galaxy server, -# but contains a redirect to a third-party server, tricking a Galaxy user to access said -# site. +# where a malicious party could provide a link that appears to reference the +# Galaxy server, but contains a redirect to a third-party server, tricking a +# Galaxy user to access said site. #enable_old_display_applications = True -# -- Next gen LIMS interface on top of existing Galaxy Sample/Request management code. +# -- Next gen LIMS interface on top of existing Galaxy Sample/Request +# management code. use_nglims = False nglims_config_file = tool-data/nglims.yaml @@ -428,18 +447,20 @@ # Format string used when showing date and time information. # The string may contain: -# - the directives used by Python time.strftime() function (see http://docs.python.org/2/library/time.html#time.strftime ), +# - the directives used by Python time.strftime() function (see +# http://docs.python.org/2/library/time.html#time.strftime ), # - $locale (complete format string for the server locale), -# - $iso8601 (complete format string as specified by ISO 8601 international standard). +# - $iso8601 (complete format string as specified by ISO 8601 international +# standard). # pretty_datetime_format = $locale (UTC) -# URL (with schema http/https) of the Galaxy instance as accessible within your local -# network - if specified used as a default by pulsar file staging and IPython docker -# container for communicating back with Galaxy via the API. +# URL (with schema http/https) of the Galaxy instance as accessible within your +# local network - if specified used as a default by pulsar file staging and +# IPython Docker container for communicating back with Galaxy via the API. #galaxy_infrastructure_url = http://localhost:8080 -# The URL of the page to display in Galaxy's middle pane when loaded. This can be -# an absolute or relative URL. +# The URL of the page to display in Galaxy's middle pane when loaded. This can +# be an absolute or relative URL. #welcome_url = /static/welcome.html # The URL linked by the "Galaxy/brand" text. @@ -470,7 +491,7 @@ # The URL linked by the "Galaxy Q&A" link in the "Help" menu # The Galaxy Q&A site is under development; when the site is done, this URL # will be set and uncommented. -#qa_url = +#qa_url = # Serve static content, which must be enabled if you're not serving it via a # proxy server. These options should be self explanatory and so are not @@ -527,9 +548,9 @@ # will cause modern web browsers to not allow Galaxy to be embedded in # the frames of web applications hosted at other hosts - this can help # prevent a class of attack called clickjacking -# (https://www.owasp.org/index.php/Clickjacking) If you configure a +# (https://www.owasp.org/index.php/Clickjacking) If you configure a # proxy in front of Galaxy - please ensure this header remains intact -# to protect your users. Uncomment and leave empty to not set the +# to protect your users. Uncomment and leave empty to not set the # `X-Frame-Options` header. #x_frame_options = SAMEORIGIN @@ -545,10 +566,10 @@ #nginx_upload_path = False # Have Galaxy manage dynamic proxy component for routing requests to other -# services based on Galaxy's session cookie. It will attempt to do this by +# services based on Galaxy's session cookie. It will attempt to do this by # default though you do need to install node+npm and do an npm install from -# `lib/galaxy/web/proxy/js`. It is generally more robust to configure this -# externally managing it however Galaxy is managed. If True Galaxy will only +# `lib/galaxy/web/proxy/js`. It is generally more robust to configure this +# externally managing it however Galaxy is managed. If True Galaxy will only # launch the proxy if it is actually going to be used (e.g. for IPython). #dynamic_proxy_manage=True @@ -564,7 +585,8 @@ # Enable verbose debugging of Galaxy-managed dynamic proxy. #dynamic_proxy_debug=False -# The dynamic proxy is proxied by an external proxy (e.g. apache frontend to nodejs to wrap connections in SSL) +# The dynamic proxy is proxied by an external proxy (e.g. apache frontend to +# nodejs to wrap connections in SSL). #dynamic_proxy_external_proxy=False # -- Logging and Debugging @@ -582,28 +604,28 @@ # Turn on logging of application events and some user events to the database. #log_events = True -# Turn on logging of user actions to the database. Actions currently logged are -# grid views, tool searches, and use of "recently" used tools menu. The +# Turn on logging of user actions to the database. Actions currently logged +# are grid views, tool searches, and use of "recently" used tools menu. The # log_events and log_actions functionality will eventually be merged. #log_actions = True -# Sanitize All HTML Tool Output By default, all tool output served as -# 'text/html' will be sanitized thoroughly. This can be disabled if -# you have special tools that require unaltered output. WARNING: -# Disabling this does make the Galxy instance susceptible to XSS -# attacks initiated by your users. +# Sanitize all HTML tool output. By default, all tool output served as +# 'text/html' will be sanitized thoroughly. This can be disabled if you have +# special tools that require unaltered output. WARNING: disabling this does +# make the Galaxy instance susceptible to XSS attacks initiated by your users. #sanitize_all_html = True # By default Galaxy will serve non-HTML tool output that may potentially -# contain browser executable JavaScript content as plain text. This will for +# contain browser executable JavaScript content as plain text. This will for # instance cause SVG datasets to not render properly and so may be disabled # by setting the following option to True. #serve_xss_vulnerable_mimetypes = False -# Set the following to True to use ipython nbconvert to build HTML from IPython -# notebooks in Galaxy histories. This process may allow users to execute arbitrary -# code or serve arbitrary HTML. If enabled ipython must be available and on Galaxy's -# PATH, to do this run `pip install jinja2 pygments ipython` in Galaxy's virtualenv. +# Set the following to True to use IPython nbconvert to build HTML from IPython +# notebooks in Galaxy histories. This process may allow users to execute +# arbitrary code or serve arbitrary HTML. If enabled, IPython must be +# available and on Galaxy's PATH, to do this run +# `pip install jinja2 pygments ipython` in Galaxy's virtualenv. #trust_ipython_notebook_conversion = False # Debug enables access to various config options useful for development and @@ -659,7 +681,7 @@ # if testing shows that Galaxy is able to create files using these formats. # Specific formats can be disabled with this option, separate more than one # format with commas. Available formats are currently 'zip', 'gz', and 'bz2'. -#disable_library_comptypes = +#disable_library_comptypes = # Some sequencer integration features in beta allow you to automatically # transfer datasets. This is done using a lightweight transfer manager which @@ -710,10 +732,11 @@ #remote_user_header = HTTP_REMOTE_USER # If use_remote_user is enabled, anyone who can log in to the Galaxy host may -# impersonate any other user by simply sending the appropriate header. Thus a +# impersonate any other user by simply sending the appropriate header. Thus a # secret shared between the upstream proxy server, and Galaxy is required. -# If anyone other than the Galaxy user is using the server, then apache/nginx should -# pass a value in the header 'GX_SECRET' that is identical the one below +# If anyone other than the Galaxy user is using the server, then apache/nginx +# should pass a value in the header 'GX_SECRET' that is identical to the one +# below. #remote_user_secret = USING THE DEFAULT IS NOT SECURE! # If use_remote_user is enabled, you can set this to a URL that will log your @@ -798,8 +821,9 @@ #api_allow_run_as = None # Master key that allows many API admin actions to be used without actually -# having a defined admin user in the database/config. Only set this if you need -# to bootstrap Galaxy, you probably do not want to set this on public servers. +# having a defined admin user in the database/config. Only set this if you +# need to bootstrap Galaxy, you probably do not want to set this on public +# servers. #master_api_key = changethis # Enable tool tags (associating tools with tags). This has its own option @@ -807,7 +831,7 @@ # large servers. #enable_tool_tags = False -# Enable a feature when running workflows. When enabled, default datasets +# Enable a feature when running workflows. When enabled, default datasets # are selected for "Set at Runtime" inputs from the history such that the # same input will not be selected twice, unless there are more inputs than # compatible datasets in the history. @@ -843,7 +867,7 @@ # File where Data Managers are configured (.sample used if default does not # exist) #data_manager_config_file = config/data_manager_conf.xml -# File where Tool Shed based Data Managers are configured +# File where Tool Shed based Data Managers are configured #shed_data_manager_config_file = config/shed_data_manager_conf.xml # Directory to store Data Manager based tool-data; defaults to tool_data_path #galaxy_data_manager_data_path = tool-data @@ -870,7 +894,8 @@ # following option to True or False. #track_jobs_in_database = None -# This enables splitting of jobs into tasks, if specified by the particular tool config. +# This enables splitting of jobs into tasks, if specified by the particular tool +# config. # This is a new feature and not recommended for production servers yet. #use_tasked_jobs = False #local_task_queue_workers = 2 @@ -921,7 +946,8 @@ # Optional file containing job resource data entry fields definition. # These fields will be presented to users in the tool forms and allow them to -# overwrite default job resources such as number of processors, memory, and walltime. +# overwrite default job resources such as number of processors, memory and +# walltime. #job_resource_params_file = config/job_resource_params_conf.xml # If using job concurrency limits (configured in job_config_file), several @@ -940,7 +966,7 @@ # the following lines. tool_* filters will be applied for all users # and can not be changed by them. user_tool_* filters will be shown # under user preferences and can be toogled on and off by -# runtime. Example shown below are not real defaults (no custom +# runtime. Example shown below are not real defaults (no custom # filters applied by defualt) but can be enabled with by renaming the # example.py.sample in the filters directory to example.py. @@ -972,11 +998,12 @@ # ---- Galaxy External Message Queue ------------------------------------------------- -# Galaxy uses AMQ protocol to receive messages from external sources like -# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -# For Galaxy to receive messages from a message queue the RabbitMQ server has -# to be set up with a user account and other parameters listed below. The 'host' -# and 'port' fields should point to where the RabbitMQ server is running. +# Galaxy uses Advanced Message Queuing Protocol (AMQP) to receive messages from +# external sources like barcode scanners. Galaxy has been tested against +# RabbitMQ AMQP implementation. For Galaxy to receive messages from a message +# queue, the RabbitMQ server has to be set up with a user account and other +# parameters listed below. The 'host' and 'port' fields should point to where +# the RabbitMQ server is running. [galaxy_amqp] 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: Update tag latest_2015.01.13 for changeset a481d17c0448
by commits-noreply＠bitbucket.org 29 Jan '15

29 Jan '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d386cf71d4f7/ Changeset: d386cf71d4f7 Branch: stable User: natefoo Date: 2015-01-29 14:00:24+00:00 Summary: Update tag latest_2015.01.13 for changeset a481d17c0448 Affected #: 1 file diff -r a481d17c04482b069e6b2ebdda4fbca01448fa9c -r d386cf71d4f71faeb49ec871b742e81011bee266 .hgtags --- a/.hgtags +++ b/.hgtags @@ -22,4 +22,4 @@ 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 9bd6f8b5b8153db752f4e61ed62f2b6c01ae4a11 latest_2014.10.06 2e8dd2949dd3eee0f56f9a3a5ebf1b2baca24aee release_2015.01.13 -1b96d3a4ff28da2bd547b65ad86c5ad5a9bbfb90 latest_2015.01.13 +a481d17c04482b069e6b2ebdda4fbca01448fa9c latest_2015.01.13 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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